Re: [PyMOL] Selecting ASP and GLU

For me, color red, resn asp+glu works. Maia Martin Hediger wrote: Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh# remove water h_add # add hydrogens as

Re: [PyMOL] Selecting ASP and GLU

Hi, Seems to work fine for me. I'm using version 1.3, although I doubt that this could be a version compatibility problem. Could you give more specifics on how it doesn't work for you (ASPs not colored red or GLUs not colored red, etc.) ? Note that the parenthesis around 'resn glu' aren't

[PyMOL] R: Re: Re: labeling by a pseudoatom

Hi Jason, sorry for last message .. To label a residue by an mdo command cmd.mdo(int frame, string command) I can pass as command one among these strings: 1) 'label %s, %s %s' % (..) works fine but prints a message (I don't want) to the output window 1+) 'label %s, %s %s, quiet=1' %

[PyMOL] Question about the .obj file saved by Pymol

Hello, If I use save myscene.obj and I was looking at the surface representation of a molecule, does the file contains only the external surface of the protein, or are the internal cavities also included? Thanks, F.

Re: [PyMOL] R: Re: Re: labeling by a pseudoatom

Dear all thanks for the feedback. Indeed, after thinking for a second its totally clear why 'select identifyer, (resn asp and resn glu)' returns { }. So, speaking of syntax, '+' is OR and '' is AND? Thanks again Martin Am 02.03.11 01:35, schrieb rv...@libero.it: Hi Jason, sorry for last

Re: [PyMOL] Rendering Large Scene Crashes Pymol

Hi Ian, You can try to set hash_max (set hash_max,200) to put a limit on memory usage. Then again, an immediate crash can also mean the scene just isn't going to fit in memory. Complex scenes I usually write in parts to povray format, which I then combine and raytrace with povray. Hope it helps,

[PyMOL] Question about the .obj file saved by Pymol

Hello, If I use save myscene.obj and I was looking at the surface representation of a molecule, does the file contains only the external surface of the protein, or are the internal cavities also included? Thanks, F.

Re: [PyMOL] Selecting ASP and GLU

I believe the confusion is caused by the simplified selection expression in PyMOL (and some other visualization tools as well). I remember that one of my colleagues once questioned strongly the reason of using OR instead of AND in such situation. The expression: select resn GLU or resn ASP

[PyMOL] How to color aligned structures by equivalent SSE?

I'm looking for a quick way to color two superimposed structures such that SSEs for which there is an equivalent in both structures are colored and the non-matching SSEs and loops are grey. Also, the colored SSEs would be rainbow (e.g. the first matching SSE colored blue, second colored green,

Re: [PyMOL] R: Re: Re: labeling by a pseudoatom

Hi Martin, You're in the wrong thread! In addition, + is not OR. OR merges expressions, + 'merges' identifiers in an expression. Further, in the code you gave it said 'or'. It seems from this post you wrote 'and' in your script, signifying a mismatch between what you were doing and what you

[PyMOL] FW: help

Hi, I have couple of questions for you, which could be very silly. I downloaded the movie.py from http://www.rubor.de/, which is rTools 0.7.2 and put it to the right directory. When I did run movie.py, nothing seemed wrong. And then I did mv_clear, and still good. But when I do like : mv_move

Re: [PyMOL] Selecting ASP and GLU

Hey :) It's good to note that programs are written by programmers, using programmer's logic.The confusion is not so much caused by the simplified expression, but by users with little background in mathematics/logic assessing 'and' and 'or' from a linguistic background. In computer science and

Re: [PyMOL] Rendering Large Scene Crashes Pymol

Hi Ian Tsjerk, You can try to set hash_max (set hash_max,200) to put a limit on memory usage. Then again, an immediate crash can also mean the scene just isn't going to fit in memory. Complex scenes I usually write in parts to povray format, which I then combine and raytrace with povray.

Re: [PyMOL] Selecting ASP and GLU

On 03/02/2011 10:07 PM, Tsjerk Wassenaar wrote: Hey :) It's good to note that programs are written by programmers, using programmer's logic. First of all, I was not complaining about the logic of the PyMOL programmers. I tried to help find out the reason that might cause Martin's script to

Re: [PyMOL] How to color aligned structures by equivalent SSE?

Hi Eric, On Wed, Mar 2, 2011 at 1:41 PM, Eric Schreiter eric_...@mit.edu wrote: I'm looking for a quick way to color two superimposed structures such that SSEs for which there is an equivalent in both structures are colored and the non-matching SSEs and loops are grey.  Also, the colored

Re: [PyMOL] Selecting ASP and GLU

yeah, its true. We should work out a tutorial for this kind of things. Something where there is only one line of instruction and one line of command, like: 1) Download a file fetch pdb1.pdb 2) Select all ASP or GLU residues: select acids, resn ASP+GLU 3) Suggestions? Am 02.03.11 22:36,

Re: [PyMOL] select clipped atoms

Hi Johannes, Coincidentally, I found myself in need of the same functionality the other day. I came up with this: from pymol import cmd def clipped_by(at,v): x,y,z = at.coord nz = v[2]*(x-v[12])+v[5]*(y-v[13])+v[8]*(z-v[14])-v[11] return nz v[15] and nz v[16] def

Re: [PyMOL] select clipped atoms

Hi Johannes, My guess is that you missed that get_view[0:8] is a _column-major_ rotation matrix. Transpose it before using it. I decided to take a look at this problem for preparation of better clipping planes in PyMOL. I got it to work in PyMOL using Python, after much fussing about. Here's