Program : OOPS2
Version : 070222
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 596,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : generation of rebuilding macros for use with O
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt & T.A. Jones (1994). OOPS-a-daisy. CCP4/ESF-EACBM Newsletter on Protein Crystallography 30, June 1994, pp. 20-24. [http://xray.bmc.uu.se/usf/factory_3.html]
* 2 * G.J. Kleywegt & T.A. Jones (1996). Efficient rebuilding of protein structures. Acta Cryst D52, 829-832. [http://scripts.iucr.org/cgi-bin/paper?gr0469]
* 3 * G.J. Kleywegt & T.A. Jones (1996). Phi/Psi-chology: Ramachandran revisited. Structure 4, 1395-1400. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=8994966&dopt=Citation]
* 4 * G.J. Kleywegt & T.A. Jones (1997). Model-building and refinement practice. Methods in Enzymology 277, 208-230. [http://xray.bmc.uu.se/gerard/gmrp/gmrp.html]
* 5 * G.J. Kleywegt (2000). Validation of protein crystal structures. Acta Cryst. D56, 249-265 (Topical Review). [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=10713511&dopt=Citation] [http://scripts.iucr.org/cgi-bin/paper?gr0949]
* 6 * G.J. Kleywegt (2001). Validation of protein crystal structures. In: "International Tables for Crystallography, Volume F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 21.1, pp. 497-506, 526-528. Dordrecht: Kluwer Academic Publishers, The Netherlands.
* 7 * G.J. Kleywegt & T.A. Jones (2002). Homo Crystallographicus - Quo Vadis ? Structure 10, 465-472. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=11937051&dopt=Citation]
* 8 * G.J. Kleywegt (2004). Quality control and validation. In "Crystallographic Methods", S. Doublie, Ed. Submitted.
* 9 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.
990311 - 0.1 - first version, derived from OOPS version 5.3.1
990312 - 0.2 - more changes
990426 - 0.3 - more graceful recovery from inconsistent datablocks
990507 - 1.0 - included more of the old OOPS checks; updated manual;
made ready for public release
990805 -1.0.1- removed "grep -v" bit when creating the file
oops_subjectivity.table
990903 -1.0.2- header lines beginning with an exclamation mark
in input O datablock files are now skipped
991111 -1.0.3- minor bug fix
991214 - 1.1 - program runs YASSPA automatically when your PDB
file is read; secondary structure type is printed
in OOPS2 output and O macros; left-handed helical
fragments can be flagged
001114 -1.1.1- add non-breaking space to HTML table entries in
case there are no error/warning messages
001211 -1.1.2- minor changes
010926 -1.1.3- option WIF (WhatIf): if you don't use nit-picking mode
you can select a cut-off for inclusion of short
contacts (bumps); the format of the Bumps lines
in the output macros has been changed slightly
011010 -1.1.4- minor changes
011126 -1.1.5- minor changes
011204 - 1.2 - support for reading RS-fit and RS R-factor values
from a list file produced by MAPMAN; better handling
of HETATMs; better handling of nucleic acids models;
various other minor changes
020107 -1.2.1- sorting the macros "WORST-FIRST" no longer crashes
the program on Alphas and Linux boxes (thanks to David
Cooper for reporting this bug) ...
021030 -1.2.2- (while in Toronto) minor changes to default cut-offs;
centre on the CA atom if the residue has one (else
on its centre-of-mass as before)
021107 -1.2.3- minor changes
021108 -1.2.4- minor changes
021121 -1.2.5- minor changes
030703 -1.2.6- WIF: now always operates in "nit-picking mode"
030904 -1.2.7- PLA: suggested values for Omega cut-off are now printed
(3-6 degrees for CNS-refined models, 10-12 degrees
for REFMAC and other models)
031026 -1.2.8- WIF: changes to handle the slightly different format of
current what_check as compared to older versions of what_if
(in particular, the second atom in bump lines)
031103 -1.2.9- WIF: small bumping violations can now be ignored by
applying a cut-off (defaults to 0.2 Å)
040309 - 1.3 - option to use the Grab_build panel for rebuilding of
the residues flagged by OOPS2 (only works for O version
9.0.7, or later, which has the Centre_build command)
041001 - 1.4 - replaced Kabsch' routine U3BEST by quaternion-based
routine (U3QION) to do least-squares superpositioning
041021 -1.4.1- WhatCheck-handling routines now print a warning message
when there are unlisted problems (indicated by a
line such as "And so on for a total of 316 lines"
in the WhatCheck output). They can now also handle
residue names that include an insert character
(such as "A374", "A374A", "A374B", etc.)
041116 - 1.5 - print extra clear warning if any WHAT IF diagnostics
were suppressed (as well as the possible remedies);
some minor cosmetic changes
041117 -1.5.1- option to generate macros for all residues of a certain
type (protein, nucleic acid, water, heterogen)
irrespective of whether they have been flagged as
outliers (this can be handy when you want to check
all hetero compounds, or all waters, etc.)
