[PyMOL] Finding coordinates of cgo object in Pymol

2010-01-28 Thread Buz Barstow
Hi All, I'd like to be able to find the coordinates of a cgo object on the pymol screen. Here's my workflow: 1. I generate a cgo object (a criss-cross) at a defined coordinate, and then drag it to a new coordinate. 2. I'd like to find the xyz coordinates of the new location. Could anyone

[PyMOL] Extracting Amino Acid Sequence from PDB File

2009-08-13 Thread Buz Barstow
Hi All, Does anyone know of a program that can extract the amino sequence of a protein from a PDB file and output it as a FASTA file? Thanks! and all the best, --Buz -- Let Crystal Reports handle the reporting -

[PyMOL] Alignment Problems

2009-08-07 Thread Buz Barstow
Hi All, I'm having some trouble fitting to sets of residues in Pymol (1.2r0 - installed with Fink on MacOSX 10.5.8). I'm also having almost identical trouble using MacPymol as well (the version based on Pymol 1.1). I'm trying to align 2 sets of 4 cysteine residues. I have tried align,

Re: [PyMOL] homology modeling in python

2009-07-01 Thread Buz Barstow
Hi Marcus, Thanks for your advice. I actually discovered Bizkit independently, and it definitely seems to fit the bill. Thanks for your advice! and all the best, --Buz On Jun 30, 2009, at 9:41 PM, Marcus Collins wrote: Hi Buz (and everyone) The biopython package together with Bizkit

[PyMOL] Homology Modeling in Pymol

2009-06-30 Thread Buz Barstow
Hi All, I have a very large library (almost 1000) of similar genetic sequences, for which I would like to generate homology models. Does anyone know of a way to automate requests to a homology modeling server, such as SWISS-Model through pymol, or alternatively through python? Thanks!

Re: [PyMOL] Mutating an Ion in Pymol and Displaying van der waals Radii

2008-12-30 Thread Buz Barstow
-- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent: Thursday, December 18, 2008 2:30 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mutating an Ion in Pymol and Displaying van der

[PyMOL] Mutating an Ion in Pymol and Displaying van der waals Radii

2008-12-18 Thread Buz Barstow
Dear All, I'd like to mutate an ion in pymol from a potassium to a sodium. Is there an easy way to do this from the command line without having to edit the pdb file of the structure? Also, when one displays an atom (for instance a K atom) using the spheres representation, is the radius

Re: [PyMOL] Ray Tracing A Protein Gallery

2008-12-18 Thread Buz Barstow
set orthoscopic # get rid of background pixels unset opaque_background # render ray # and save save struct001.png Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent

[PyMOL] Ray Tracing A Protein Gallery

2008-12-15 Thread Buz Barstow
Dear All, I'm making a gallery of protein molecules for my PhD thesis. I'd like to find an automatic way to ensure that all of the ray traced images have the same scale. Is there an easy way to do this? Thanks! and all the best, --Buz

[PyMOL] Making Stereo Pair Graphics

2008-11-24 Thread Buz Barstow
Dear All, I'd like to make a stereo pair graphic using pymol. I'd like to know what is an appropriate size for each image in the pair, and what their separation should be. Thanks! and all the best, --Buz

Re: [PyMOL] Making Stereo Pair Graphics

2008-11-24 Thread Buz Barstow
need more details. Carsten -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent: Monday, November 24, 2008 3:01 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Making Stereo Pair Graphics Dear All, I'd like to make a stereo pair graphic using pymol. I'd like

[PyMOL] Selecting Negative Residues

2008-08-21 Thread Buz Barstow
Dear All, Does anyone know how to select residues with negative sequence numbers in Pymol? I have a protein molecule with two residues with negative sequence numbers (-2 and -1). When I issue the command: cmd.select('temp', 'resi -2 and name CA') Pymol selects the alpha carbons of

