[PyMOL] Selecting a lot of residues
Hello everyone: Please excuse this question if it is answered elsewhere. I have a structure that I would like to highlight a lot of residues with a different color and have in a spacefilling mode. These residues are listed in another (text) file. I've been doing the selection manually, but was wondering if there was anyway to automate this process at all, ie, using the text file and some sort of import control. Any ideas/directions would be appreciated. Thanks in advacne, Gwen __ Gwendowlyn S. Knapp Department of Biochemistry and Biophysics Texas AM University College Station, TX 77843-2128 mailto:g...@tamu.edu g...@tamu.edu http://www.gwenknapp.com http://www.gwenknapp.com __
[PyMOL] Selecting a lot of residues
Hi Gwen, You should really read the manual. Many of these basic questions can be answered by a few minutes of careful reading. One way of doing what you want to do is to make a small script (we will call it script.pml) that loads your PDB and then creates a selection containing all your residues of interest. This is script.pml: load your.pdb, foo create interestingstuff, ((/foo//A/27,28,141,144,148) show sticks, interestingstuff read this into PyMOL by typing: @script.pml this would display residues 27,28,141,144, and 148 of chain A of your molecule foo. You need to become familiar with the various atom selection schemas available in PyMOL to put this to best use for yuor particular PDB. Ciao, Scott On Dec 3, 2003, at 12:52 PM, Gwendowlyn S. Knapp wrote: Hello everyone: Please excuse this question if it is answered elsewhere. I have a structure that I would like to highlight a lot of residues with a different color and have in a spacefilling mode. These residues are listed in another (text) file. I've been doing the selection manually, but was wondering if there was anyway to automate this process at all, ie, using the text file and some sort of import control. Any ideas/directions would be appreciated. Thanks in advacne, Gwen __ Gwendowlyn S. Knapp Department of Biochemistry and Biophysics Texas AM University College Station, TX 77843-2128 g...@tamu.edu http://www.gwenknapp.com __ Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290
RE: [PyMOL] Selecting a lot of residues
Hi Scott, Thanks for that info. That's what i've been doing. (taken from the manual) Maybe I didn't word my question right. I have several proteins (like 15-20) that i need to do this for and i also have these lists. i was wanting to see if there was anyway to have pymol read in that list automatically so i didn't have to type in all the residues (ie, about 60 on each protein). thanks though, gwen -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Scott Classen Sent: Wednesday, December 03, 2003 3:13 PM To: g...@neo.tamu.edu; pymol-users@lists.sourceforge.net Subject: [PyMOL] Selecting a lot of residues Hi Gwen, You should really read the manual. Many of these basic questions can be answered by a few minutes of careful reading. One way of doing what you want to do is to make a small script (we will call it script.pml) that loads your PDB and then creates a selection containing all your residues of interest. This is script.pml: load your.pdb, foo create interestingstuff, ((/foo//A/27,28,141,144,148) show sticks, interestingstuff read this into PyMOL by typing: @script.pml this would display residues 27,28,141,144, and 148 of chain A of your molecule foo. You need to become familiar with the various atom selection schemas available in PyMOL to put this to best use for yuor particular PDB. Ciao, Scott On Dec 3, 2003, at 12:52 PM, Gwendowlyn S. Knapp wrote: Hello everyone: Please excuse this question if it is answered elsewhere. I have a structure that I would like to highlight a lot of residues with a different color and have in a spacefilling mode. These residues are listed in another (text) file. I've been doing the selection manually, but was wondering if there was anyway to automate this process at all, ie, using the text file and some sort of import control. Any ideas/directions would be appreciated. Thanks in advacne, Gwen __ Gwendowlyn S. Knapp Department of Biochemistry and Biophysics Texas AM University College Station, TX 77843-2128 g...@tamu.edu http://www.gwenknapp.com __ Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290
[PyMOL] Fog and ray-tracing
Hi, I want to generate a ray-traced image with a white background and a very strong fog effect. I tried to play around with the ray_trace_fog, ray_trace_fog_start and fog parameters but could not manage to do it. The image generated through the interface before ray-tracing is way clearer than the one after. Is there any solution to improve this? Thank you very much, Loïc
Re: [PyMOL] Selecting a lot of residues
On Wednesday 03 December 2003 22:25, Gwendowlyn S. Knapp wrote: Maybe I didn't word my question right. I have several proteins (like 15-20) that i need to do this for and i also have these lists. i was wanting to see if there was anyway to have pymol read in that list automatically so i didn't have to type in all the residues (ie, about 60 on each protein). I see two possibilities: 1) write a PyMol function to read the residue list and make the appropriate selections. I do not have enough experience to do this yet. 2) use an editor or script to transform the residue list into a PyMol select command that can be sourced. If the residue list looks like this: 5 10 50 51 52 100 in a file list then a command like sed -e s/^/(protein and resi / -e s/$/) or \\\/ list list.pml will create a file list.pml like this: (protein and resi 5) or \ (protein and resi 10) or \ (protein and resi 50) or \ (protein and resi 51) or \ (protein and resi 52) or \ (protein and resi 100) or \ The ^ in the sed command means beginning of the line, the $ means end of the line. The backslash at the end of each line indicates that the command continues on the next line. There should be no characters after the backslash (other than the newline). Two manual edits transform this into select group,((protein and resi 5) or \ (protein and resi 10) or \ (protein and resi 50) or \ (protein and resi 51) or \ (protein and resi 52) or \ (protein and resi 100) ) Note the additional parentheses around the complete expression. This can be executed in PyMol by typing @list.pml and should select the indicated residues in the molecule protein. Hope this helps, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
