You can subscribe to this list here.
2001 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(13) |
Nov
(22) |
Dec
(35) |
---|---|---|---|---|---|---|---|---|---|---|---|---|
2002 |
Jan
(33) |
Feb
(46) |
Mar
(56) |
Apr
(29) |
May
(56) |
Jun
(30) |
Jul
(64) |
Aug
(54) |
Sep
(86) |
Oct
(106) |
Nov
(50) |
Dec
(67) |
2003 |
Jan
(78) |
Feb
(98) |
Mar
(51) |
Apr
(95) |
May
(53) |
Jun
(103) |
Jul
(93) |
Aug
(64) |
Sep
(87) |
Oct
(93) |
Nov
(78) |
Dec
(86) |
2004 |
Jan
(83) |
Feb
(90) |
Mar
(64) |
Apr
(112) |
May
(103) |
Jun
(57) |
Jul
(101) |
Aug
(84) |
Sep
(92) |
Oct
(96) |
Nov
(86) |
Dec
(32) |
2005 |
Jan
(88) |
Feb
(108) |
Mar
(111) |
Apr
(107) |
May
(120) |
Jun
(134) |
Jul
(143) |
Aug
(129) |
Sep
(75) |
Oct
(171) |
Nov
(125) |
Dec
(65) |
2006 |
Jan
(95) |
Feb
(105) |
Mar
(114) |
Apr
(124) |
May
(87) |
Jun
(66) |
Jul
(88) |
Aug
(65) |
Sep
(71) |
Oct
(92) |
Nov
(94) |
Dec
(60) |
2007 |
Jan
(81) |
Feb
(84) |
Mar
(82) |
Apr
(68) |
May
(58) |
Jun
(80) |
Jul
(30) |
Aug
(47) |
Sep
(68) |
Oct
(92) |
Nov
(59) |
Dec
(17) |
2008 |
Jan
(69) |
Feb
(81) |
Mar
(60) |
Apr
(34) |
May
(47) |
Jun
(65) |
Jul
(46) |
Aug
(49) |
Sep
(84) |
Oct
(43) |
Nov
(33) |
Dec
(30) |
2009 |
Jan
(62) |
Feb
(48) |
Mar
(123) |
Apr
(73) |
May
(72) |
Jun
(69) |
Jul
(78) |
Aug
(72) |
Sep
(99) |
Oct
(82) |
Nov
(70) |
Dec
(53) |
2010 |
Jan
(112) |
Feb
(95) |
Mar
(127) |
Apr
(110) |
May
(135) |
Jun
(91) |
Jul
(91) |
Aug
(79) |
Sep
(136) |
Oct
(63) |
Nov
(38) |
Dec
(64) |
2011 |
Jan
(59) |
Feb
(109) |
Mar
(191) |
Apr
(130) |
May
(94) |
Jun
(90) |
Jul
(89) |
Aug
(127) |
Sep
(135) |
Oct
(113) |
Nov
(136) |
Dec
(140) |
2012 |
Jan
(158) |
Feb
(131) |
Mar
(151) |
Apr
(88) |
May
(121) |
Jun
(85) |
Jul
(82) |
Aug
(56) |
Sep
(55) |
Oct
(125) |
Nov
(87) |
Dec
(65) |
2013 |
Jan
(81) |
Feb
(64) |
Mar
(90) |
Apr
(77) |
May
(80) |
Jun
(92) |
Jul
(92) |
Aug
(70) |
Sep
(69) |
Oct
(60) |
Nov
(99) |
Dec
(50) |
2014 |
Jan
(89) |
Feb
(66) |
Mar
(52) |
Apr
(70) |
May
(68) |
Jun
(44) |
Jul
(68) |
Aug
(81) |
Sep
(152) |
Oct
(106) |
Nov
(74) |
Dec
(57) |
2015 |
Jan
(93) |
Feb
(48) |
Mar
(60) |
Apr
(107) |
May
(82) |
Jun
(64) |
Jul
(74) |
Aug
(38) |
Sep
(49) |
Oct
(99) |
Nov
(105) |
Dec
(51) |
2016 |
Jan
(68) |
Feb
(87) |
Mar
(55) |
Apr
(90) |
May
(68) |
Jun
(25) |
Jul
(25) |
Aug
(41) |
Sep
(35) |
Oct
(55) |
Nov
(24) |
Dec
(26) |
2017 |
Jan
(59) |
Feb
(49) |
Mar
(24) |
Apr
(50) |
May
(45) |
Jun
(63) |
Jul
(36) |
Aug
(26) |
Sep
(22) |
Oct
(23) |
Nov
(26) |
Dec
(29) |
2018 |
Jan
(17) |
Feb
(21) |
Mar
(30) |
Apr
(34) |
May
(24) |
Jun
(47) |
Jul
(65) |
Aug
(30) |
Sep
(24) |
Oct
(52) |
Nov
(21) |
Dec
(17) |
2019 |
Jan
(9) |
Feb
(39) |
Mar
(32) |
Apr
(22) |
May
(30) |
Jun
(69) |
Jul
(40) |
Aug
(48) |
Sep
(17) |
Oct
(26) |
Nov
(30) |
Dec
(19) |
2020 |
Jan
(32) |
Feb
(26) |
Mar
(16) |
Apr
(34) |
May
(50) |
Jun
(87) |
Jul
(51) |
Aug
(23) |
Sep
(25) |
Oct
(48) |
Nov
(32) |
Dec
(6) |
2021 |
Jan
(12) |
Feb
(31) |
Mar
(15) |
Apr
(31) |
May
(13) |
Jun
(13) |
Jul
(24) |
Aug
(9) |
Sep
(11) |
Oct
(28) |
Nov
(26) |
Dec
(25) |
2022 |
Jan
(47) |
Feb
(22) |
Mar
(22) |
Apr
(12) |
May
(4) |
Jun
(26) |
Jul
(17) |
Aug
(2) |
Sep
(13) |
Oct
(6) |
Nov
(13) |
Dec
(4) |
2023 |
Jan
(7) |
Feb
(6) |
Mar
(13) |
Apr
(2) |
May
(25) |
Jun
(13) |
Jul
(12) |
Aug
(10) |
Sep
(5) |
Oct
(13) |
Nov
(19) |
Dec
(7) |
2024 |
Jan
(3) |
Feb
(12) |
Mar
(1) |
Apr
(13) |
May
(11) |
Jun
|
Jul
(20) |
Aug
(4) |
Sep
|
Oct
|
Nov
|
Dec
|
From: Buz B. <bu...@co...> - 2004-02-18 22:00:03
|
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: bu...@co... Phone: 607 255 8678 Fax: 607 255 8751 |---------------------------------------------------------| |
From: Nick S. <sk...@ge...> - 2004-02-18 20:41:45
|
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:wa...@de... >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=1356&alloc_id=3438&op=click >_______________________________________________ >PyMOL-users mailing list >PyM...@li... >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: sk...@ge... Tel. (650) 225 6402 FAX (650) 225 3734 |