Re: [PyMOL] Selecting Negative Residues

2008-08-21 Thread Buz Barstow
Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Buz Barstow Sent: Thursday, August 21, 2008 12:32 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL

[PyMOL] Graphics Workstation

2008-06-11 Thread Buz Barstow
Dear All, I'm considering purchasing a new graphics workstation for molecular graphics and macromolecular refinement. I'm considering buying a machine with 2 quad core xeon processors, and a nVidia Quadro FX graphics card with 1.5 Gb of memory. Can the current generation of software, and

Re: [PyMOL] Pymol Crash in X11 on MacOSX 10.5

2008-02-12 Thread Buz Barstow
to 2.1.1, so updating that might solve the problem ... On Mon, 11 Feb 2008, Buz Barstow wrote: Hi All, I've been having a lot of trouble with Pymol since upgrading to the X11 included with MacOS 10.5. Of late (using X11 2.1.3), Pymol built with fink, and ipymol 1.0 have

[PyMOL] Pymol Crash in X11 on MacOSX 10.5

2008-02-11 Thread Buz Barstow
Hi All, I've been having a lot of trouble with Pymol since upgrading to the X11 included with MacOS 10.5. Of late (using X11 2.1.3), Pymol built with fink, and ipymol 1.0 have been crashing after a small amount of viewing and rotating an object in the program (a few rotations and zooms).

[PyMOL] MSMS Cavity Visualization in Pymol

2008-01-30 Thread Buz Barstow
Hi All, Does anyone know of a script that is capable of displaying the surfaces identified by msms in pymol? It would be nice to have a program that could read in existing .vert and .face files. I've included small starting sections of these .face and .vert files as examples: # MSMS

Re: [PyMOL] Algorithm to Rotate One Set of Vectors onto Another

2008-01-29 Thread Buz Barstow
). Hope it helps, Tsjerk On Jan 25, 2008 10:55 PM, Buz Barstow b...@mac.com wrote: Dear All, I'm looking for an algorithm that will allow me to derive a transformation matrix that superimposes one set of orthogonal vectors onto another set of orthogonal vectors, that I can then use to transform

[PyMOL] Algorithm to Rotate One Set of Vectors onto Another

2008-01-25 Thread Buz Barstow
Dear All, I'm looking for an algorithm that will allow me to derive a transformation matrix that superimposes one set of orthogonal vectors onto another set of orthogonal vectors, that I can then use to transform another set of orthogonal vectors. Thanks! and all the best, --Buz

[PyMOL] Rigimol Output

2008-01-10 Thread Buz Barstow
Dear All, Does anyone know the exact meaning of the output from the first rigimol processing step? For instance, if I give the rigimol program two structures that are very similar (structure #1 and structure #2), the program identifies several domains and gives the following output:

[PyMOL] Principal axes and moment of inertia matrix

2008-01-09 Thread Buz Barstow
Dear All, Does anyone have a python routine that can be used to calculate the moment of inertia matrix, and principal axes of a collection atoms? Thanks! and all the best, --Buz

[PyMOL] Calculation of Domain Volume in Pymol

2008-01-04 Thread Buz Barstow
Dear all, I'd like to very accurately calculate the volume of a selection in pymol, or with tools that are callable by pymol? Could anyone suggest a program or algorithm? Thanks! and all the best, --Buz

[PyMOL] Adding Hydrogens to GFP Chromophore

2005-03-23 Thread Buz Barstow
PyMol to recognize the double bonds? All the best, --Buz |-| Buz Barstow 192 Clark Hall Cornell University Ithaca, NY 14853, USA Email: b...@cornell.edu Phone: 607 255 8678 Fax: 607 255 8751 |-|

[PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-18 Thread Buz Barstow
|-| Buz Barstow 192 Clark Hall Cornell University Ithaca, NY 14853, USA Email: b...@cornell.edu Phone: 607 255 8678 Fax: 607 255 8751 |-|