[PyMOL] Bond lengths
Dear People, I was wondering if if people could recommend 1) a way of generating all bond lengths and bond angles for a molecule automatically(atm I'm using the measurement wizard) 2) a method for increasing the size of the font produced by the measurement wizard If I have missed something previously posted, can you please refer me to a valid url. Thanks for your help Andy -- If you're not part of the solution, you're part of the precipitate.
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] Ray, png
Hi, On the subject of larger image sizes, I had a question a while back; I'd like to know if it's been addressed or anyone has a quick(er) workaround- Basically, is there in inverse to the viewport command? i.e., if I manually resize the Pymol window to fit around the molecule I'm displaying, how can I get the relative dimensions of the new window? These dimensions are needed for the Ray command to keep proper perspective. What I've done in the past is save a small image of what's displayed in the window, used a graphics program to determine the x y dimensions, and then used these to generate a high-resolution ray traced image with the same x/y ratio. I figure I'm missing something. Regards, - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm http://www1.wfubmc.edu/biochem/faculty/Horita.htm/
RE: [PyMOL] Ray, png
David, In recent builds, you don't need to specify both dimensions for the ray command -- just give it height or width and it will compute the other based on the current aspect ratio. Regardless, to get the current window, here is one way: print cmd.get_session()['main'] 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 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A. Horita Sent: Tuesday, January 03, 2006 2:39 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Ray, png Hi, On the subject of larger image sizes, I had a question a while back; I'd like to know if it's been addressed or anyone has a quick(er) workaround- Basically, is there in inverse to the viewport command? i.e., if I manually resize the Pymol window to fit around the molecule I'm displaying, how can I get the relative dimensions of the new window? These dimensions are needed for the Ray command to keep proper perspective. What I've done in the past is save a small image of what's displayed in the window, used a graphics program to determine the x y dimensions, and then used these to generate a high-resolution ray traced image with the same x/y ratio. I figure I'm missing something. Regards, - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm http://www1.wfubmc.edu/biochem/faculty/Horita.htm/
[PyMOL] ray
Here's another question about ray. At what level in pymol is it implemented? Is it part of what's provided by OpenGL, or done at some higher/other level? Terry
[PyMOL] Drawing surfaces in pymol?
I've been using PyQt/Coin/SoQt/pivy to draw surfaces using SoNurbsSurface. I'm wondering if something like this is possible in pymol? I.e., I specify a set of points in 3D space and use pymol to lay an interpolated surface over them. I don't want the surface to fully envelop the points in the way that pymol can show surfaces around a series of points. If this is possible, can I also trim such a surface (in Coin this is done using an SoNurbsCurve)? I've put a image showing the sort of thing I'm already generating at http://jones.tc/other/surface.png (Ignore the grid at bottom). Thanks for any help or suggestions. Terry
RE: [PyMOL] Drawing surfaces in pymol?
| This isn't really something PyMOL was designed to do. You could construct | such a surface using Python CGO facility, but that means doing the | tesselation, surface normal calculation, and any culling yourself. Thanks. Is this what you do already in pymol to make surfaces that envelop points? Thanks too for the ray answer. Terry
[PyMOL] Feedback on New Macs w/ Stereo3D
MacPyMOL Users, If you've recently bought a Stereo 3D-equipped G5 Single/Dual/Quad for running MacPyMOL and other scientific codes, please let me know -- I'd like some candid real-world feedback on how well these systems are performing... 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