070222 -1.5.2- changed output a bit so it's easier to 'grep' a
summary of the results; increased dimensioning
OOPS2 is the successor of ye olde faithful OOPS program as described in: G.J. Kleywegt & T.A. Jones (1996). Efficient rebuilding of protein structures. Acta Cryst D52, 829-832. This new version has been streamlined, making it much less tedious to use, and it has some enhancements that make it more useful than OOPS. The old OOPS will no longer be developed, although it remains available for those who find it easier to use.
What is the idea behind OOPS2 ? It is a tool that can be used by beginning and experienced protein crystallographers alike to streamline and speed up their model rebuilding efforts. In essence, all OOPS2 does is to read a load of information with respect to the quality of the current model, and to write a set of O macros that will take the crystallographer from one suspect residue to the next. In this way, your attention is focussed on those residues with which something appears to be amiss, and since OOPS2 tells you what the potential problem is (e.g., poor fit to the density, unusual side-chain conformation) you can use the appropriate tools in O to take action if you deem that this is necessary to improve the model.
Before you run OOPS2, you will need the following:
- your current model (typically, the output from a refinement
cycle) in a PDB file
- information regarding the quality of your current model (e.g.,
an O datablock with pep-flip values, or a WHAT IF quality
report)
- a subdirectory called "oops". This is where OOPS2 stores the
O macros it produces. The program will quit immediately if this
subdirectory does not exist. To create it, under Unix you
can type: mkdir oops
At present OOPS2 can check the criteria listed below. An "[O]" indicates that a check requires input in the form of an O datablock, whereas "[WHAT IF]" means that this check requires input of a WHAT IF quality report. All other checks are done by OOPS2 itself, calculating information as required on-the-fly.
A - main-chain geometry:
- [O] residues with bad pep-flip values
- residues with PHI-PSI values outside the allowed regions
- Proline residues with PHI not near -65.4 +/- 11.2 degrees
- non-Gly residues with positive PHI
- residues with non-planar peptides
- residues with unusual omega torsion
- residues with a cis-peptide
B - side-chain geometry:
- [O] residues with bad RSC-fit (Rotamer Sidechain) values
- residues with poor C-alpha chirality
- D-amino acids
C - real-space-fit of model to density:
- [O] RSCC (real-space corr. coeff.) for all atoms
- [O] RSCC for the main chain atoms only
- [O] RSCC for the side chain atoms only
- [O] RS R-factor for all atoms
D - temperature factors and occupancies:
- residues with at least one atom with a too low B-factor
- ditto, with a too high B-factor
- residues with too high an RMS delta-B for bonded atoms
- residues with at least one atom with a too low occupancy
- ditto, with a too high occupancy
E - comparison with a previous model:
- positional shifts, changes in temperature factors and occupancies,
large shifts in Phi/Psi and Chi1/Chi2, as well as newly inserted
and mutated residues are flagged since they might warrant your
inspection
F - miscellaneous:
- residues with at least one atom which sticks out of the mask
- residues which violate user-defined criteria
- disulfide bridges
- disulfides with S=S distance not near 2.06 +/- 0.10 A
- disulfides with CB-S-S-CB not near 96.8 +/- 10.1 degree (right-handed)
or -85.8 +/- 8.6 degrees (left-handed)
- [WHAT IF] a subset of WHAT IF diagnostics can be extracted from the file
"pdbout.txt" (which is generated if the "check ful file.pdb x y"
command is executed in WHAT IF)
Alternatively, OOPS2 can be used to generate informative macros for all residues in your protein, and the macros may even have the same name as the residue. So, to centre on residue A273, and to get a message about what is suspicious about this residue, all you need to type is: @oops/a273
The program will print some general information and an overview of the array dimensions (e.g., maximum number of atoms).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 507 gerard sarek 16:55:38 progs/oops2 > run oops2*** OOPS2 *** OOPS2 *** OOPS2 *** OOPS2 *** OOPS2 *** OOPS2 *** OOPS2 ***
Version - 990507/1.0 (C) 1992-1999 Gerard J. Kleywegt, Dept. Cell Mol. Biol., Uppsala (S)
[...]
