Re: [PyMOL] problems cloring sticks
Ariel, I would just add to Andreas' reply that in my case (onboard intel GMA-HD, Suse linux, core i3) either using ray (and if you have a lot of memory, set setting-rendering-memory- use most) or saving the pse and making images on a windows PC (or a linux PC with an nvidia graphics card) are the workarounds I use. Not a solution per se, but this seems to be an issue between OpenGL and Intel (although I've only seen problems with Pymol, and not vmd). -David David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston Salem, NC 27157, USA From: Andreas Spitzmüller [andreas.spitzmuel...@staff.uni-marburg.de] Sent: Sunday, June 05, 2011 11:09 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] problems cloring sticks Hi Ariel, I'm facing the same problem on my Ubuntu laptop with an onboard Intel graphics chip. And as far as I know it is a problem of the linux graphics driver. From my side this is a huge problem for making figures. However, I found that ray tracing is not affected by this bug. I know that this is for sure not convenient, but still it is possible to make figures for publication or presentation slides. Just try the 'ray' command to see if this yields correct coloring for you, too. Regards, Andreas Am 05.06.2011, 08:29 Uhr, schrieb Ariel Talavera talav...@cim.sld.cu: Hi Jason, After some struggle, I finally compiled the last open source version, Pymol 1.4.1. Unfortunately, the same problem persist. I still not able to properly colored residues shown as sticks. From my side this is a huge problem for making figures. Best regards, Ariel On Wed, 2011-06-01 at 12:35 -0500, Jason Vertrees wrote: Hi Ariel, This is a known problem on some machines with ATI or Intel video cards. You can try upgrading to a newer version of PyMOL. Also, please check that your video driver is the newest for your video card. If I find a solution on our side that fixes this, I'll update the open-source. Cheers, -- Jason On Wed, Jun 1, 2011 at 12:04 PM, Ariel Talavera talav...@cim.sld.cu wrote: Hi Pymolers, I am having problems coloring residues when they are shown as stick. The coloring is properly working for the other representations like, lines, surface or spheres. I am using Pymol 1.2r2 under Ubuntu 11,04. Thanks in advanced, best regrads, Ariel Centro de Inmunologia Molecular phone: +537 2717933 e-mail: c...@cim.sld.cu web:www.cim.co.cu Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -- Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Data protection magic? Nope - It's vRanger. Get your free trial download today. http://p.sf.net/sfu/quest-sfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Centro de Inmunologia Molecular phone: +537 2717933 e-mail: c...@cim.sld.cu web:www.cim.co.cu Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -- Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Discover what all the cheering's about. Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Andreas Spitzmüller, M.Sc (Bioinformatics) Group Prof. Gerhard Klebe Institute of Pharmaceutical Chemistry Philipps-Universität Marburg Marbacher Weg 6 D-35037 Marburg Phone: +49-6421-28-21339 Email: andreas.spitzmuel...@staff.uni-marburg.de www.agklebe.de -- Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Discover what all the cheering's about. Get your free
[PyMOL] can't save pdb from within pymol
Hi, I've apparently managed to create a pse of a protein that loads fine but won't save the pdb coordinates (I get a file with END in it, and nothing else). Any ideas how to get the coordinates out? pymol 1.1b3 linux, windows (same pse has same result under both OS's) Thanks, Dave - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edumailto:dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htmhttp://www1.wfubmc.edu/biochem/faculty/Horita.htm/ -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] cd in windows
Hi, How does one change directories in Windows when the directory name has a space in it? I've tried double and single quotes as well as backslash space (I'd like to run a script that's in such a directory). Thanks David - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm http://www1.wfubmc.edu/biochem/faculty/Horita.htm/ -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] cd in windows