From: Warren D. <wa...@de...> - 2004-02-18 20:19:08
|
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:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 |
From: Warren D. <wa...@de...> - 2004-02-18 18:25:57
|
> -----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 |
From: Eric Z. <zo...@ca...> - 2004-02-18 17:27:42
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1"> <title></title> </head> <body text="#000000" bgcolor="#ffffff"> Anyone who works with nucleic acids will certainly prefer the current situation. From the PDB format guidelines:<br> <p>* 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.<br> </p> <p>Eric<br> </p> <br> <br> David A. Horita wrote:<br> <blockquote type="cite" cite="midFA3BADF3FDED7140B92BF82F82CDA00906C28B10@EXCHVS1.medctr.ad.wfubmc.edu"> <pre wrap="">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: <a class="moz-txt-link-abbreviated" href="mailto:pym...@li...">pym...@li...</a> [<a class="moz-txt-link-freetext" href="mailto:pym...@li...">mailto:pym...@li...</a>] On Behalf Of Warren DeLano Sent: Wednesday, February 18, 2004 10:56 AM To: 'John Berrisford'; <a class="moz-txt-link-abbreviated" href="mailto:pym...@li...">pym...@li...</a> 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 </pre> <blockquote type="cite"> <pre wrap="">-----Original Message----- From: <a class="moz-txt-link-abbreviated" href="mailto:pym...@li...">pym...@li...</a> [<a class="moz-txt-link-freetext" href="mailto:pym...@li...">mailto:pym...@li...</a>] On Behalf Of John Berrisford Sent: Wednesday, February 18, 2004 3:42 AM To: <a class="moz-txt-link-abbreviated" href="mailto:pym...@li...">pym...@li...</a> 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! <a class="moz-txt-link-freetext" href="http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click">http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click</a> _______________________________________________ PyMOL-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:PyM...@li...">PyM...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/pymol-users">https://lists.sourceforge.net/lists/listinfo/pymol-users</a> </pre> </blockquote> <pre wrap=""><!----> ------------------------------------------------------- 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! <a class="moz-txt-link-freetext" href="http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click">http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click</a> _______________________________________________ PyMOL-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:PyM...@li...">PyM...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/pymol-users">https://lists.sourceforge.net/lists/listinfo/pymol-users</a> ------------------------------------------------------- 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! <a class="moz-txt-link-freetext" href="http://ads.osdn.com/?ad_id56&alloc_id438&op=click">http://ads.osdn.com/?ad_id56&alloc_id438&op=click</a> _______________________________________________ PyMOL-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:PyM...@li...">PyM...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/pymol-users">https://lists.sourceforge.net/lists/listinfo/pymol-users</a> </pre> </blockquote> </body> </html> |
From: David A. H. <dh...@wf...> - 2004-02-18 16:39:32
|