Max nr of residues : 7000 Max size of mask : 4194304 Max nr of atoms : 70000 Max nr of disulfide bridges : 100 Max nr of WHAT IF messages : 10000 Max nr of user-defined criteria : 10 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you reply "Y", then for every item (where relevant), some statistics and a histogram of the encountered values are printed. This may help you in finding a proper cut-off value. For most criteria, OOPS2 comes up with fixed (sensible) defaults. However, for RS-fit cut-offs are calculated, IF you said YES to this question, as follows:
CUTOFF = MAX (RSFmin+0.1, MIN(RSFmax-0.1,RSFave-2*RSFsigma)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Print statistics and histograms ? (Y) y ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you said YES to the statistics question, you may also opt to get O2D plot files for some of the properties (e.g., pep-flip, rs-fit, rsc, bad-counts)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Auto-generate (some) O2D plot files ? (N) no ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Name of the current molecule (in O !!), e.g.: M9. This will be used to centre on the correct residues when you run the O macros created by OOPS2, and to validate the name of O datablocks that you read in OOPS2
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Molecule name in O ? (M1) m9 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Provide the name of the PDB file that contains your current model
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- PDB file ? (m9.pdb) m8.pdb REMARK ( Created by MOLEMAN V. 950223/5.8.2 at Tue Feb 28 03:43:36 1995 for user) REMARK ( M8 XPLOR 950228 R 0.180 Rfree 0.211) REMARK ( FILENAME="/nfs/gerard/proteins/cbh2/xplor/m1_2mbsmb.pdb") REMARK ( Uses *NO* sigma or amplitude cut-offs) REMARK ( DATE:28-Feb-95 02:17:48 created by user: gerard) CRYST1 ( 49.100 75.800 92.900 90.00 103.20 90.00) ORIGX1 ( 1.000000 0.000000 0.000000 0.00000) ORIGX2 ( 0.000000 1.000000 0.000000 0.00000) ORIGX3 ( 0.000000 0.000000 1.000000 0.00000) SCALE1 ( 0.020367 0.000000 0.004777 0.00000) SCALE2 ( 0.000000 0.013193 0.000000 0.00000) SCALE3 ( 0.000000 0.000000 0.011056 0.00000) END ( ) Nr of residues read : ( 1250) Nr of atoms read : ( 6210) Nr of HETATM cards : ( 0) Nr of Hs stripped : ( 0) Nr of residues with C : ( 726) Nr of residues with CA : ( 726) Nr of residues with N : ( 726) Nr of residues with O : ( 726) Nr of residues with CB : ( 666) Total nr of residues : ( 1250) Max CA-CA distance for neighbours : ( 4.500) Nr of WATERs : ( 506) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you made use of the option to annotate your previous model's residues with your own subjective assessment of the quality of the model and density, OOPS2 will read the results of that. If you don't have the foggiest what I'm on about - don't worry your pretty little head :-)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Reading old subjective score table Lines read from table : ( 20) Residues recognised : ( 20) Unexamined : ( 1230) Good dens, good fit : ( 11) Good dens, poor fit : ( 5) Poor dens, poor fit : ( 1) No dens, no fit : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
At this stage, the old OOPS would continue to ask you a zillion questions. In OOPS2 the initiative has been put into the hands of the user instead. OOPS2 enters a command loop, and you add (or remove, if you made a mistake) those quality checks you want to include. If external information (e.g., an O datablock) is required, the program will ask you for the filename. For some criteria a cut-off value is required, but OOPS2 attempts to come up with reasonable default values.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- POSSIBLE COMMANDS : PEP = include pep-flip RSC = include rotamer RAM = include Ramachandran WIF = include WHAT IF diagnostics RSR = include real-space R (all atoms) CCA = include real-space CC (all) CCM = include real-space CC (main) CCS = include real-space CC (side) BFA = include B-factors OCC = include occupancies MSK = include mask fit DIS = include disulfides PRE = include previous model CAC = include CA chirality PLA = include peptide planarity -------------------------------------- -------------------------------------- GO = get going ! QUI = quit without doing anythingNext command ? (?) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you select this option, OOPS2 will terminate without writing any files or doing anything at all for that matter.
Switch the analysis of pep-flip values on or off. If you include it, provide the name of the pep-flip datablock file and a cut-off of what you consider to be "bad pep-flips" (e.g., 2.5 Å).
References:
- Jones, T.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard, M. (1991).
Improved methods for building protein models in electron density maps
and the location of errors in these models. Acta Cryst A47, 110-119.
- Kleywegt, G.J. and Jones, T.A. (1997). Model-building and refinement
practice. Meth Enzymol 277, 208-230.
- Kleywegt, G.J. and Jones, T.A. (1998). Databases in protein
crystallography. Acta Cryst D54, 1119-1131.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) pep O data block with pep-flip values ? (pepflip.o) Datablock : (M9_RESIDUE_PEPFLIP) Data type : (R) Number : (1250) Format : ((10(x,f7.5)))*************************************************************************** Analysis of Pep-flip values (>0) ***************************************************************************
Number of values .................... 718 Average value ....................... 0.774 Standard deviation .................. 0.621 Minimum value observed .............. 0.109 Maximum value observed .............. 3.506
Nr < 0.0000 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.0000 and < 0.2500 : 131 ( 18.25 %; Cum 18.25 %) Nr >= 0.2500 and < 0.5000 : 145 ( 20.19 %; Cum 38.44 %) Nr >= 0.5000 and < 0.7500 : 155 ( 21.59 %; Cum 60.03 %) Nr >= 0.7500 and < 1.0000 : 121 ( 16.85 %; Cum 76.88 %) Nr >= 1.0000 and < 1.2500 : 50 ( 6.96 %; Cum 83.84 %) Nr >= 1.2500 and < 1.5000 : 37 ( 5.15 %; Cum 89.00 %) Nr >= 1.5000 and < 1.7500 : 16 ( 2.23 %; Cum 91.23 %) Nr >= 1.7500 and < 2.0000 : 13 ( 1.81 %; Cum 93.04 %) Nr >= 2.0000 and < 2.2500 : 17 ( 2.37 %; Cum 95.40 %) Nr >= 2.2500 and < 2.5000 : 11 ( 1.53 %; Cum 96.94 %) Nr >= 2.5000 and < 2.7500 : 12 ( 1.67 %; Cum 98.61 %) Nr >= 2.7500 and < 3.0000 : 4 ( 0.56 %; Cum 99.16 %) Nr >= 3.0000 and < 3.2500 : 4 ( 0.56 %; Cum 99.72 %) Nr >= 3.2500 and < 3.5000 : 1 ( 0.14 %; Cum 99.86 %) Nr >= 3.5000 and < 3.7500 : 1 ( 0.14 %; Cum 100.00 %) Nr >= 6.0000 : 0 ( 0.00 %; Cum 100.00 %)
Pep-flip cut-off ? ( 2.500) Nr of outliers : ( 22) Percentage : ( 3.064) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Switch the analysis of RSC values on or off (RSC = Rotamer Side Chain fit, a measure of how closely your side-chain conformation resembles that of the most similar rotamer in the O database; not used for Gly and Ala residues). If you include it, provide the name of the rsc datablock file and a cut-off value (e.g., 1.0 Å).
