[Pymol] cuting a Brix map
Hi list, I was wondering if there is a way to select some part of an electron microscopy map (brix format) within the pymol environment. To give you a precise exemple: I have a protein consisting of two different chains which are clearly identified on the screen and I would like to display only one chain and then save its coordinates. Do anyone know if it is possible under Pymol or should I use a EM specific software ? cheers Thibault Géoui
RE: [PyMOL] putty/sausage NMR figure
One way to do this would be to calculate RMSD between your models (using whatever package) and replace the B-factor column with those values (make sure you respect the PDB format (B-factors are in columns 61 - 66, with first column as 1 - see http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html for details), load that into pymol, and voila. If the effect isn't enough, you could always multiply your RMS values by some value (eg. 10). Good luck! JP Cartailler -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Douglas Kojetin Sent: Tuesday, July 19, 2005 3:48 PM To: pymol Subject: [PyMOL] putty/sausage NMR figure Hello All- From what I've read, the 'cartoon putty' command uses the PDB B- factor value to determine the appearance of the sausage diagram. How can I use the 'cartoon putty' command with NMR structures in a way that represents the structure ensemble, similar to that as the MOLMOL sausage diagram? Thanks, Doug --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477alloc_id=16492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] One-Button Mice on Macs
Mac Users: We strongly recommend (require?) use of a three-button mouse with MacPyMOL and PyMOLX11Hybrid. However, it is possible to use MacPyMOL in a limited way on Macs that have a single button mouse thanks to some built-in mouse remapping in the Mac OS X GLUT implementation. Her is how that works... If the Mac is hooked up to a 1-button mouse (only) when MacPyMOL or HybridX11PyMOL are launched, then Mac OS X itself will furnish translations as follows: Rotate: Click Drag XY-Translate: Option-Click Dreg Zoom: Control-Click Drag Select: Click Release Box-Select: Shift-Click Drag Box-Deselect: Shift-Option-Click Drag Clipping:Control-Shift-Click Drag with... - near plane controlled by vertical motion - far plane controlled by horizontal motion Note that not all mouse actions are possible with a one-button mouse. For example, I don't think molecular editing is possible with a one-button mouse. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com
[PyMOL] (no subject)
Hi, I've just started using PyMol for making some figures. I'm very happy that it is so easy to use. However the resolution of my pictures is very bad even after rendering them. When I print them they are very pixellated. I'm sure there is something I'm not doing right. Any help, suggestions will be appreciated. Thanks. Regards, Madhavi Kolli Graduate Student UMass Medical School Worcester
Re: [PyMOL] (no subject)
Check out the post on High end graphics. This will solve the problem. Basically you can ray-trace your molecule at a resolution bigger tahn teh screen size and then cut it down afterwards effectively generating a high resolution graphic from a 72 dpi starting point Cheers J Kolli, Madhavi wrote: Hi, I’ve just started using PyMol for making some figures. I’m very happy that it is so easy to use. However the resolution of my pictures is very bad even after rendering them. When I print them they are very pixellated. I’m sure there is something I’m not doing right. Any help, suggestions will be appreciated. Thanks. Regards, Madhavi Kolli Graduate Student UMass Medical School Worcester -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034
[PyMOL] movies in MacOSX
Hi, I've produced a series of png files using PyMOL, and I want to compress them to produce a movie. I was considering to use mencoder (following the suggestions in the PyMOL wiki), but I'm having some problems in running it under MacOSX Briefly, mencoder complains because it can't find the mpng codec. I downloaded a codecs.conf file and copied to ~/.mplayer, but it doesn't help. Are any of you using mencoder in a mac? If so, I'd like to get some advice. Thanks in advance, Xavier -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: xavier.de...@stanford.edu Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021
Re: [PyMOL] movies in MacOSX
Of course, this assumes you have purchased a QuickTime Pro (tm) key for £20 ($25)... gilleain On 20/7/05 23:44, Reinhold Penner rpen...@hawaii.edu wrote: Xavier, since you're on a Mac, it's easy enough to just fire up QuickTime Player and select File-Open Image Sequence. This will prompt you to select the first png file in a folder and load all other pngs with the same base name in that folder. Then simply export these frames as a movie with any of the available quicktime codecs at a frame rate you like. It's totally simple. HTH, -Reinhold On Jul 20, 2005, at 12:14 PM, Xavier Deupi wrote: Hi, I've produced a series of png files using PyMOL, and I want to compress them to produce a movie. I was considering to use mencoder (following the suggestions in the PyMOL wiki), but I'm having some problems in running it under MacOSX Briefly, mencoder complains because it can't find the mpng codec. I downloaded a codecs.conf file and copied to ~/.mplayer, but it doesn't help. Are any of you using mencoder in a mac? If so, I'd like to get some advice. Thanks in advance, Xavier -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: xavier.de...@stanford.edu Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021 --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477alloc_id=16492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477alloc_id=16492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
