Re: [PyMOL] question on differential coloring of protein chains
On Tuesday, February 17, 2004, at 02:57 PM, ALEX DAJKOVIC wrote: hello- i am new to pymol and am trying to figure out how to differentially color different chains (i.e. different proteins) in the structure i am viewing. the structure i am working with is actually a structure of two proteins that were co-crystalized and i would like assign different colors to them. thanks for your help. alex dajkovic Hello Alex, I think what you want is to use the 'select' function in combination with the 'resi' function. This is documented in the reference manual. Following is a helpful summary that was sent to me by Robert L. Campbell, Ph.D. Let's say I wanted to create a single residue selection for Lysine 465 (and I choose to call the selection 'K465'), so that I could color and display it the way I wanted: (insert your particular atom coordinates file name where you see square brackets below) ___ select K465, ([filename] and chain A and resi 465) or you could shorten the selection string: select ak465, (abc c. a and r. 465) or use the shorthand notation: select ak465, /abc//a/465 ___ ˜ Now to create multiple residue selections, just separate the start and end residue numbers by a colon, I think, following the word 'resi' Once you create your unique selections they show up in the right panel list and you can further manipulate their display properties as you see fit. Regards, --Michael
[PyMOL] selecting multiple atoms ie oxygen
I wish to select multiple oxygens (labelled O1, O2 etc.. within my pdb file) and colour them red for example. Is there any easy way of doing this other than typing out a list of all the oxygens I wish to select? eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p)) I know in molscript its posible to use a o* label to select all oxygens, is such a switch possible in pymol. It doesn't work, or I am using the wrong syntax if its possible. Any thoughts would be appreciated. John
RE: [PyMOL] selecting multiple atoms ie oxygen
John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names is that some ill-conceived PDB files actually use them in atom names. However, PyMOL does support the use of a terminal wildcard in some cases, such as with the delete command... create obj01, none create obj02, none delete obj* And with residue names color red, as* color blue, gl* color pink, hi* Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of John Berrisford Sent: Wednesday, February 18, 2004 3:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] selecting multiple atoms ie oxygen I wish to select multiple oxygens (labelled O1, O2 etc.. within my pdb file) and colour them red for example. Is there any easy way of doing this other than typing out a list of all the oxygens I wish to select? eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p)) I know in molscript its posible to use a o* label to select all oxygens, is such a switch possible in pymol. It doesn't work, or I am using the wrong syntax if its possible. Any thoughts would be appreciated. John --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
FW: [PyMOL] selecting multiple atoms ie oxygen
Warren, Personally, I'd much rather have wild-card selections in atom names and have to deal individually with the ill-conceived PDB files than the other way around. Regards, David Horita -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren DeLano Sent: Wednesday, February 18, 2004 10:56 AM To: 'John Berrisford'; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] selecting multiple atoms ie oxygen John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names is that some ill-conceived PDB files actually use them in atom names. However, PyMOL does support the use of a terminal wildcard in some cases, such as with the delete command... create obj01, none create obj02, none delete obj* And with residue names color red, as* color blue, gl* color pink, hi* Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of John Berrisford Sent: Wednesday, February 18, 2004 3:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] selecting multiple atoms ie oxygen I wish to select multiple oxygens (labelled O1, O2 etc.. within my pdb file) and colour them red for example. Is there any easy way of doing this other than typing out a list of all the oxygens I wish to select? eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p)) I know in molscript its posible to use a o* label to select all oxygens, is such a switch possible in pymol. It doesn't work, or I am using the wrong syntax if its possible. Any thoughts would be appreciated. John --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] wild card
Anyone who works with nucleic acids will certainly prefer the current
situation. From the PDB format guidelines:
* The asterisk (*) is used in place of the prime character (')
for naming atoms of the sugar group. The prime was avoided historically
because of non-uniformity of its external representation.
Eric
David A. Horita wrote:
Warren,
Personally, I'd much rather have wild-card selections in atom names and have to deal individually with the ill-conceived PDB files than the other way around.