References:
- Jones, T.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard, M. (1991).
Improved methods for building protein models in electron density maps
and the location of errors in these models. Acta Cryst A47, 110-119.
- Kleywegt, G.J. and Jones, T.A. (1997). Model-building and refinement
practice. Meth Enzymol 277, 208-230.
- Kleywegt, G.J. and Jones, T.A. (1998). Databases in protein
crystallography. Acta Cryst D54, 1119-1131.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) rsc O data block with RSC values ? (rsc.o) Datablock : (M9_RESIDUE_RSC) Data type : (R) Number : (1250) Format : ((10(x,f7.5)))[...]
RSC cut-off ? ( 1.000) Nr of outliers : ( 101) Percentage : ( 17.782) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Switch analysis of main-chain phi-psi torsion angles on or off. The definition of core Ramachandran areas (for non-glycine residues only) is that of: Kleywegt, G.J. and Jones, T.A. (1996). Phi/psi-chology: Ramachandran revisited. Structure 4, 1395-1400. In addition, prolines with unusual phi torsions, and all residues with positive phi torsions can be flagged if you like.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) ram Checking allowed PHI-PSI areas Nr of residues with defined PHI : ( 724) Nr of residues with defined PSI : ( 724) Nr of residues considered : ( 662) Nr of outliers : ( 23) Percentage outliers : ( 3.474)Check unusual Pro PHI ? (N)
Check positive non-Gly PHI ? (N) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
OOPS2 can read "pdbout.txt" files created by WHAT IF (with the command: "check ful filename.pdb x y"). A subset of the diagnostics is used literally by OOPS2. If you don't use "nit-picking mode" some diagnostics will be ignored. For literature references, see the WHAT IF output file.
Note: as of version 1.2.6, the program always operates in "nit-picking mode".
Note: if the program prints a warning message telling you something like ""And so on for a total of 316 lines" occurred in the WhatIf or WhatCheck output you should take action. It means that there are more diagnostic messages than WhatIf is allowed to print, and hence that you will miss possibly important information during rebuilding ! You can increase the number of messages that WhatIf is allowed to print by either issuing the command "setwif 593 100000" before you run the check, or by editing the program's parameter file (PARAMS.FIG) and changing the value of parameter number 593 (which is 50 by default) to a large number, e.g. 100000.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) wif WHAT IF report file ? (pdbout.txt) Cut-off for short contacts (bumps) ? ( 0.200)No rounded coordinates detected
No incorrect Valine nomenclature
No incorrect Threonine nomenclature
No incorrect Isoleucine nomenclature
No incorrect Leucine nomenclature
Ouch : (# 21 # Warning: Arginine nomenclature problem) Incorrect Arginine nomenclature : ( 11)
No chirality deviations
No impossible occupancies
No missing atoms
No unusual bond lengths
Ouch : (# 37 # Warning: Unusual bond angles) Unusual bond angles : ( 43)
No non-planar side chains
No atoms not co-planar with rings
Ouch : (# 43 # Warning: Torsion angle evaluation shows unusual residues) Unusual torsion angles : ( 54)
Ouch : (# 44 # Warning: Backbone torsion angle evaluation shows unusual conformations) Unusual backbone torsions : ( 110)
No atoms near symmetry axes
Ouch : (# 59 # Error: Abnormally short interatomic distances) Bumps : ( 38)
Ouch : (# 60 # Warning: Abnormal packing environment for some residues) Abnormal packing environments : ( 91)
Ouch : (# 74 # Warning: Backbone oxygen evaluation) Unusual peptide oxygens : ( 12)
Ouch : (# 75 # Warning: Unusual rotamers) Unusual rotamers : ( 21)
Ouch : (# 76 # Warning: Unusual backbone conformations) Unusual backbone conformations : ( 151)
No isolated water clusters
Ouch : (# 79 # Warning: Water molecules need moving) Waters in wrong asymmetric unit : ( 1)
Ouch : (# 80 # Error: Water molecules without hydrogen bonds) Water molecules without H-bonds : ( 7)
Ouch : (# 86 # Error: HIS, ASN, GLN side chain flips) H/N/Q side chain flips : ( 38)
Ouch : (# 88 # Warning: Buried unsatisfied hydrogen bond donors) Unsatisfied H-bond donors : ( 316)
Ouch : (# 89 # Warning: Buried unsatisfied hydrogen bond acceptors) Unsatisfied H-bond acceptors : ( 19)
Nr of WHAT IF diagnostics : ( 912) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Switch the analysis of real-space R-factors (assumed for all atoms) on or off. If you include it, provide the name of the rsr-factor datablock file and a cut-off of what you consider to be "bad rs R-factors" (e.g., 0.3). If you want to include checks for real-space R-factors of main-chain and side-chain atoms separately as well, enter them as user-defined criteria.
