Re: : [PyMOL] Surface Vertex Coordinates

. Of course it would be a whole lot easier if PyMol output VRML directly . Warren ? Laurence Pearl On 15 Mar 2006, at 17:01, Benjamin Hitz wrote: I am interested in the coordinates of the vertices of the mesh representation of the molecular surface. Is there any method to read them

[PyMOL] Slow transparency

Is it just me or has the new release of MacPyMol gone very slow when rendering transparent surfaces ? -- Laurence H. Pearl Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories,

Re: [PyMOL] Slow transparency

It was just me - loading a .pse created with the previous version seemed to be the problem. When I loaded a new coordinate file into that session, everything seemed to click back to normal. On 23 May 2005, at 12:56, Laurence Pearl wrote: Is it just me or has the new release of MacPyMol

[PyMOL] cylindrical helix problem

When I set 'cartoon_cynlindrical_helices' to 1, I'm getting cylinders with coloured ends, but black sides I'm using version 0.92 on OSX 10.2.8 any ideas ?? -- Laurence H. Pearl Section of Structural

Re: [PyMOL] wild card

, liberating * to its otherwise universal role as wild-card. Laurence Pearl On Wednesday, February 18, 2004, at 05:25 pm, Eric Zollars wrote: Anyone who works with nucleic acids will certainly prefer the current situation.  From the PDB format guidelines: * The asterisk (*) is used

[PyMOL] VRML output

file optionally generated by PyMol's ray command. Laurence Pearl Laurence H. Pearl Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Phone +44

Re: [PyMOL] you know what would be cool?

I'm still not sure about all this 'cool' stuff - Python looks to me like the illegitimate spawn of C and BASIC, but then I used to program in 6502 machine code so what do I know . Below is a variant of camera_travel (as Pythonised by Lieven Buts) which takes an explicit final view matrix

Re: [PyMOL] you know what would be cool?

-like routine - feel free to improve it. # camera_travel - Laurence Pearl, November 2003 import cmd import math def camera_travel(first,nframes=30,sel='(all)',zflag=0,zlevel=2): # first - start frame # nframes - duration # sel - atom selection that defines the orientation at the end

[PyMOL] turn light routine

I'm having a problem with the routine described a few months ago for rotating the direction of the light source when the picture is rotated for making a stereo pair. The problem is as follows : PyMOLrun turn_y_light.py Traceback (most recent call last): File

[PyMOL] secondary structure colouring

Can anyone help me with the selection commands in PyMOL to select (and subsequently colour) residues by their secondary structure ? Many Thanks, Laurence -- --- Laurence H. Pearl Section of Structural Biology,