Re: [PyMOL] Focus depth
Implementing DOF in PyMol wouldn't be trivial and I'm not sure it's a priority/necessity. There are excellent open-source (and proprietary) rendering engines out there that can render better and faster than PyMol. Why re-invent the wheel... my 2 cents' worth :) However, aside from exporting to PovRay, you can do DOF from PyMol ray-traced PNG's (32-bit, i.e. w/ alpha channel) in post-production using the alpha channel as a Z-depth channel. If there is interest, I don't mind writing up a tutorial, but note that it does involve other software aside from PyMol, such as Photoshop. Best, JP From: pymol-users-boun...@lists.sourceforge.net on behalf of Thomas Blicher Sent: Wed 5/23/2007 5:32 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Focus depth Dear PyMOL users, I was wondering if it is possible to implement focus depth (also known as depth of field or DOF) in PyMOL. I have come across several links to DOF and it appears to be a common feature of ray-tracing programs. I imagine that it could work like the fog function - possibly in combination with this - to give an even more realistic feeling of depth/perspective, especially in close-ups. It is probably most useful for making artistic molecular graphics, i.e. for ray-traced images, so it wouldn't have to work real-time. Does anyone have ideas on how to implement this in PyMOL (other than exporting files and rendering them in POVRay)? Best regards, Thomas Blicher
Re: [PyMOL] WRL Output
My 2 cents' worth: How about skipping over the ancient and limiting WRL format and adopt a cross-platform solution. For example, Collada is gaining momentum in the 3D community (https://collada.org/public_forum/welcome.php) and provides an open standard digital asset schema for interactive 3D applications. Thanks, JP Cartailler -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Markus Wahl Sent: Friday, March 02, 2007 11:28 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] WRL Output Dear all, I wondered whether there is a possibility in PyMol to export the rendered polygon data in any kind of 3D format such as wrl or inventor? Best, Markus -- PD Markus Wahl, Ph.D. Max-Planck-Institut fuer Biophysikalische Chemie Abteilung Zellulaere Biochemie/Roentgenkristallographie Am Fassberg 11 D-37077 Goettingen Germany Phone: +49 (0)551-201-1046 Fax: +49 (0)551-201-1197 eMail: mw...@gwdg.de Homepage: http://www.mpibpc.mpg.de/groups/wahl - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDE V ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Command:turn
Greetings, Does anyone know if the camera commands (turn move) can be constrained to the reference (global) axes? I would imagine that the turn command (http://pymol.sourceforge.net/newman/ref/S1000comref.html#2_166) would cause a camera of 45 degrees about the reference axis: PyMOL turn x, 45 However, it appears to turn the camera about the viewport orientation, i.e. about the (horizonal) x-axis axis of the viewport. Note - this is pretty clear if you use Robert Campbell's axes_cyl.py to visualize the reference axis. According to the manual, it is also supposed to be constrained to the origin as well but doesn't appear to do so, at least not in my hands Are its constraints possibly overridden by such commands as center, orient, origin? Reason for asking this is that it would be very nice (at least for me) to be able to perform local transformations (i.e. about local object axes, be it the camera or other) that are bound to locally-defined axes - that are independent of the global or viewport orientation. Using winXP/Pymol 0.98. Thanks! JP Cartailler
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
RE: [PyMOL] transparent background
Set the ray_opaque_background to off The PNG file format supports transparency. Render your scene with the above, open up in an image editor and you should have a transparent background. JP -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Douglas Kojetin Sent: Thursday, August 12, 2004 11:04 AM To: pymol Subject: [PyMOL] transparent background Hi All- Is it possible to create an image in PyMOL with a transparent background (without having to feed it through a second program, such as the ImageMagick suite)? rant: MS PowerPoint has the ability to make images transparent, however Apple's Keynote does not -- a missing feature that's likely to make me switch back from switching (presentation software; I'm not giving up OS X). Thanks, Doug --- SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 Save 50% off Retail on Ink Toner - Free Shipping and Free Gift. http://www.shop4tech.com/z/Inkjet_Cartridges/9 _108_r285 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/p ymol-users
RE: [PyMOL] Cavity display?
Related the issue of inside-surface coloring, a useful feature to add to pymol would be the ability to flip surface normals for selected surfaces. Just a thought. JP Cartailler -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Lari Lehtiö Sent: Thursday, July 22, 2004 9:07 AM To: Dirk Kostrewa Cc: PyMOLBB Subject: Re: [PyMOL] Cavity display? I was looking for such a program couple of days ago, and I found pass. http://www.ccl.net/cca/software/UNIX/pass/overview.shtml I saw the cavities in couple of minutes in pymol :) I'm not familiar with voidoo, so I don't know if you will find this usefull or not... My current problem is related to this one, so I'll post it here also. I would like to calculate surface of the cavity with pymol and show this as a cavity going in to the protein. But the surface is all grey, because it is the inside. Is there a way to map the colours also to the other side of the surface? best regards, ~Lari~ »» Lari Lehtiö University of Helsinki Institute of Biotechnology Macromolecular X-ray crystallography P.O.Box 65 00014 HY Finland »» Quoting Dirk Kostrewa dirk.kostr...@psi.ch: # Dear PyMol users, # # I'm looking for a program that can calculate and write out cavities in a # # format that can be converted such that I can display it with PyMol (I'm # not # satisfied with the results from VOIDOO). Could you please send me any # pointer # to a program that you found useful? BTW, this would be my wish for a # next # release of PyMol! # # Best regards, # # Dirk. # # -- # # # Dirk Kostrewa # Paul Scherrer Institut # Life Sciences, OFLC/110 # CH-5232 Villigen PSI, Switzerland # Phone: +41-56-310-4722 # Fax:+41-56-310-5288 # E-mail: dirk.kostr...@psi.ch # http://sb.web.psi.ch # # # # # --- # This SF.Net email is sponsored by BEA Weblogic Workshop # FREE Java Enterprise J2EE developer tools! # Get your free copy of BEA WebLogic Workshop 8.1 today. # http://ads.osdn.com/?ad_id=4721alloc_id=10040op=click # ___ # PyMOL-users mailing list # PyMOL-users@lists.sourceforge.net # https://lists.sourceforge.net/lists/listinfo/pymol-users # --- This SF.Net email is sponsored by BEA Weblogic Workshop FREE Java Enterprise J2EE developer tools! Get your free copy of BEA WebLogic Workshop 8.1 today. http://ads.osdn.com/?ad_idG21alloc_id040op=ick ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] map size/memory/crashing
Hello list, I've been working on making some figures from ultrahigh resolution data. I have some dense maps and pymol just bombs away when I try to 'ray' away. It's pymol 0.93, BRIX maps, tried it on two machines both with 1GB RAM (not enough, I know...), 6 month old P4's, win2000 and RH7.x. The raytracing begins, I see the little bar at the top left appear, then pymol crashes without error. I have tried setting the hash_max to 70 (slower setting, less memory), but pymol is just taking every last bit of RAM possible (not much left after it finishes loading the map, actually) and then ungracefully quits. Are there ways around this, other than buying more memory (not an option at this time)? Any ideas would be interesting to hear. Thanks. JP
[PyMOL] Alpha channel support gone?
What has happened to alpha channel support in PNG output? I could have sworn it used to be there. I'm now working in version 0.9. thanks Jean-Philippe Cartailler Vanderbilt University Medical Center S-3223 Medical Center North 1161 21st Avenue South Nashville, TN 37232-2372 Phone: 615.322.7729 FAX: 615.343.7156 email: jp.cartail...@vanderbilt.edu www: http://www.cartailler.com