Reference:
- Jones, T.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard, M. (1991).
Improved methods for building protein models in electron density maps
and the location of errors in these models. Acta Cryst A47, 110-119.
Switch the analysis of real-space correlation coefficients on or off. Provide the name of an appropriate datablock file and a cutoff value.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) cca O data block with RS-fit values ? (rsfit_all.o) Datablock : (M9_RESIDUE_RSFIT) Data type : (R) Number : (1250) Format : ((10(x,f7.5)))[...]
RS-fit cut-off ? ( 0.657) 0.7 Nr of outliers : ( 88) Percentage : ( 7.040) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Switch the check for too high and/or too low isotropic temperature factors on or off.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) bfa*************************************************************************** Analysis of Temperature factors (all ATOMS !) ***************************************************************************
[...]
Threshold for low Bs ? ( 5.000) Threshold for high Bs ? ( 40.000) Threshold for high Bs WATERs ? ( 50.000) 40 Checking low Bs ... Residues with low Bs : ( 8) Checking high Bs ... Residues with high Bs : ( 203) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Switch the check for too high and/or too low occupancies on or off.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) occ[...]
Threshold for low Qs ? ( 0.300) Threshold for high Qs ? ( 1.000) Checking low Qs ... Residues with low Qs : ( 0) Checking high Qs ... Residues with high Qs : ( 0) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You may check if disulfides are present, and if they have an unusual conformation.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) dis Checking disulfides Nr 1 Cys A176 - A235 S=S (A) = 2.03 Nr 2 Cys A368 - A415 S=S (A) = 2.04 Nr 3 Cys K176 - K235 S=S (A) = 2.03 Nr 4 Cys K368 - K415 S=S (A) = 2.03 Nr of disulfide bridges : ( 4) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You may check if any of the atoms in your model perhaps stick out of your averaging mask (in O/MAMA format).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) msk Mask file ? (m9.mask) Reading mask (O format) Format : compressed Grid points : ( 1631520) Stretches : ( 14082) Mask points : ( 90702) Number of points in mask : ( 90702)Radius to check around atoms ? ( 2.000) 1.5 Checking if mask is too tight Residues with mask problems : ( 0) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Switch the CA chirality check on or off. CA chirality is assessed
through the value of the improper torsion angle:
CA(i) - N(i) - C(i) - CB(i)
This angle should be near +33.9 degrees (for L-amino acids). Supply
a cut-off for the absolute deviation from +33.9.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) cac Calculating improper twist angle CA(i) - N(i) - C(i) - CB(i) This angle should be +33.9, sigma = 3.5, for standard L-amino acids Nr of residues with defined improper : ( 620)[...]
Maximum absolute deviation ? ( 3.500) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Switch analysis of peptide planarity on or off. Peptide planarity is
assessed through the absolute value of the improper torsion angle:
C(i) - CA(i) - N(i+1) - O(i)
This angle is 0.0 for planar peptides. Supply a cut-off for the
absolute deviation from zero .
The omega torsion (CA-C-N-CA) is also checked, and any cis-peptides
are flagged as well (these are not necessarily errors, of course,
but you may want to have a look at them anyway).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) pla Calculating improper twist angle C(i) - CA(i) - N(i+1) - O(i) This angle should be ZERO, sigma = 5.8Also calculating OMEGA torsion angle CA(i) - C(i) - N(i+1) - CA(i+1) This angle should be +178, sigma = 6 for TRANS peptide links. Nr of residues with defined improper : ( 724) Nr of residues with defined omega : ( 724)
[...]
Max deviation improper ? ( 5.800)
Max deviation OMEGA ? ( 6.000) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Switch comparison with a previous model on or off. If you include
it, provide the name of the PDB file containing that model.
The following items are checked for each residue of the
current model:
o has the residue newly been inserted ?
o has the residue newly been mutated ?
If not:
o has it shifted "a lot" ?
o have the temperature factors changed a lot ?
o have the occupancies changed a lot ?
o have the Phi and/or Psi angles changed a lot ?
o have the Chi1 and (if present) Chi2 angles changed a lot ?
You have to provide a cut-off for each of these checks in order to define what "a lot" actually is. In all cases, when a large shift has occurred (either during rebuilding or refinement), you want to have a closer look at the residue. The same is true, of course, if you have recently mutated or inserted a residue.
Delta-dihedral angles are calculated as: dihedral (now) - dihedral (previous) and moved to fall in the range <-180,+180].