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: pym...@li... = [mailto:pym...@li...] On Behalf Of Warren = DeLano Sent: Wednesday, February 18, 2004 10:56 AM To: 'John Berrisford'; pym...@li... Subject: RE: [PyMOL] selecting multiple atoms ie oxygen John, =20 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.=20 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: pym...@li... > [mailto:pym...@li...] On Behalf Of=20 > John Berrisford > Sent: Wednesday, February 18, 2004 3:42 AM > To: pym...@li... > Subject: [PyMOL] selecting multiple atoms ie oxygen >=20 > I wish to select multiple oxygens (labelled O1, O2 etc.. > within my pdb file) and colour them red for example. Is there=20 > any easy way of doing this other than typing out a list of=20 > all the oxygens I wish to select? >=20 > eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p)) >=20 > 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=20 > work, or I am using the wrong syntax if its possible. >=20 > Any thoughts would be appreciated. >=20 > John >=20 >=20 > ------------------------------------------------------- > SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and=20 > deploy apps & Web services for Linux with a free DVD software kit from = > IBM. Click Now! = http://ads.osdn.com/?ad_id=3D1356&alloc_id=3D3438&op=3Dclick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 ------------------------------------------------------- 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=3D1356&alloc_id=3D3438&op=3Dclick _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Warren D. <wa...@de...> - 2004-02-18 16:01:30
|
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: pym...@li... > [mailto:pym...@li...] On Behalf Of > John Berrisford > Sent: Wednesday, February 18, 2004 3:42 AM > To: pym...@li... > 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=1356&alloc_id=3438&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: John B. <j.b...@sh...> - 2004-02-18 11:47:01
|
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 |
From: Michael B. <mb...@uv...> - 2004-02-18 10:16:02
|
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=20= > 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=20 combination with the 'resi' function. This is documented in the=20 reference manual. Following is a helpful summary that was sent to me by Robert L.=20 Campbell, Ph.D. Let's say I wanted to create a single residue selection for Lysine 465=20= (and I choose to call the selection 'K465'), so that I could color and=20= display it the way I wanted: (insert your particular atom coordinates=20 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 _______________________________________ =98 Now to create multiple residue selections, just separate the start and=20= 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=20= list and you can further manipulate their display properties as you see=20= fit. Regards, --Michael |
From: Panepucci, E. <zac@SLAC.Stanford.EDU> - 2004-02-18 07:21:19
|
> Thanks for sharing this. my pleasure > Will your python script, along with powermate.py, work on other > platforms like OSX where the default driver/kernel extensions that > come with the powermate have been installed, or is this specific to > the linux driver? as far as I know, the code I wrote uses the linux generic event interface so it will only work under linux, but then again, I only touch Macs every now and then so it could be that porting is easy for a MacOS X expert. Cheers, Zac |
From: <wg...@ch...> - 2004-02-18 05:36:05
|
Hi Zac: Thanks for sharing this. I just bought one of these for MacOSX and it works great with O. Will your python script, along with powermate.py, work on other platforms like OSX where the default driver/kernel extensions that come with the powermate have been installed, or is this specific to the linux driver? Thanks in advance. Bill William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA |
From: Ezequiel P. <zac@SLAC.Stanford.EDU> - 2004-02-18 01:15:28
|
Hello There, I've written a very little piece of python code that uses William R Sowerbutts's rudimentary (his own words) python interface to the powermate device. BE WARNED!! This hack will crash your pymol session when you type "quit" to terminate your pymol session. this wouldn't be a problem if it didn't leave python threads floating around...Anyone knows a workaround? The safest way to quit is to "CTRL-C" the prompt that started pymol. This a first announcement. /dev/input/event* is indeed the future... Cheers, Zac HOWTO: 1) put the python interface (powermate.py) in ${PYMOL_PATH}/modules http://www.sowerbutts.com/powermate/powermate.py 2) put the code below in your $HOME/.pymolrc.py 3) tweak the line that says CONFIGURE to match your setup # # code below starts here # def powermate_reader(): # thread for reading powermate dial import sys from pymol import cmd from powermate import PowerMate dial_down = 0 pm1 = PowerMate('/dev/input/event1') #CONFIGURE while 1: event = pm1.WaitForEvent(1) if event == None: continue sec,usec,type,code,value = event if code == 256: dial_down = not dial_down continue if dial_down: cmd.turn('x',value) else: cmd.turn('y',value) pm = threading.Thread(target=powermate_reader) print 'PowerMate' pm.setDaemon(1) pm.start() |
From: Mario S. <sa...@if...> - 2004-02-17 20:28:54
|
Hi Alex. > 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 t= wo > proteins that were co-crystalized and i would like assign different > colors to them. > thanks for your help. > alex dajkovic > As long as I know you can do that by creating copies of the same molecule= . Do=20 like this: load molecule.pdb, mole create copy, (mole) Then assign different colors to each (for example): color blue, mole color red, copy Finally show each chain separately: show cartoon, (mole & c;A) show cartoon, (copy & c;B) (in the case you what a cartoon representation of chains A and B). I hope that helps you. --=20 Mario Sanches, PhD Student Protein Crystallography Group S=E3o Paulo University, S=E3o Carlos Physics Institute Phone: +55 (16) 273 9868 sa...@if... |
From: ALEX D. <ada...@ku...> - 2004-02-17 20:02:47
|
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 |
From: Warren D. <wa...@de...> - 2004-02-15 22:10:28
|
Bjorn, Whoops! That is definitely an oversight -- I'll see what I can do to correct this. In the meantime, you may need to save a separate = session file for each labeled scene. Cheers, Warren =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Bj=F6rn Kauppi > Sent: Sunday, February 15, 2004 1:59 PM > To: pym...@li... > Subject: [PyMOL] Labels not stored in scenes >=20 > Hi, > I noticed today that labels (other than distances) is not=20 > stored in scenes. Could be very handy in a "live"=20 > presentation to have pre-labeled residues. Is this hard to=20 > implement, or just an oversight? >=20 > Bj=F6rn Kauppi >=20 > ************************************************************** > ************* > This e-mail may contain confidential information proprietary=20 > to Karo Bio AB and is meant for the intended addressee(s)=20 > only. Any unauthorized review, use, disclosure or=20 > distribution is prohibited. If you have received this message=20 > in error, please advise the sender and delete the e-mail and=20 > any attachments from your files. Thank you! > ************************************************************** > ************* >=20 |
From: <bjo...@ka...> - 2004-02-15 22:02:09
|
Hi, I noticed today that labels (other than distances) is not stored in scenes=2E Cou= ld be very handy in a "live" presentation to have pre-labeled residues=2E Is this= hard to implement, or just an oversight? Bj=F6rn Kauppi *************************************************************************** This e-mail may contain confidential information proprietary to Karo Bio AB and is meant for the intended addressee(s) only=2E Any unauthorized review, use, disclosure or distribution is prohibited=2E If you have received this message in error, please advise the sender and delete the e-mail and any attachments from your files=2E Thank you! *************************************************************************** |
From: Warren D. <wa...@de...> - 2004-02-14 01:52:30
|
