Re: [ccp4bb] making high res image in pymol
Thank you all for the suggestions. I lowered the hash-max and could get ray tracing to complete for line or even ribbon modes (to be honest line mode worked even without lowering the hash-max). But as Matthew pointed out, I could not get it to work in the cartoon mode. I think I am restricted here with my hardware limitations... Alex On Tue, Jan 28, 2014 at 2:20 PM, Yong Wang wang_yon...@lilly.com wrote: Hi Alex, If you don't mind forgoing the ray tracing, you may try the draw command to specifically set the resolution (and antialiasing) to your needs, and then save the image. Yong -- *Yong Wang, Ph.D. Research Advisor, Discovery Chemistry Research* Eli Lilly Company Phone: 317-655-9145 Lilly Corporate Center DC 0403 Fax: 317-651-6333 Indianapolis, IN 46285 wang_y...@lilly.com CONFIDENTIALITY NOTICE: This e-mail message from Eli Lilly and Company (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *A K *Sent:* Tuesday, January 28, 2014 10:27 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] making high res image in pymol Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex
[ccp4bb] making high res image in pymol
Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex
Re: [ccp4bb] making high res image in pymol
CCP4MG? On 28 Jan 2014, at 15:27, A K wrote: Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] making high res image in pymol
Hi Alex - I'm not surprised you're having memory issues. I just tried this test with one of my molecules. Simply generating and displaying the symmetry mates in a 250 A radius required 4 G of memory, and the raytracing would have needed a lot more (I only have 8 G on this computer, so I didn't finish that job). Unless you're running your job on a server-scale computer with 32 G or more of memory, I think you'll have trouble with so many molecules. However, that's with cartoon rendering. I assume you're trying to show unit cell packing, and the molecules will be so tiny that it doesn't matter what they look like. Use ribbon rendering instead, and the memory demands are greatly reduced. I was able to raytrace a 2000 x 2000 pixel image (which should be more than adequate for a poster - that's 10 x 10 inches at 200 dpi) in 40 seconds with peak memory usage under 2 G. This is with the Fink compiled version of Pymol - version 1.6.9.0. Hope that helps, Matt On 1/28/14 10:27 AM, A K wrote: Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] making high res image in pymol
Hi Alex - You can also try reducing the value of `hash_max`http://www.pymolwiki.org/index.php/Hash_max (e.g. `set hash_max, 50`). The default value is 130; a lower number reduces the memory PyMOL tries to obtain for ray tracing. The trace will take longer, but hopefully will get you through without crashing. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.eduhttp://kong.med.nyu.edu/ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of A K [alek6...@gmail.com] Sent: Tuesday, January 28, 2014 10:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] making high res image in pymol Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] making high res image in pymol
Hi Alex, If you don't mind forgoing the ray tracing, you may try the draw command to specifically set the resolution (and antialiasing) to your needs, and then save the image. Yong -- Yong Wang, Ph.D. Research Advisor, Discovery Chemistry Research Eli Lilly Company Phone: 317-655-9145 Lilly Corporate Center DC 0403 Fax: 317-651-6333 Indianapolis, IN 46285 wang_y...@lilly.com CONFIDENTIALITY NOTICE: This e-mail message from Eli Lilly and Company (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of A K Sent: Tuesday, January 28, 2014 10:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] making high res image in pymol Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex
