RE: [PyMOL] saving images
Thanks Scott. I have tried sticks (and it works) but it doesn't look very good for what I'm trying to show. The really annoying part about this lines issue is that it doesn't ALWAYS happen. And i can't seem to find any relation between the times it does save the lines versus the times it doesn't save the lines.THanks again -GC Greg Caputo Ph.D. Postdoctoral Research Associate Department of Medical Biochemistry Genetics Texas AM University College Station, TX 77840 (979) 862 3188 (lab) (979) 324 8645 (cell) From: Scott Classen clas...@uclink.berkeley.edu To: pymol-users@lists.sourceforge.net Subject: [PyMOL] saving images Date: Mon, 13 Sep 2004 09:38:45 -0700 Hi Greg, You might need to display your sidechains as sticks rather than lines in order for them to be visible when you write out your image file. Or perhaps, if you are not already doing it, you should raytrace your scene by hitting the "ray" button before you write out your image file. Scott On Sep 13, 2004, at 8:03 AM, Greg C wrote: Hello all, I'm having a problem saving the pymol output as an image. I'm working with asingle alpha helix (~25 residues) with the residues displayed as lines, the backbone as a ribbon, and one or more of the residues as spheres. When i go to save the image, the lines are no longerpresent in the image, but still there in the pymol window. I should also note it's not a consistent problem. This happens about 60% of the time i try to save these images.Sometimes if i re-savethe picture, it works. ANy ideas? Thanks -GC Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 --- This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 Project Admins to receive an Apple iPod Mini FREE for your judgement on who ports your project to Linux PPC the best. Sponsored by IBM. Deadline: Sept. 13. Go here: http://sf.net/ppc_contest.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Express yourself instantly with MSN Messenger! Download today - it's FREE!
[PyMOL] Pymol and virtual reality (freeVR)
I am seeking the most direct route to protein visualization in a Virtual Reality environment. If possible, I would like to integrate pymol visualization with freeVR (www.freevr.org). Any experience or thoughts?
[PyMOL] graphics with GeForce4 card in windows vs. linux
Hi All, I have a machine running WindowsXP and RedHat 9 with an Albatron GeForce 4 Ti4800se graphics card. I notice that when I run pymol in windows it is much faster and smoother than when I run in linux. When I open PyMol in windows, it says Adapting to GeForce hardware... but does not say this when I open it in linux. Any thoughts on how I can get pymol to run more smoothly in linux? Thanks for your help. Cheers, Eric
[PyMOL] saving images
Hi Greg, So when you say that sticks don't look very good I assume you mean they are too thick? If this is the case you know that you can change the stick thickness by changing the stick_radius value set stick_radius, 0.1 Ciao, Scott On Sep 13, 2004, at 10:56 AM, Greg C wrote: Thanks Scott. I have tried sticks (and it works) but it doesn't look very good for what I'm trying to show. The really annoying part about this lines issue is that it doesn't ALWAYS happen. And i can't seem to find any relation between the times it does save the lines versus the times it doesn't save the lines. THanks again Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290
Re: [PyMOL] graphics with GeForce4 card in windows vs. linux
You will need to download linux driver for GeForce 4 and install it under linux. The linux is not using the 3D-hardware accelaration without the manufacture's driver. On Tue, 14 Sep 2004, Eric Schreiter wrote: Hi All, I have a machine running WindowsXP and RedHat 9 with an Albatron GeForce 4 Ti4800se graphics card. I notice that when I run pymol in windows it is much faster and smoother than when I run in linux. When I open PyMol in windows, it says Adapting to GeForce hardware... but does not say this when I open it in linux. Any thoughts on how I can get pymol to run more smoothly in linux? Thanks for your help. Cheers, Eric --- This SF.Net email is sponsored by: thawte's Crypto Challenge Vl Crack the code and win a Sony DCRHC40 MiniDV Digital Handycam Camcorder. More prizes in the weekly Lunch Hour Challenge. Sign up NOW http://ad.doubleclick.net/clk;10740251;10262165;m ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (primary) (410)455-2718 (secondary) fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