Eric, For now, set retain_order, on Before writing out your PDB file -- that will insure that nothing changes. I'll look into whether the default behavior can be changed before the next release... Cheers, Warren > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Eric Zollars > Sent: Friday, February 13, 2004 3:59 PM > To: 'pym...@li...' > Subject: [PyMOL] save molecule format > > All- > When using the Pymol ability to save a structure as a PDB > file it appears that the "standard" PDB format is changed in > at least one instance. When a sidechain has more than one > conformation in the crystal structure (A, B), the saved PDB > file will have the two conformations before the amide of the > group instead of after. > Doing nothing more than loading and then saving a > structure to a new file yields the following results. > Original file: > ATOM 87 N SER A 13 2.735 9.167 21.169 1.00 > 9.31 N > ATOM 88 CA SER A 13 2.455 9.048 19.752 1.00 > 10.35 C > ATOM 89 C SER A 13 1.623 10.233 19.278 1.00 > 9.48 C > ATOM 90 O SER A 13 1.775 10.681 18.144 1.00 > 10.31 O > ATOM 91 CB ASER A 13 1.719 7.737 19.462 0.34 > 10.21 C > ATOM 92 CB BSER A 13 1.705 7.743 19.467 0.66 > 14.26 C > ATOM 93 OG ASER A 13 2.552 6.621 19.728 0.34 > 11.15 O > ATOM 94 OG BSER A 13 0.474 7.699 20.166 0.66 > 22.03 O > > After saving to pdb: > ATOM 87 CB ASER A 13 1.719 7.737 19.462 0.34 > 10.21 C > ATOM 88 OG ASER A 13 2.552 6.621 19.728 0.34 > 11.15 O > ATOM 89 CB BSER A 13 1.705 7.743 19.467 0.66 > 14.26 C > ATOM 90 OG BSER A 13 0.474 7.699 20.166 0.66 > 22.03 O > ATOM 91 N SER A 13 2.735 9.167 21.169 1.00 > 9.31 N > ATOM 92 CA SER A 13 2.455 9.048 19.752 1.00 > 10.35 C > ATOM 93 C SER A 13 1.623 10.233 19.278 1.00 > 9.48 C > ATOM 94 O SER A 13 1.775 10.681 18.144 1.00 > 10.31 O > > As far as I can tell it only happens with those sidechains > with multiple conformations. Anyone else have this problem? > Is there a quick fix? > > Pymol 0.93 on Fedora Core 1. > > Thanks. > Eric Zollars > > ------------------------------------------------------- > 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=1356&alloc_id=3438&op=click > _______________________________________________ PyMOL-users > mailing list PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Eric Z. <zo...@ca...> - 2004-02-13 23:57:33
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1"> <title></title> </head> <body text="#000000" bgcolor="#ffffff"> <span style="font-family: monospace;">All-</span><br style="font-family: monospace;"> <span style="font-family: monospace;"> When using the Pymol ability to save a structure as a PDB file it appears that the "standard" PDB format is changed in at least one instance. When a sidechain has more than one conformation in the crystal structure (A, B), the saved PDB file will have the two conformations before the amide of the group instead of after.</span><br style="font-family: monospace;"> <span style="font-family: monospace;"> Doing nothing more than loading and then saving a structure to a new file yields the following results.</span><br style="font-family: monospace;"> <span style="font-family: monospace;">Original file:</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 87 N SER A 13 2.735 9.167 21.169 1.00 9.31 N</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 88 CA SER A 13 2.455 9.048 19.752 1.00 10.35 C</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 89 C SER A 13 1.623 10.233 19.278 1.00 9.48 C</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 90 O SER A 13 1.775 10.681 18.144 1.00 10.31 O</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 91 CB ASER A 13 1.719 7.737 19.462 0.34 10.21 C</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 92 CB BSER A 13 1.705 7.743 19.467 0.66 14.26 C</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 93 OG ASER A 13 2.552 6.621 19.728 0.34 11.15 O</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 94 OG BSER A 13 0.474 7.699 20.166 