Re: [PyMOL] Saving Images
If you would like appropriately scaled images then you can set up your viewer to the appropriate dimensions eg for a square viewport 700,700 or rectangle viewport 800,400 If using a square I then use ray 1800,1800 this ray traces an image larger than your pymol window and allows you to save it. This will help with higher resolution images. Newer versions show a preview. You canuop the resolution by increasing the ray pixels Hope this helps J Peter Adrian Meyer wrote: Hi everyone, Each time I try to save images, Pymol writes 640x480 pixel image to the file. I wonder if there is a way to save images (png format) other than 640X480 pixel that is default. Any help will be appreciated. Thanks. Images are saved as either the size of the viewer window, or the ray traced size. The easiest way to get a larger image is to maximize the viewer window, and then save. To get an arbritray size, use the ray-tracer (ray 1024,768 ; png BigImage.png). Pete Pete Meyer Fu Lab BMCB grad student Cornell University --- 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://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- 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] Saving Images
Hi everyone, Each time I try to save images, Pymol writes 640x480 pixel image to the file. I wonder if there is a way to save images (png format) other than 640X480 pixel that is default. Any help will be appreciated. Thanks. __ Yahoo! for Good - Make a difference this year. http://brand.yahoo.com/cybergivingweek2005/
Re: [PyMOL] Saving Images
Hi everyone, Each time I try to save images, Pymol writes 640x480 pixel image to the file. I wonder if there is a way to save images (png format) other than 640X480 pixel that is default. Any help will be appreciated. Thanks. Images are saved as either the size of the viewer window, or the ray traced size. The easiest way to get a larger image is to maximize the viewer window, and then save. To get an arbritray size, use the ray-tracer (ray 1024,768 ; png BigImage.png). Pete Pete Meyer Fu Lab BMCB grad student Cornell University
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] 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
[PyMOL] saving images
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 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) Express yourself instantly with MSN Messenger! Download today - it's FREE!
[PyMOL] saving images
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 longer present 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-save the 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