Thanks for the replies/suggestions. Looks like I may need to upgrade from v1.1, but: cd \program files, \program files, and \program?files give a variant of PyMOLcd \program files Traceback (most recent call last): File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\externing.py, line 46, in cd os.chdir(dir) # raises on error OSError: [Errno 22] Invalid argument: '\\program files' cd \progra~1 does work, however. Pymol 1.1r1 running on Vista (32-bit) Business. -David -Original Message- From: Edward A. Berry [mailto:ber...@upstate.edu] Sent: Mon 9/20/2010 2:03 PM Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] cd in windows David A. Horita wrote: Hi, How does one change directories in Windows when the directory name has a space in it? I've tried double and single quotes as well as backslash space (I'd like to run a script that's in such a directory). Thanks David These all work for me: cd \program files cd \program files cd \program?files dir/x \prog* 06/05/2010 10:02p DIR PROGRA~1 cd \progra~1 Or run in your data directory using full path of the executable: \program files\seamonkey\seamonkey.exe (seamonkey is artemia the brine shrimp, you understand. Diminutive alternative to thunderbird and firefox) -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Feature Request/Ideas
Hi, I would definitely not like to see a default representation to be any more than lines (as it is now). Opening one of my 100,000 atom MD trajectory frames would take far longer than it's worth. Regarding png output, I think this is in there already (but don't remember) - I'd like to be able to specify one dimension (usually width) and have the other automatically calculated. If I'm trying to frame a molecule and adjust the size of the screen window I'll want output to keep the same aspect ratio. Also, I see a major slowdown when running remotely as compared to VMD, especially with regards to using the menus (top and right). I get an unable to create direct context rendering message, and while I don't expect it to perform as well as when running locally, I get very adequate performance running VMD over the same connection. This is useful when checking of MD or NMR calculations on a remote cluster from my lab machines. The slowdown (especially the view descriptor menu on the right side) is apparent even over a gigE lan. I'll add another voice for a better undo function. In my specific case I can think of a number of times where I've highlighted a collection of residues as spheres and then accidentally added spheres to the whole molecule instead of the next selection. Being able to get back from that (even one step) would be a time-saver. Dave - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm -Original Message- From: David Hall [mailto:dwash59_2...@yahoo.com] Sent: Thursday, January 21, 2010 9:20 AM To: Jason Vertrees; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL on the Mac Alright, here's a feature request that might convince people who still don't believe, despite your first commit to pymol trunk post-acquisition including Fixed a GL build bug on OSX (see http://pymol.svn.sourceforge.net/viewvc/pymol?view=revrevision=3887 ) A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Hopefully I'm out of ideas nows, David -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to plot residu with a number 9999
Stephane, What I've done in these situations is broken the many-residue blocks (typically water) into different chainID's and segid's. Then select with by both residue number and segid (or chainID or both). That said, I don't think segid's are a part of the official pdb specification anymore (although pymol doesn't have a problem with them). As for getting around the 5-digit limit in overall atoms, I think different packages have different tricks, including * (not particularly useful) and hexadecimal (vmd/namd). Overall, this points out a glaring problem with fixed-width fields, but that's another discussion... Regards, David - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Monday, June 08, 2009 8:01 PM To: Stephane Abel; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to plot residu with a number Stephane, As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB residue identifier field is only four characters wide. So how could you possibly have a PDB file with residue identifiers larger than ? Cheers, Warren -Original Message- From: Stephane Abel [mailto:stephane.a...@cea.fr] Sent: Monday, June 08, 2009 7:30 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to plot residu with a number Hi pymol users It seems that the command select, residue xxx to plot residue xxx where xxx is greater than does not work in pymol version 0.99rc6 Indeed for a pdb file with ~ 13800 residue, if i use the command: select water1846, residue 1846 - the water molecule with the residue number 1846 is plotting But when i use the same command (say select water11100, residue 11100) for plotting the residue 11100 the previous command does not work How to tackle this problem. Thanks in advance for your help Stephane -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] hydrogen naming