0.66 22.03 O</span><br style="font-family: monospace;"> <br style="font-family: monospace;"> <span style="font-family: monospace;">After saving to pdb:</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 87 CB ASER A 13 1.719 7.737 19.462 0.34 10.21 C</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 88 OG ASER A 13 2.552 6.621 19.728 0.34 11.15 O</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 89 CB BSER A 13 1.705 7.743 19.467 0.66 14.26 C</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 90 OG BSER A 13 0.474 7.699 20.166 0.66 22.03 O</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 91 N SER A 13 2.735 9.167 21.169 1.00 9.31 N</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 92 CA SER A 13 2.455 9.048 19.752 1.00 10.35 C</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 93 C SER A 13 1.623 10.233 19.278 1.00 9.48 C</span><br style="font-family: monospace;"> <span style="font-family: monospace;">ATOM 94 O SER A 13 1.775 10.681 18.144 1.00 10.31 O</span><br style="font-family: monospace;"> <br> As far as I can tell it only happens with those sidechains with multiple conformations. Anyone else have this problem? Is there a quick fix?<br> <br> Pymol 0.93 on Fedora Core 1.<br> <br> Thanks.<br> Eric Zollars<br style="font-family: monospace;"> </body> </html> |
From: Jason V. <tr...@ve...> - 2004-02-13 06:36:31
|
From: "Murray, Jeremy" <Jer...@ch...> > To: "'pym...@li...'" > <pym...@li...> > Date: Thu, 12 Feb 2004 10:50:57 -0800 > Subject: [PyMOL] png2avi command line jiffy > > After searching far and wide for a freeware jiffy > to convert png files to an animation (contrary to > popular belief scientists in industry operate under > tight fiscal constraints), I found imgcon which I find > very useful: > > http://www.fmrib.ox.ac.uk/~yongyue/imgcondl.html Jeremy (et. al.) May I also suggest you investigate ImageMagick if you haven't already. I think this a very popular command line based image processing package used under *nix (and supported under MS Windows as well). Main website: http://www.imagemagick.org/ It's released under a very 'loose' or 'open' ($FREE$) license; if you want to read it check out http://www.imagemagick.org/www/Copyright.html. Regards, |
From: Murray, J. <Jer...@ch...> - 2004-02-12 18:52:36
|
After searching far and wide for a freeware jiffy to convert png files to an animation (contrary to popular belief scientists in industry operate under tight fiscal constraints), I found imgcon which I find very useful: http://www.fmrib.ox.ac.uk/~yongyue/imgcondl.html Jeremy M. Murray Chiron Corporation | SMDD 4560 Horton Street M.S. 4.4 Emeryville CA 94608-2916 Tel: 510.923.6946 Fax: 510.923.5550 jer...@ch... |
From: Warren D. <wa...@de...> - 2004-02-11 23:13:45
|
Jose, Thanks to some recent and much appreciated development assistance from PyMOL user, this is something I hope we can deliver in the next release... For now, save your ray-traced images as PNG files and then annotate manually in PowerPoint, Photoshop, or Keynote. Sorry for the inconvenience. Cheers, Warren > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Jose Avalos > Sent: Wednesday, February 11, 2004 1:01 PM > To: Warren DeLano > Cc: pym...@li... > Subject: [PyMOL] labels > > > Dear all: > > What do I need to do avoid losing the labels when I ray trace? > > Thank you again > > Jose > > > > ------------------------------------------------------- > 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=1356&alloc_id=3438&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Jose A. <ja...@gr...> - 2004-02-11 21:02:57
|
Dear all: What do I need to do avoid losing the labels when I ray trace? Thank you again Jose |
From: Warren D. <wa...@de...> - 2004-02-11 20:56:21
|