If only one of Phi and Psi can be calculated, then the "Phi/Psi distance" is simply the absolute value of the delta-dihedral; if both can be calculated, the distance is calculated as SQRT (0.5 * (dPhi**2 + dPsi**2) ). A similar method is used for the Chi1/2 distance.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) pre Nr of residues with defined PHI : ( 179) Nr of residues with defined PSI : ( 179)PDB file of previous model ? (m16_prev.pdb) m15.pdb REMARK ( Written by O version 6.2.3) REMARK ( Fri Apr 16 01:53:59 1999) CRYST1 ( 45.050 51.850 79.970 90.00 90.00 90.00) ORIGX1 ( 1.000000 0.000000 0.000000 0.00000) ORIGX2 ( 0.000000 1.000000 0.000000 0.00000) ORIGX3 ( 0.000000 0.000000 1.000000 0.00000) SCALE1 ( 0.022198 -0.000001 -0.000001 0.00000) SCALE2 ( 0.000000 0.019286 -0.000001 0.00000) SCALE3 ( 0.000000 0.000000 0.012505 0.00000) END ( ) Nr of atoms read : ( 1536) Nr of atoms found : ( 1536)
Name of this previous model ? (Prev Model) Include WATERs in comparison ? (N) y
Comparing with previous model
*************************************************************************** Analysis of RMSD current/previous model ***************************************************************************
[...]
*************************************************************************** Analysis of RMS delta-B current/previous model ***************************************************************************
[...]
*************************************************************************** Analysis of RMS delta-Q current/previous model ***************************************************************************
[...]
*************************************************************************** Analysis of Phi/Psi distance ***************************************************************************
[...]
*************************************************************************** Analysis of Chi1/2 distance ***************************************************************************
[...]
Maximum RMSD (A) ? ( 0.500) Maximum RMS delta-B (A2) ? ( 5.000) Maximum RMS delta-Q (A2) ? ( 0.100) Maximum Phi/Psi distance ? ( 20.000) Maximum Chi1/2 distance ? ( 20.000) Do you want an O datablock file ? (N) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you select the "GO " command, OOPS2 will start producing its output files. But a few more questions will have to be answered first.
You can check one or more (up to ten) user-defined criteria ? provide a file name (this MUST be an O-style datablock; both Integer and Real datablocks can be read, but the values are always stored as REAL), a name for the property, and the message to print in O when a residue has a "bad" value for this property. You must also make clear WHEN a residue has a bad value, i.e. whether VALUE > CUT-OFF or VALUE < CUT-OFF is considered bad. In order to do this, you must supply a comparison operator (either < or >) and a cut-off value.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Next command ? (?) goUser-definable criteria Max number of them : ( 10)
Enter file with user datablock (<CR> to stop): ( )
Nr of user criteria : ( 0) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
An "electronic notebook file" will automatically be created. Just edit this file as you go along rebuilding your model. At the end, print the file and stick it in your real notebook.
In addition, an HTML model critique file, which contains a residue-by-residue critique of your model to put on your web site or intranet server will also automatically be created.
The names of these files are fixed, so no user input is required.
You can enter one line of O commands to execute for each residue.
It is handy to draw your maps and a sphere object, for example:
fm_dr sigma fm_dr diff obj sph sphere 10 end bell
If you want to execute an awful lot of commands for every
"baddy", put them in a macro and just execute that:
@do_all_this_for_every_baddy.omac
If you don't want to do anything, supply a comment line:
! don't do anything
or a dummy message:
message Check this one out, babe !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You may enter one line of O commands which will be executed by EVERY macro generated by OOPS. O command(s) to execute in every macro ? (bell save print DONE and SAVED) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- do you want macros for ALL or only for the BAD residues ? If you want to be use OOPS as an information-macro-generator, choose ALL; for rebuilding of only suspicious residues, choose BAD
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You may opt to get macros for ALL or merely the BAD residues. Do you want macros for ALL residues ? (N) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- if you don't want macros for all residues, you may still want macros for all residues of a certain kind (e.g., all heterogens). This can be accomplished from version 1.5.1 on:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Alternatively, you may opt to get macros for all residues (good or bad) of a certain type (protein, nucleic acid, water, heterogen). Do you want macros for certain types ? (N) y Macros for all amino acids ? (N) Macros for all nucleotides ? (N) Macros for all waters ? (N) y Macros for all heterogens ? (N) y ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- decide on whether or not to use user feedback information (assuming you have generated such information in an earlier cycle of OOPS2 followed by rebuilding):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- If you wish, residues that you have previously flagged as "good density, good fit" can be skipped by OOPS, even if they would normally be flagged as "bad" (e.g., due to an unusual side-chain conformation). Skip good residues ? (N) yConversely, residues that you have previously flagged as having poor density or a poor fit can be flagged by OOPS, even if they are not flagged as "bad". Include poor residues ? (N) y ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- do you want CHAINED macros ? If so, each macro will "point to" the next one; it will put an O instruction on the O menu to execute the next macro. If you want to be use OOPS as an information-macro-generator, select NO; for rebuilding of only suspicious residues, select YES
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You may opt to get chained macros or individual macros without instructions to put the next macro on the menu. Do you want CHAINED macros ? (Y) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- do you want macros to be executed "from N to C terminus" or do you want to start with the residues that have the largest number of diagnostics ? One could use the latter option if one is in a hurry and only wants to inspect those residues that seem to have the most serious problems.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The macros can be executed either from first residue to
last, or starting with the residue with the highest
number of possible problems ("worst-first").
