[PyMOL] GUI output font size too small

Hi, How do I control the GUI output window font size? It is too small for my eyes on a 1600x1200 screen. I can change it manually to 12 points in the GUI window Setting/Output size, but I can not find a command to do it for my .pymolrc! Preferably to more than 12 points as well... I use 0.99be

RE: [PyMOL] Super-smooth surfaces

Hi Stephen I also use smooth surfaces - for visualizing results from small angle xray scattering, which is a low resolution technique. I use: set solvent_radius, 4 alter my_protein, vdw=4 sort show surface, my_protein Maybe you can set solvent_radius a little bit higher, but not much, as you

Re: [PyMOL] Quadro-based 3D Mac Feedback

On Mon, Jan 16, 2006 at 04:34:44PM -0800, Warren DeLano wrote: > > Through extensive travel, contacts, and personal experiences over past > few years, I have come to understand just how poorly Linux is doing at > meeting the needs of the scientific visualization community. Despite my > unabashed

[PyMOL] selection disordered

Hi there, i have the following problem: selecting all ca atoms in chain A of 1ao0 the amino acids in the selection are disordered with respect to their occurrence in the protein. After loading the protein i tried the following: numbers=[] iterate (chain a)&(name ca),(numbers.append(res

[PyMOL] reinitialize fails to clear PyMOL Viewer

Hi all, I've run into a small glitch that I was wondering if anyone else had seen (or knew of a way to fix). At somewhat unpredicatable intervals, the reinitialize command doesn't actually clear the viewer display (objects show as deleted, but are still visible). Any ideas? Pete Pete Meyer Fu

Re: [PyMOL] selection disordered

pymol-users-ad...@lists.sourceforge.net wrote on 01/19/2006 06:55:11 AM: > Hi there, > > i have the following problem: selecting all ca atoms in chain A of 1ao0 > the amino acids in the selection are disordered with respect to their > occurrence in the protein. > (snip) > > So the 56th amino acid

RE: [PyMOL] Quadro-based 3D Mac Feedback

HI Tim! Thank you for making the pro-Linux case. > I thought the mailing list was for discussions regarding the > usage of a program, not a forum for polemicism. Indeed it is, and thank you also for that reminder -- let's all try to stick to the real-world practical issues surrounding use of Py

[PyMOL] Labels throw shadows in Ray traced images - possible to turn off?

Hi, I noticed that Ray traced output of images containing text labels will show the shadows thrown by and on these labels. This is a nice feature but is there also an easy way to turn this off (i.e. selectively turn off shadows from/on text while mantaining global shadows)? Thanks, -Alex

[PyMOL] Possible to select the nth residue?

One more question. Someone asked me this: is it possible in Pymol to select the nth (e.g. the 3rd) residue in a molecule/chain without knowing the pdb residue # itself? -Alex __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam pro

Re: [PyMOL] Possible to select the nth residue?

I just needed to do this and this was my solution NTH_RESIDUE=3 cmd.select("myselection", "molecule1 and chain A and resi %s" % (cmd.get_model("molecule1 and chain A").atom[NTH_RESIDUE])) will create a selection named myselection and contain only the NTH_RESIDUE of molecule1 and chain A. H

Re: [PyMOL] Possible to select the nth residue?

Sorry the below actually won't work, you'll need something more... nth_residue = 3 previous = -1 cur_res = 0 nth_resi = 0 for at in cmd.get_model("molecule1 and chainA").atom: if (at.resi != previous): cur_res++ if (cur_res == nth_residue): nth_resi = at.resi break

RE: [PyMOL] Labels throw shadows in Ray traced images - possible to turn off?

In the current development version, shadows are off for labels by default... set label_shadow_mode, 0 If that doesn't work in your build, it will in the next release. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Poin

RE: [PyMOL] Labels throw shadows in Ray traced images - possible to turn off?

Thanks, that works. I missed that option (didn't look far enough to the right when i hit set label "tab"). And, yes, in build 33, they are on by default (I think). -Alex --- Warren DeLano wrote: > In the current development version, shadows are off for > labels by > default... > > set l

RE: [PyMOL] reinitialize fails to clear PyMOL Viewer

Pete, Does tbe image go away as soon as you drag the mouse in the viewer area? Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942

RE: [PyMOL] selection disordered

Frank, That PDB file has bogus/inconsistent segment identifiers that are screwing up atomic ordering (since atoms are sorted into segments by default). set ignore_pdb_segi before loading the pdb file and then everything should work file. Cheers, Warren -- Warren L. DeLano, Ph.D.

RE: [PyMOL] Possible to select the nth residue?

res_list = [] iterate name ca, res_list.append(chain+"/"+resi+"/") cmd.indicate(res_list[2]) -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942

[PyMOL] RE: Program or Script to Calculate Atom-Atom Distances in pdb files

Irida, > I am looking for a free program > or script that can calculate all sulfur-sulfur distances in > pdb files from the Protein Data Bank. This is the kind of problem you can solve in PyMOL with just a few lines of Python code. For example: from pymol import cmd from glob import glob for

RE: [PyMOL] GUI output font size too small

Hi Bjorn, Unfortunately, this isn't configurable at runtime yet. We'll need to do something about this... For now, you'll need to directly edit the code in modules/pmg_tk/skins/normal/__init__.py look for self.font and text.configure. Cheers, Warren -- Warren L. DeLano, Ph.D.