Uppsala Software Factory

Uppsala Software Factory - XVRML Manual

1 XVRML - GENERAL INFORMATION

Program : XVRML
Version : 970722
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 590, SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : generate VRML files from PDB files
Package : X-UTIL

2 REFERENCES

Reference(s) for this program:

* 1 * G.J. Kleywegt (1992-1999). Uppsala University, Uppsala, Sweden. Unpublished program.

* 2 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.

3 VERSION HISTORY

970722 - 0.2 - first documented version

4 INTRODUCTION

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  - 970722/0.2
 (C) 1992-97 Gerard J. Kleywegt, Dept. Mol. Biology, BMC, 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  - Tue Jul 22 22:28:34 1997
 User     - gerard
 Mode     - interactive
 Host     - sarek
 ProcID   - 28296
 Tty      - /dev/ttyq28

   
 *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML ***

   
 Reference(s) for this program:

   
 *  1 * G.J. Kleywegt,
        Uppsala University, Uppsala, Sweden,
        Unpublished program.

   
 For manuals and complete references, check:
 http://alpha2.bmc.uu.se/usf/

   
 *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML *** XVRML ***

   
 Initialising : (XVRML - 970717/0.1)
 Nr of predefined colours : (        411)

   
 PDB file name ? (test.pdb) rea.pdb
 Nr of atoms read : (         22)
 Looking for bonds ...
 Nr of unique bonds : (         22)

   
 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 -----

5 OPTIONS

5.1 0 - quit


Stop working with the program.

5.2 99 - change background colour

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (       1) 99

   
 Background 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 -----

5.3 98 - change default drawing colour

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (      99) 98

   
 Default 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 -----

5.4 97 - colour atoms by element


This assumes that the first two characters of every atom name define the chemical (i.e., carbon atoms called "AC1*" will be interpreted as Actinium atoms, "NO12" will be Nobelium, "OSC3" is Osmium, etc. !). 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (      98) 97
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

5.5 96 - scale atomic radii


Applies a scale factor to the atomic radii. The default radii are the covalent bond radii which are quite a bit smaller than the van der Waals radii. For CPK models, scale by a factor of 1.5-2; for ball-and-stick models, use a factor of ~0.5. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (      97) 96

   
 Scale factor (>0) ? (   1.000) 0.5
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

5.6 95 - list predefined colours

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (      96) 95

   
 Nr 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 -----

5.7 94 - RGB from colour name


Enter a colour name and the program will return the corresponding RGB values (Red-Green-Blue, three numbers between 0 and 1). 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (      95) 94

   
 Colour name ? (red) dodgerblue2
 dodgerblue2                    =    991454330 = RGB    0.110   0.525   0.933
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

5.8 93 - colour code from RGB


Enter RGB values, and the program will return an integer code for the colour. Not intended for users. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (      94) 93

   
 RGB values ? (   0.110    0.525    0.933)
 Code =    991453306 for RGB    0.110   0.525   0.933
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5.9 8 - read new PDB file


Re-start the program with a new PDB file. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (      93) 8

   
 PDB file name ? (rea.pdb) trp.pdb
 Nr of atoms read : (        252)
 Looking for bonds ...
 Nr of unique bonds : (        270)
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

5.10 1 - monochrome CPK model

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (       1)

   
 VRML file name ? (test.wrl)
 Opened VRML file
 Closed VRML file
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

5.11 2 - atom-coloured CPK model


This requires that you have first used option 97 to colour the atoms by element type ! 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (       1) 2

   
 VRML file name ? (test.wrl)
 Opened VRML file
 Closed VRML file
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

5.12 3 - monochrome wire model


Draws a wire model of all atoms. Atoms not bonded to any others will be shown as 3D crosses. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (       2) 3

   
 VRML file name ? (test.wrl)
 Opened VRML file
 Closed VRML file
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

5.13 4 - atom-coloured wire model


This requires that you have first used option 97 to colour the atoms by element type ! 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (       3) 4

   
 VRML file name ? (test.wrl)
 Opened VRML file
 Closed VRML file
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

5.14 5 - monochrome ball-and-stick

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (       4) 5

   
 VRML file name ? (test.wrl)
 Opened VRML file
 Stick radius ? (   0.200)
 Closed VRML file
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

5.15 6 - atom-coloured ball-and-stick


This requires that you have first used option 97 to colour the atoms by element type ! 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (       5) 6

   
 VRML file name ? (test.wrl)
 Opened VRML file
 Stick radius ? (   0.200)
 Closed VRML file
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

5.16 7 - monochrome CA trace


Only works for proteins ;-) 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Option ? (       6) 7

   
 VRML file name ? (test.wrl)
 Opened VRML file
 CA-CA cut-off distance ? (   4.500)
 Closed VRML file
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6 KNOWN BUGS

None, at present ("peppar, peppar").

7 UNKNOWN BUGS

Does not compute.

Uppsala Software Factory Created at Fri Dec 18 19:42:28 1998 by MAN2HTML version 971024/1.6