Do you want the macros "WORST-FIRST" ? (N)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- do you want to use the Grab_build panel in O to rebuild the residues flagged by the program ? Depending on your choice here, two symbols are defined in the "oops.omac" macro, namely oops_c_atom and oops_c_zone. If you use Grab_build, then both symbols will be set to "centre_build"; otherwise they will be set to "centre_atom" and "centre_zone", respectively. You can always redefine these symbols if you regret your choice while you are rebuilding.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- From O version 9.0.7 on, you can opt to use the Grab_build panel for every residue flagged by OOPS2. Do you want to use GRAB_BUILD ? (Y) n ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
OOPS2 will now loop over all residues. If a residue has a bad pep-flip or rs-fit value etc., a macro will be written to the oops subdirectory (unless you requested macros for ALL residues). In addition, a start-up macro called "oops.mac" will be put in your current directory.
In the case of pepflip values etc., only residues which have absolute values greater than 0.01 are considered (this is to prevent OOPS from flagging all your waters as having bad RS-fit values, or your terminal residues as having bad PHI/PSI values). Similar safe-guards are applied for other attributes (e.g.: RS-fit side-chain not for GLYs; RSC not for GLY/ALA; phi/psi not for N- and C-terminal residues, etc. etc.).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- [...] OOPS - (LEU D385 [Loop or turn] [Protein]) Bad Phi-Psi = 65.42 -113.06 Unusual torsion angles : 2521 LEU ( 385 ) D -2.5982 Unusual backbone torsions : 2521 LEU ( 385 ) D Poor phi/psi Abnormal packing environments : 2521 LEU ( 385 ) D -5.56 OOPS - (TPQ D387 [Beta strand] [Protein]) Too high temperature factor = 60.04 OOPS - (ALA D407 [Beta strand] [Protein]) Unsatisfied H-bond donors : 2542 ALA ( 407 ) D N [...]OKAY - (CA2 M1 [-] [Heterogen]) OKAY - (CU2 M2 [-] [Heterogen]) OKAY - (CA2 M3 [-] [Heterogen]) OKAY - (CL1 M4 [-] [Heterogen])
Nr of macros generated : ( 1478) Nr of baddies : ( 909) Generated macros for 865 out of 2816 amino acids Generated macros for 0 out of 0 nucleotides Generated macros for 557 out of 557 water molecules Generated macros for 56 out of 56 heterogens
Start by typing @oops.omac in O !!!
Crystallographic indicators: Bad B (low) : ( 2) Bad B (high) : ( 308) Bad Q (low) : ( 4) Bad Q (high) : ( 0)
Geometric indicators: Bad Phi/Psi : ( 138) Left-handed helical residues : ( 18) Bad peptide planarity : ( 0) Bad omega torsion : ( 4) Cis-peptides : ( 12) Bad C-alpha chirality : ( 0) D-amino acids : ( 0) Disulfide bridges : ( 11) Bad disulfide S=S distance : ( 0) Bad disulfide CB-S-S-CB : ( 10) Flagged by WHAT IF : ( 673)
Residues without problems : ( 569)
Writing oops_badcounts.o ... Read oops_badcounts.o into O and use the residue property badcounts to colour your molecule, or plot this file, to reveal areas where the structure may be poor.
*************************************************************************** Analysis of Bad counts ***************************************************************************
Number of values .................... 3429 Average value ....................... 0.402 Standard deviation .................. 0.825 Minimum value observed .............. 0.000 Maximum value observed .............. 6.000
Nr < 0.0000 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.0000 and < 1.0000 : 2530 ( 73.78 %; Cum 73.78 %) Nr >= 1.0000 and < 2.0000 : 611 ( 17.82 %; Cum 91.60 %) Nr >= 2.0000 and < 3.0000 : 161 ( 4.70 %; Cum 96.30 %) Nr >= 3.0000 and < 4.0000 : 79 ( 2.30 %; Cum 98.60 %) Nr >= 4.0000 and < 5.0000 : 37 ( 1.08 %; Cum 99.68 %) Nr >= 5.0000 and < 6.0000 : 6 ( 0.17 %; Cum 99.85 %) Nr >= 6.0000 and < 7.0000 : 5 ( 0.15 %; Cum 100.00 %) Nr >= 24.0000 : 0 ( 0.00 %; Cum 100.00 %)
Writing oops_remarks.pdb ...
[...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
When OOPS2 is finished (and if there were any bad residues), all you have to do is type: "@oops.omac" from within O. This will then automatically centre on the first bad residue and print a message which tells you what is suspicious about this residue. In addition, a new menu item "@oops/2" will be added to your menu. When you're finished with the first residue, just click on this new menu item to go the second suspicious residue automatically, etc. ad infinitum. When the second macro is executed, you again will be centred on this residue's C-alpha atom, a diagnostic message is printed, the previous menu item "@oops/2" is deleted and a new one, "@oops/3" is inserted. Again, when you're finished, just click on "@oops/3" and voila.
After the last "baddy", the terminal bell will ring and a message that there aren't any more of them is printed.
In OOPS2, a facility has been implemented that enables you to keep track of your subjective judgement of all the residues you inspect with the OOPS2 macros.