Regards,
David Horita
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren DeLano
Sent: Wednesday, February 18, 2004 10:56 AM
To: 'John Berrisford'; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] selecting multiple atoms ie oxygen
John,
color red, 5paa and elem o
The problem with using asterices as wildcards in atom names is that some ill-conceived PDB files actually use them in atom names.
However, PyMOL does support the use of a terminal wildcard in some cases, such as with the delete command...
create obj01, none
create obj02, none
delete obj*
And with residue names
color red, as*
color blue, gl*
color pink, hi*
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
John Berrisford
Sent: Wednesday, February 18, 2004 3:42 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] selecting multiple atoms ie oxygen
I wish to select multiple oxygens (labelled O1, O2 etc..
within my pdb file) and colour them red for example. Is there
any easy way of doing this other than typing out a list of
all the oxygens I wish to select?
eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p))
I know in molscript its posible to use a o* label to select
all oxygens, is such a switch possible in pymol. It doesn't
work, or I am using the wrong syntax if its possible.
Any thoughts would be appreciated.
John
---
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RE: [PyMOL] selecting multiple atoms ie oxygen
-Original Message- From: Charlie Sent: Wednesday, February 18, 2004 8:56 AM To: Warren DeLano Subject: Re: [PyMOL] selecting multiple atoms ie oxygen Warren DeLano wrote: John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names is that some ill-conceived PDB files actually use them in atom names. However, PyMOL does support the use of a terminal wildcard in some cases, such as with the delete command... create obj01, none create obj02, none delete obj* And with residue names color red, as* color blue, gl* color pink, hi* Cheers, Warren Hi Warren, I've struggled with this a couple of times. Could it be worth finding another way round, so that a consistent role for * exists. Might it not be better to require users to somehow escape *'s in atom names and then allow * as a wildcard. Although this might be less clear for newbies, the lack of * as a wilcard in atom names is currently unclear. I don't know much about python, but the unix system of escaping special chars with a backslash would be an option, then one could select foo,(bar//A/50/*1\*) to get atoms O1* and C1* from the molecule. You've probably been through this and have a perfectly sound reason for not doing it ! The newbie issue is what troubled me. Unix hacks know how to edit PDB files to replace asterisks with something more benign, and they know to escape common wildcards -- but the ordinary person does not. Clearly we can't make everyone happy, so perhaps consistency should be the guide? But on the other hand, we are talking about a huge portion of the PDB. Nearly every nucleic acid structure seems to suffer from this unfortunate naming convention (~5000 PDB entries contain C1\* according to grep of a recent copy of the PDB). It is true that well-established conventions already exist for handling asterisks, but I don't believe in following conventions blindly, particularly when so many people would be negatively affected. I welcome further discussion on this point. Guidance from the community will be crucial, since I don't have a good solution in mind yet. Some food for thought: 1) Are atom name wildcards really needed when a more precise way of selecting by element symbol already exists? 2) If so, then what are the proposals? a. Escape non-wildcard asterisks with backslash? (regexp convention, but would trip-up newbies, break current PyMOL scripts, and inconvenience a whole field of research) b. Escape wildcard asterisks in atom names with a backslash (that would be very backwards from the standard convention and create further confusion). c. Add a configurable atom_name_wildcard toggle? d. Support alternative wildcards for atom names? Would . or .* work? Also note that currently PyMOL doesn't have a regexp engine, and it doesn't support full wildcards -- just terminal astericks in a few situations. Full regexps matching (and thus full convention adherence) would be a nice addition in the future, but it will need to be configured somehow as well, probably via some global setting like regexp_based_matching. Cheers, Warren
Re: [PyMOL] PyMOL/MacPyMOL Beta Feedback