Leigh, Get_dihedral can do what you need -- I think the problem is that you need to be more narrow in your atom selections. Otherwise, 9/C will match every atom named "C", in every residue "9", and in every protein loaded. With two proteins loaded: load prot1.pdb load prot2.pdb You'll need to restrict each atom selection to just one of the two proteins: get_dihedral prot1///9/C, prot1///10/N, prot1///10/CA, prot1///10/C Cheers, Warren > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > le...@rs... > Sent: Wednesday, February 11, 2004 12:18 PM > To: pym...@li... > Subject: [PyMOL] get_dihedral & multiple objects > > I am trying to use the get_dihedral routine. If I've got > just one object it works as expected. For example: > > PyMOL>get_dihedral 9/C, 10/N, 10/CA, 10/C (I type in) > cmd.get_dihedral: -49.721 degrees. (pymol replies) > > But if I've got MORE than one object loaded, which I usually > do, pymol gives me this error: > > GetDihedral-Error: Selection 1 doesn't contain a single atom/vertex. > GetDihedral-Error: Selection 2 doesn't contain a single atom/vertex. > GetDihedral-Error: Selection 3 doesn't contain a single atom/vertex. > GetDihedral-Error: Selection 4 doesn't contain a single atom/vertex. > > I **need** to be able to call get_dihedral when I've got more > than one object loaded. De-selecting all but one object > doesn't work either. I have tried everything that I can think of. > Loading multiple pdb files into one object DOES Work (and > then I specify a state to get_dihedral), but again this is > not what I want to do. > > Can someone please help me? > > Leigh Willard > le...@rs... > University Laval > > > > ------------------------------------------------------- > 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=1356&alloc_id=3438&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Robert C. <rl...@po...> - 2004-02-11 20:48:09
|
Leigh, * le...@rs... <le...@rs...> [2004-02-11 15:18] wrote: > I am trying to use the get_dihedral routine. If I've got just one object > it works as expected. For example: > > PyMOL>get_dihedral 9/C, 10/N, 10/CA, 10/C (I type in) > cmd.get_dihedral: -49.721 degrees. (pymol replies) > > But if I've got MORE than one object loaded, which I usually do, > pymol gives me this error: > > GetDihedral-Error: Selection 1 doesn't contain a single atom/vertex. > GetDihedral-Error: Selection 2 doesn't contain a single atom/vertex. > GetDihedral-Error: Selection 3 doesn't contain a single atom/vertex. > GetDihedral-Error: Selection 4 doesn't contain a single atom/vertex. > You need to specify the object in the atom spec above. If your object is called "obj1", then: PyMOL>get_dihedral obj1///9/C, obj1///10/N, obj1///10/CA, obj1///10/C should work. Or using the other atom specification syntax for those that find it clearer, if more verbose: PyMOL>get_dihedral obj1 & i. 9 & n. c, obj1 & i. 10 & n. n, obj1 & i. 10 & n. ca, obj1 & i. 10 & n. c Cheers, Rob -- Robert L. Campbell, Ph.D. <rl...@po...> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 |
From: <le...@rs...> - 2004-02-11 20:19:53
|
I am trying to use the get_dihedral routine. If I've got just one object it works as expected. For example: PyMOL>get_dihedral 9/C, 10/N, 10/CA, 10/C (I type in) cmd.get_dihedral: -49.721 degrees. (pymol replies) But if I've got MORE than one object loaded, which I usually do, pymol gives me this error: GetDihedral-Error: Selection 1 doesn't contain a single atom/vertex. GetDihedral-Error: Selection 2 doesn't contain a single atom/vertex. GetDihedral-Error: Selection 3 doesn't contain a single atom/vertex. GetDihedral-Error: Selection 4 doesn't contain a single atom/vertex. I **need** to be able to call get_dihedral when I've got more than one object loaded. De-selecting all but one object doesn't work either. I have tried everything that I can think of. Loading multiple pdb files into one object DOES Work (and then I specify a state to get_dihedral), but again this is not what I want to do. Can someone please help me? Leigh Willard le...@rs... University Laval |