Hi, How do I get proper (HN,HA, HE1, etc) hydrogen naming when using h_add (instead of H01, H02, ...)? Worst case I can build them in Xplor/CNS; second worst would be if there is a uniform rule per residue that I could write a script to convert on a residue type basis. Thanks, Dave - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm http://www1.wfubmc.edu/biochem/faculty/Horita.htm/
[PyMOL] pymol nstall problems
Hi, I've been unable to install Pymol recently on an XP Pro-SP2 system. I'll start setup.exe, and ntvdm.exe starts running but nothing progresses from there (no error messages and installshield doesn't start). I'm not sure if it's a software conflict with something else running, but it's likely (and the PC is managed/regulated by the IS department, so I have limited ability to muck around with it, and they like to push patches in the middle of the night). At one time I successfully installed 0.99rc6, but now that install also fails, so something has changed. I've seen other posts where people have had problems with the 5.10.130.0 version of installshield on xp; I've cleaned out my temp directory, and tried running setup in various compatibility modes and with its own memory space, and in safe mode. Has anyone else seen/fixed this problem? Thanks, Dave - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm http://www1.wfubmc.edu/biochem/faculty/Horita.htm/
[PyMOL] low-end graphics cards/laptops
Hi, While I've seen a number of examples of good graphics cards to use with Pymol, I'd like some feedback on what an acceptable low-end is for a Windows laptop computer. Specifically, is the Intel GMA950 completely useless or just not very good. Likewise, does the X3100 help (this seems to be weak on driver support)? My current system uses an ATI Mobility Radeon 9200, which is a few years old and not a high-end gaming/workstation card, but lets me spin a molecular cartoon or surface of a ~300 residue protein without any problems (if the 950 or X3100 equal this level, I'll be satisfied). Many of the current crop of 5 lb notebooks use integrated graphics for price and battery life. If these units don't provide sufficient graphics power for Pymol/VMD/Deepview, the useful market shrinks substantially. Thanks, David - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm http://www1.wfubmc.edu/biochem/faculty/Horita.htm/
RE: [PyMOL] GUI
Hi- I'd second this; my brain doesn't do well keeping track of whether I'm, for example, in maximum or reasonable performance mode. David - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Mark A Saper Sent: Friday, January 20, 2006 3:01 PM To: Pymol Subject: [PyMOL] GUI Hi Warren, Why can't we have little check marks in the main menu that indicate the current setting? For example, SettingRenderingAntialias gets a check, but selecting SettingRenderingShadowsNone doesn't give a check (as do any of the other rendering options). Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Ray, png
Hi, On the subject of larger image sizes, I had a question a while back; I'd like to know if it's been addressed or anyone has a quick(er) workaround- Basically, is there in inverse to the viewport command? i.e., if I manually resize the Pymol window to fit around the molecule I'm displaying, how can I get the relative dimensions of the new window? These dimensions are needed for the Ray command to keep proper perspective. What I've done in the past is save a small image of what's displayed in the window, used a graphics program to determine the x y dimensions, and then used these to generate a high-resolution ray traced image with the same x/y ratio. I figure I'm missing something. Regards, - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm http://www1.wfubmc.edu/biochem/faculty/Horita.htm/
RE: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver
Hi, I Haven't tried VMD yet, but Windows XP-pro pymol crashes upon file open under the 71.84 drivers, but not the 70.78 drivers. (Quadro 1300, XP-Pro servicepack 2) David Horita -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of John Stone Sent: Monday, March 28, 2005 10:10 AM To: Sabuj Pattanayek Cc: pymol-users@lists.sourceforge.net; vm...@ks.uiuc.edu Subject: Re: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver Hi, Have you reported the crashes to NVidia? I'd suggest sending an email to their linux-b...@nvidia.com mail address. The fact that multiple packages crash with the new driver indicates that they may have a new bug in their drivers. You mentioned that making a licorice rep crashes your VMD on that driver, what about VDW or bonds? Do they have a similar effect? John Stone v...@ks.uiuc.edu On Sat, Mar 26, 2005 at 04:42:42PM -0600, Sabuj Pattanayek wrote: Yeah I have the same problem in the beta pymol, haven't tried the stable version: OpenGL-based graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro4 750 XGL/AGP/SSE/3DNOW! GL_VERSION: 1.5.3 NVIDIA 71.67 Hardware stereo capability detected. Adapting to Quadro hardware... Detected 2 CPUs. Enabled multithreaded rendering. /usr/bin/pymol: line 14: 8852 Segmentation fault $PYMOL_PATH/pymol.exe $* and 7167 won't compile on 2.6.10-11? kernels either, need 2.6.12-rc1, haven't tested others. I get similar crashes in VMD 1.8.2+ using 7167 also. For instance, if you load a pdb and try to make a licorice representation, vmd just closes/crashes. I also think this maybe a Quadro problem and not a a problem with GeForce cards. I have a GeForce 5500 FX on another machine and it doesn't have these programs, and realtime GLSL rendering works very nicely in vmd 1.8.3. Sorry for posting this on both mailing lists, just trying to avoid reposting. ..Sabuj Pattanayek HuiZhe Li wrote: just upgraded nvidia driver from 6629 to 7167 (Linux, RHEL 4) and pymol crashes when a molecule is load. is there a fix? (pymol worked fine with 6629 driver). OpenGL-based graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro FX 1400/PCI/SSE2 GL_VERSION: 1.5.3 NVIDIA 71.67 Adapting to Quadro hardware... /usr/local/bin/pymol: line 14: 4575 Segmentation fault (core dumped) $PYMOL_PATH/pymol.exe $* __ Do you Yahoo!? Yahoo! Small Business - Try our new resources site! http://smallbusiness.yahoo.com/resources/ --- SF email is sponsored by - The IT Product Guide Read honest candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595alloc_id=14396op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: jo...@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 --- SF email is sponsored by - The IT Product Guide Read honest candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595alloc_id=14396op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] rotating molecules
Hi, Let's say I load 4 molecules, A, B, C, D. A and B are a heterodimer pair, as are C and D. I'd like to move/rotate A and B together, maintaining their respective orientations, while holding C and D fixed (e.g., manually overlaying dimer structures). How do I do this? I might have hit on the appropriate combination of protecting/freezing/creating objects/etc. once, but can't seem to repeat the routine. Thanks for any tips, David Horita - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/
RE: [PyMOL] ray command
Hi, Regarding the use of the ray command, is there a way to automatically set either the x or y value to maintain the same aspect ratio as displayed in the window? For that matter, how do you determine the number of x and y points displayed (other than making a bitmap and loading that into another program)? -David Horita Mohammed, ray width, height png filename.png for example, for a 5x4 figure at 300 dpi: ray 1600,1200 png hires.png (or use Save image... from the File menu after the ray command) Cheers, Warren
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] unsetting cartoon_colors
Hi all, I have a collection of molecules and want to color a particular helix (in cartoon mode) a specific color different from other helices. Unfortunately, I had previously set cartoon_color from default to another color, so now specifying a color for that helix (or even color red, ss h) has no impact. (it does change the color of the Calpha, but not the cartoon itself). So, the question is, how do I unset the cartoon_color variable (without wiping out my scene)? The variable setting comes with the .pse file, set cartoon_color, default gives an error about not knowing what color default is. Thanks, Dave Horita - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/
[PyMOL] Nuvision stereo glasses?
Hi, Is anyone using the Nuvision 60GX stereo glasses with FireGL Z1 or QuadroFX 500 cards under linux? Or any other non-nVidia card which supports quad-buffered stereo but doesn't have a mini-din connector on-board (i.e., not the 256 Mb FireGL X1). It would be nice to avoid the problems with the nVidia stereo drivers, but I'd rather not buy the FX1000+/FireGL X1 level card, and FireGL2/4 are getting old (and hard to find). The Nuvision guys told me that their VGA passthrough (the -100 model, not the -NSR model), picks up the stereo sync from nVidia cards coming through the 15-pin VGA connector. Is this signal present on ATI cards (or even on dual-DVI-I output cards)? Thanks, Dave Horita - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/
