Program : XVRML
Version : 990924
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 : generate VRML files from PDB files
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt (1992-2004). Uppsala University, Uppsala, Sweden. Unpublished program.
* 2 * 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.
970722 - 0.2 - first documented version
990806 - 0.3 - minor bug fix (set atomnr to 1 if unknown element)
990924 - 0.4 - allow addition to atomic radii (option 96)
NOTE: more sophisticated VRML "worlds" can be created with MOLEMAN2 (version 2.0 and on) !
This program is just a quick-and-dirty jiffy to produce VRML files of molecules from PDB files. Operation is pretty simple:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML ***Version - 990924/0.4 (C) 1992-1999 Gerard J. Kleywegt, Dept. Cell Mol. Biol., Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
Started - Mon Oct 11 19:40:23 1999 User - gerard Mode - interactive Host - sarek ProcID - 13663 Tty - /dev/ttyq12
*** XVRML *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML ***
Reference(s) for this program:
* 1 * G.J. Kleywegt (1992-1999). Uppsala University, Uppsala, Sweden. Unpublished program.
* 2 * G.J. Kleywegt, J.Y. Zou, M. Kjeldgaard & T.A. Jones (1999 ?). Chapter 25.2.6. Around O. Int. Tables for Crystallography, Volume F. Submitted.
==> For manuals and up-to-date references, visit: ==> http://xray.bmc.uu.se/usf
*** XVRML *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML ***
Initialising : (XVRML - 990924/0.7) Nr of predefined colours : ( 411)
PDB file name ? (test.pdb) 1cbs.pdb ==> Found file in GKPATH : (/nfs/pdb/full/1cbs.pdb) Nr of atoms read : ( 1213) Looking for bonds ... Nr of unique bonds : ( 1129)
Select: 0 = QUIT 1 = monochrome CPK model 2 = atom-coloured CPK model 3 = monochrome wire model 4 = atom-coloured wire model 5 = monochrome ball-and-stick 6 = atom-coloured ball-and-stick 7 = monochrome CA trace 8 = read new PDB file 93 = colour code from RGB 94 = RGB from colour name 95 = list predefined colours 96 = scale atomic radii 97 = colour atoms by element 98 = change default drawing colour 99 = change background colour Option ? ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 1) 99Background colour (RGB) ? ( 0.500 0.500 0.500) 0 0 0 Background colour (RGB) : ( 0.000 0.000 0.000) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 99) 98Default colour (RGB) ? ( 1.000 1.000 1.000) 1 1 0 Default colour (RGB) : ( 1.000 1.000 0.000) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 98) 97 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 97) 96Scale factor (>0) ? ( 1.000) 0.5 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 96) 95Nr of colours : ( 411) # 1 (black ) = 12595212 RGB 0.000 0.000 0.000 # 2 (red ) = 12596212 RGB 1.000 0.000 0.000 # 3 (green ) = 13619212 RGB 0.000 1.000 0.000 # 4 (blue ) = 1061171212 RGB 0.000 0.000 1.000 ... # 408 (lightsteelblue3 ) = 855328391 RGB 0.635 0.709 0.803 # 409 (green3 ) = 13417484 RGB 0.000 0.803 0.000 # 410 (orangered4 ) = 12745261 RGB 0.545 0.146 0.000 # 411 (mediumorchid1 ) = 1061582714 RGB 0.878 0.401 1.000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 95) 94Colour name ? (red) dodgerblue2 dodgerblue2 = 991454330 = RGB 0.110 0.525 0.933 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 94) 93RGB values ? ( 0.110 0.525 0.933) Code = 991453306 for RGB 0.110 0.525 0.933 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 93) 8PDB file name ? (rea.pdb) trp.pdb Nr of atoms read : ( 252) Looking for bonds ... Nr of unique bonds : ( 270) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 1)VRML file name ? (test.wrl) Opened VRML file Closed VRML file ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 1) 2VRML file name ? (test.wrl) Opened VRML file Closed VRML file ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 2) 3VRML file name ? (test.wrl) Opened VRML file Closed VRML file ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 3) 4VRML file name ? (test.wrl) Opened VRML file Closed VRML file ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 4) 5VRML file name ? (test.wrl) Opened VRML file Stick radius ? ( 0.200) Closed VRML file ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 5) 6VRML file name ? (test.wrl) Opened VRML file Stick radius ? ( 0.200) Closed VRML file ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 6) 7VRML file name ? (test.wrl) Opened VRML file CA-CA cut-off distance ? ( 4.500) Closed VRML file ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present ("peppar, peppar").
Does not compute.