As you execute the "oops.omac" start-up macro, four new commands
will be added to your menu:
- @Good_fit
- @Poor_fit
- @Poor_dens
- @No_dens
Also, a new datablock will be created (and filled with zeros)
that is called MOLNAM_residue_quality (MOLNAM is the name
of the molecule you are scrutinising, e.g. M9). Now, whenever
you inspect a residue, you can click on any of the four new
commands, and the entry of the current residue will be set
to:
o 0 if you click on @Good_fit: the density is good, and the fit
of the model to the density is good
o 1 if you click on @Poor_fit: the density is good, but the fit
of the model to the map is not, i.e. you need to do some
rebuilding
o 2 if you click on @Poor_dens: the density is poor, so you cannot
fit the residue any better than it is
o 3 if you click on @No_dens: there is no density, so you cannot
reasonably fit the residue at all
While you are still working on the same residue, you can revise
your judgement, and press another of the four commands.
When you are done, a new CA-object will be generated (called QUAL), where residues with quality value 0 are green, value 1 red (these should have been fixed by you), value 2 magenta (may have been rebuilt in the hopes of better density next cycle), and value 3 white (no density, little hope at present). You can use this object, for example, to ask a colleague or your supervisor to have a (quick) look at the problematic residues. (Residues which you have not judged have a value of -1 and will be drawn in blue.)
You can also use it in a next rebuilding cycle to quickly skip over residues that are flagged as outliers (e.g., in pepflip or rotamer analysis), but for which you know that the density and the fit to it are rock solid, and conversely to include residues that were a problem in the previous cycle even though OOPS2 may not have found anything wrong with them this time around.
The results of your assessment are stored in a file called "oops_subjectivity.table" (once you have executed the final OOPS2 macro), and read the next time you run the program.
The file may looks as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ASN A158 0 ASN A161 1 TYR A169 0 ASP A170 0 ASP A189 0 GLU A219 1 SER A222 3 TRP A269 0 GLN A319 2 ASN A369 3 SER A380 3 ASN K158 0 ASN K161 1 ASP K170 0 ASP K189 0 GLU K219 0 SER K222 0 TRP K269 1 ASN K305 1 ASN K369 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The next time you start the program:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Reading old subjective score table Lines read from table : ( 20) Residues recognised : ( 20) Unexamined : ( 1230) Good dens, good fit : ( 11) Good dens, poor fit : ( 5) Poor dens, poor fit : ( 1) No dens, no fit : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
And when you're about to generate new macros:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- If you wish, residues that you have previously flagged as "good density, good fit" can be skipped by OOPS, even if they would normally be flagged as "bad" (e.g., due to an unusual side-chain conformation). Skip good residues ? (N) yConversely, residues that you have previously flagged as having poor density or a poor fit can be flagged by OOPS, even if they are not flagged as "bad". Include poor residues ? (N) y ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
colouring your molecule according to the number of violations:
EXAMPLE 1:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > read oops_badcounts.o O > mol m6a O > pai_ramp residue_badcounts ; blue red O > obj bad ca ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
EXAMPLE 2:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > read oops_badcounts.o O > mol m6a O > pai_prop atom_name = ca blue O > pai_prop residue_badcounts > 0 red O > obj bad ca ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
EXAMPLE 3:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > read oops_badcounts.o O > mol m6a O > pai_case residue_badcounts 5 0 1 2 3 4 blue green yellow orange red O > obj bad ca ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
use ODBM or ODBMAN to create O-style datablock files from ASCII files.
ODBMAN and ODBM can also be used to extract several types of
datablock from a PROCHECK output file (see their manuals) !
when prompted by OOPS2 to supply a line of O commands which
will be executed for every bad residue, be clever and execute
a macro ! For example: @do_all.omac
You may then change the contents of this macro later on without
having to re-run OOPS2.
Use the OMAC/pre_oops.omac macro to take some work out of your hands.
Converting the O2D plot files generated by OOPS2 into PostScript format is conveniently done with the OMAC/o2dps script.
OOPS2 always checks if the names of datablocks are consistent, to help you prevent using a datablock belonging to an old model:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Analyse RS R-factor (all atoms) ? (Y) O data block with RS R-factors ? (rsrfac_all.o) Datablock : (M18_RESIDUE_RSRCONV) Data type : (R) Number : (238) Format : ((f10.3)) WARNING - inconsistent datablock name Expected : (m18_residue_rsfit) Encountered : (m18_residue_rsrconv) Continue anyway ? (Y) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
There is a problem with entities that only occur in one alternate
location that is not " " or "A" (e.g., waters associated with the
"B" location of some residue). O will put these in a separate molecule
and therefore not generate an RS-fit value for them etc. This leads
to a mismatch between O and OOPS2. The simplest way around this is
the rename the alt. loc. indicator of such entities to "A" or " "
before reading the file into O and OOPS2 (but use the correct file
in WHAT IF to make sure the bump checks are carried out correctly).
Created at Thu Feb 22 14:20:30 2007
by MAN2HTML version 070111/2.0.8 . This manual
describes OOPS2, a program of the Uppsala
Software Factory (USF), written and maintained by Gerard Kleywegt. © 1992-2007.