[PyMOL] Detecting holes/cavities in surface

Hi all, I haven't used this list before but can't find an answer to my question elsewhere. I am selecting the antibody binding site automatically to calculate the surface area of the binding sites. However, some of the binding sites have holes/cavities in the surface - I would like to be able to

Re: [PyMOL] Detecting holes/cavities in surface

at > > detects cavities. Potentially this offers an approach for you. > > > > On Jul 20, 2016 12:05 AM, "Daniel James" > wrote: > >> > >> Hi all, > >> > >> I haven't used this list before but can't find an answer to my que

[PyMOL] Re:2 questions about Summit drivers w/ Radeon8500 card for stereo...

" missing on display ":0.0". I'm wondering what this problem means (if anything), and how it may be corrected?? Thanks for any advice! Cameron Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 Unive

Re: [PyMOL] Nuvision stereo glasses?

ail: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/ =20 Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463

[PyMOL] pymol crash on linux opening a .pse saved session file

saved, then the screen goes weird on the monitor the viewing window is on, the mouse pointer vanished and the keyboard is non responsive, forcing us to press the reset button to reboot. Looks like a big Xserver crash. Any ideas? cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell

[PyMOL] Re: ATI radeon 8500 and Linux quad buffered stereo

he left is a digital video output and I need to shop for the stereo enabler cable... ulrich Re: [PyMOL] Nuvision stereo glasses? * From: "Dr. Daniel James White PhD" * Date: Fri, 18 Jul 2003 11:59:17 +0300 * In-reply-to: * List-archive: <http://sourceforge.ne

[PyMOL] energy minimisation in python

learn Dan On Tuesday, September 9, 2003, at 09:08 PM, pymol-users-requ...@lists.sourceforge.net wrote: We'd all like to see a real forcefield in PyMOL, but no one has written the code yet. Cheers, Warren Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biol

[PyMOL] Re: 3 button editing and viewing, modifier button clicking not working

pendent molecules out of them? The following commands will move the heteroatoms into a separate object: create hetobj, hetatm remove hetatm and not hetobj Cheers, Warren --__--__-- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net

[PyMOL] Re: Need advice on graphic card

just one framebuffer for both display, so fool the system thinking it's only a "single-head" presented. No, Xinerama won't work with DRI. That's why i used merged mode, but it messed up nmrview's font. Seems nobody else out there using two screens? Thanks anyway, Marc

[PyMOL] rebuilding icosohedral virus structure - symexp?

he file ok... So suppose it is a bodil problem... anyway, can i use symexp to do this automatically. you have to do it by hand 1 by 1 in SwissPDBviewer (and the linux version is a bit funny...i did it on a mac) cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of

Re: [PyMOL] save icosohedral virus structure with all subunits present?

vie->Show All States. ~Todd Geders On Fri, 2004-04-02 at 07:14, Dr. Daniel James White PhD wrote: Hi, I have a virus envelope protein structure pdb entry, and I want to rebuild the whole virus protein shell using the symmetry transformations given in the 180 (60 trimers) REMARK 350 BIO

[PyMOL] Re: split_states

d for this task, and it still takes a dual 2 Ghz G5 85 seconds to render... Cheers, Warren Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +3

[PyMOL] save all not working for multiple objects from split_states?

dnt want, leaving 15 molecules around one of the 5 fold symmetry axes. now I want to save these molecules to a pdb file. so I did save 5fold.pdb, all this gave no errors, but the pdb file written only contains END what am I doing wrong? I expect it is my simple mistake? cheers Dan Dr. Danie

[PyMOL] Re: give unique chain identifiers

segi 0001 zoom segi 0001 http://delsci.com/img/1c8e-subunit.jpg Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dr. Daniel James White PhD Sent: Tuesday, April 06, 2004 6:22 AM

[PyMOL] enable direct rendering DRI on fedora core 2

Option "dpms" EndSection Section "Device" Identifier "Videocard0" Driver "radeon" VendorName "Videocard vendor" BoardName "ATI Radeon 8500LE" EndSection Section "Screen"

[PyMOL] ATI fglrx 3.11 drivers for Radeon 8500 LE with linux 2.6 kernel, quad buffered stereo on sony G520???

sony G520 monitor , stereo graphics enabler cable and e2 emitter box. or am I flogging a dead horse cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260

[PyMOL] sony (sgi) monitorGDM-20D11 flashing LEDs, no picture

monitor blink together. I can use the machine via VNC from my Mac, so I can see it is running ok. any idea what the problem might be? I can't find the manual here, or any useful info on the internet just though someone might have seen this before...sometime.. cheers Dan Dr. Daniel

[PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2

eware/bin/c++ are these ok? will the hardware stereo work with pymol? this is really all I need this machine for, good for students (unless I can get a new licensed version of insightII on it ... from the csc here in finland) cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Bi

Re: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2

From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dr. Daniel James White PhD Sent: Thursday, September 16, 2004 10:41 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2 Hi Warren and all,

Re: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2, external sources python build fails

rix6.5 from sgi freeware won't install (of course, and only python 1.5 is available for irix 6.3 on sgi freware) cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology, Ambiotica C242 Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 4

[PyMOL] red blue stereo?

Hi Warren, Is there any chance of enabling open GL red-blue anaglyph stereo to pymol? As seen in VMD. cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Bioimaging Coordinator Nanoscience Centre and Department of Biological and Environmental science Division of Molecular Recognition

[PyMOL] Re: hardware stereo in IRIX

lease 6.5 - Model Indigo 2 Impact 1 - Main Mem: 128 MB - CPU: 175 MHz =20 Thanks a lot, =20 Nicolas Ambert. --=20 Dr. Daniel James White BSc. (Hons.) PhD Bioimaging Coordinator Nanoscience Centre and Department of Biological and Environmental science Division of Molecular Recogn