Hi there Warren, I have been using the v0.94 MacPyMOL that we got from you last december. It has been very stable on my desktop system: dual cpu G4867 MHz power PC (version 2.1) OSX 10.2.8 (6R73) v0.94 However, using the same version on my lap top has not been so reliable G4 powerbook 6.2 version 1.1 OSX 10.2.8 (6R73) v0.94 Not sure about the graphics cards as they are not listed by the system profiler. It may be purely circumstantial, but I most often see the crash on my lap top after I have run dss to get secondary structure. I will keep an eye on this behaviour and let you know if I see any trends. Nick Warren DeLano wrote: MacPyMOL beta testers: Are the latest beta builds of MacPyMOL still exhibiting a significant number of spontaneous crashes in your hands? http://delsci.com/macpymol So far, I have been utterly unable to reproduce the reported instability on my G4 and G5 test systems. Thus, I am wondering whether the problems might be related to some sort of hardware or OS variability. If you are still experiencing consistent problems, then please provide specific details on your system: - Processor/Mac Model - Graphics Card - Specific MacOS version #. - Latest beta version used. For Windows Linux users: I have also posted a couple of equivalent beta builds for Linux and Windows. If you would like to cautiously play around with and provide feedback on the development versions, then you may do so via: http://delsci.com/beta. However, please do not treat these build as formal releases. They are not too stable and certain aspects of the user interface remain fluid as old demons are exorcized and new demons understood. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Nick Skelton, Ph.D. Department of Medicinal Chemistry Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080 E-mail: ske...@gene.com Tel.(650) 225 6402 FAX (650) 225 3734
[PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
Hi, I've been using Pymol 0.93 on SuSE Linux 8.2 for a few hours now, and I'm having trouble ray tracing graphics. I installed Pymol from the source file pymol-0_93-src.tgz. Each time I start the ray tracer Pymol quits with a segmentation fault error; /usr/local/pymol/pymol.com: line 2: 29720 Segmentation fault /usr/bin/python /usr/lib/python2.2/site-packages/pymol/__init__.py $* I've tried setting max_threads to 1, and this doesn't resolve the problem. I've also downloaded the patch for glibc from SuSE and this doesn't help the problem either. Can anyone help? Best, --Buz |-| Buz Barstow 192 Clark Hall Cornell University Ithaca, NY 14853, USA Email: b...@cornell.edu Phone: 607 255 8678 Fax: 607 255 8751 |-|
[PyMOL] molecular surface colored by hydrophobicity
Dear all, I am preparing a figure of a molecualr surface, colored by the hydrophobicity of surface residues. Can pymol do this job? How about showing atom C* in a color, and N* and O* in another color? In fact I have tried GRASP but failed in coloring the surface. I used r=hyd, but could not color the surface of those redisues. This is an old version of grasp (1.0?). I am not familiar with this program. If anybody can tell me the correct way of doing it in grasp, it will also be greatly appreciated. Rongjin Guan
Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
Dear Buz, I've been using Pymol 0.93 on SuSE Linux 8.2 for a few hours now, and I'm having trouble ray tracing graphics. Each time I start the ray tracer Pymol quits with a segmentation fault error; I guess you are running into a compiler bug (or a bug in PyMol which gets exposed only by some compiler versions). For me PyMol on SuSE 8.2 crashed always when raytracing a line element. The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) solved the problem for me. See PyMol bugreport 806361. Thomas -- Thomas Siegmund, Ph.D. DeveloGen AG Bioinformatics and Data Management Phone: +49(551) 505 58 651 E-Mails können unvollständig oder fehlerhaft oder manipuliert sein. Sie dienen daher stets nur der Information. Rechtsverbindliche Willenserklärungen müssen in Schriftform, d.h. mindestens per Telefax mit Unterschrift des Erklärenden, abgegeben werden, um wirksam zu sein. Unsere E-Mails sind stets vertraulich und nur für den angegebenen Adressaten bestimmt. Andere Empfänger werden gebeten, diese Nachricht zu löschen. Jede unberechtigte Weiterleitung ist untersagt. Trotz ergriffener Vorsichtsmaßnahmen gegen Viren kann keine Haftung für etwaige Schäden aus der Verwendung dieser E-Mail übernommen werden. E-mails may be incomplete or be subject to change without notice. Therefore the content of this E-mail is not binding unless confirmed by letter or by telefax with signature of the author. Our E-mails are confidential and dedicated to the intended recipient only. If you are not an intended recipient, please delete the original message and all copies. Any unauthorized distribution is strictly prohibited. Although precautions have been taken to prevent the existence of viruses in this E-mail, the company cannot accept any responsibility for any damage arising out of or from the use of this E-mail.
