[PyMOL] polar surface area with pymol

Hi List! Is there any way I can calculate the PSA of a molecule with pymol? Will be grateful for any hints. Thanks and regards, -- Ramesh Sistla Science Fellow This email and its attachments are confidential and proprietary to AURIGENE Discovery Technologies and are meant for the intended re

[PyMOL] RE: sequences view

This question just came in about the sequence viewer...I'm anonymously copying it to the mailing list since it is bound to come up frequently: > Hey Warren, > > I just downloaded the new version of PyMOL and was playing > with the new sequence view. Is it possible to do a > structural alignmen

RE: [PyMOL] polar surface area with pymol

Ramesh, You can do something like this... For a solvent accessible PSA approximation: set dot_density, 3 remove hydro remove solvent show dots set dot_solvent, on get_area elem N+O get_area elem C+S get_area all For molecular PSA approximation set dot_density, 3 remove hydro remove solvent set

[PyMOL] Align/pair_fit question

Hi all, Is it possible to get access to the transformation matrix resulting from an align or pair_fit command? I want to transform a collection of objects according to superposition parameters determined from one of them. I thought I had it working by defining a composite object, and while

Re: [PyMOL] PyMOL 0.96 Released

Hi, just wondering if this is a bug or just my system. I was just exploring the new PyMOL, there is a menu item "plugin", when I clicked the pull-down menu "about plugins", PyMOL quit, gives out segmentation fault error. Thanks! Chen -- === Yu Chen How

[PyMOL] align function in MacPyMOL (v0.95) and the X11 hybrid version

Dear all, I noticed that MacPyMOL (v0.95) or the X11 hybrid version (v0.95 and v0.96) crashes when aligning relatively large protein molecules (over 2,000 residues). After issuing the align command, the PyMOL process in the Activity Monitor turns red. This did not happen when I aligned smal

[PyMOL] pymol crash!

Dear List! I grabbed 0.96and installed. It is a beauty. Only that when I clicked on getview button, it copied the matrix to clipboard and crashed. The error it returned is: PyMOL: Viewing matrix copied to clipboard. unable to alloc 1869182081d bytes /usr//bin/pymol: line 14: 24056 Aborted

RE: [PyMOL] pymol crash!

Ramesh, Thanks for this report. So far I haven't been able to reproduce the crash under Linux or IRIX... If other people encounter this same problem or other problems with the new releases, then please send a report to supp...@delsci.com that includes your operating system details. If pattens e