Re: [PyMOL] Database with protein experimental pKa values, with possibility to search for Cysteines and .pdb structure.

Hi Troels, about 8 month again I used their dataset: PINT: Protein-protein Interactions Thermodynamic Database. Kumar MD, Gromiha MM. Department of Biochemical Engineering and Science, Kyushu Institute of Technology Iizuka 820-8502, Fukuoka, Japan. sh...@bse.kyutech.ac.jp http://www.ncbi.nlm.ni

[PyMOL] Fwd: pdb-l: one question about using pymol

This question fits better the pymol list. -- Forwarded message -- From: 李雅雯 Date: 16 August 2010 12:31 Subject: pdb-l: one question about using pymol To: pd...@sdsc.edu Hi, thanks for your attention. I am using pymol to do structural alignment. Pymol will return this sentence

[PyMOL] Fwd: [ccp4bb] How to orient molecules in pymol according to the crystal orientation during data collection?

Someone on the pymol list might be able to help you with this. -- Forwarded message -- From: Anja Pomowski Date: Wed, Jul 7, 2010 at 08:22 Subject: [ccp4bb] How to orient molecules in pymol according to the crystal orientation during data collection? To: ccp...@jiscmail.ac.uk

Re: [PyMOL] modelling

Hi Lies, here a few among many options: http://www.salilab.org/modeller/ http://swissmodel.expasy.org/ http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi On Mon, Jun 28, 2010 at 06:15, Lies Van Nieuwenhove wrote: > Dear Sir, Ms, > > I don't know enough about bio-informatics but I need a

Re: [PyMOL] (no subject)

Hi Chris, the emails are only sent to you because you subscribed to the pymol-users list. If you don't want them anymore you need to unsubscribe. Click on "Show details" at the top of this email. Click then on: unsubscribe Unsubscribe from this mailing-list That will do the magic. On Fri,

Re: [PyMOL] some help

Hi Ashok, there are several ways to visualise alignments. Here is a nice overview: Visualization of multiple alignments, phylogenies and gene family evolution James B Procter, Julie Thompson, Ivica Letunic, Chris Creevey, Fabrice Jossinet & Geoffrey J Barton Nature Methods 7, S16 - S25 (2010) htt

Re: [PyMOL] CEalign - PyMOL Build

+3 from me and people to busy writing grant applications. Built-in CE would be awesome! Thomas On Tue, Feb 2, 2010 at 12:19, Thomas Stout wrote: > > I thought that I had +1'd to this last week, but I don't see that > note... > > If legal, I'm also +1-ing for 5 additional people here that do not

Re: [PyMOL] Help Needed

Dear Kousik, Sue Jones PROTORP server should do the trick: http://bioinformatics.sussex.ac.uk/protorp Cheers, Thomas On Wed, Dec 9, 2009 at 14:57, Kousik Kundu wrote: > > Dear Sir, >         I, Kousik Kundu, am a Ph.D student at university of Freiburg, > Germany. I am using Pymol for my rece

[PyMOL] Fwd: Warren L Delano Memorial Award

>Dear friends and colleagues: > >It's now been over a week since Warren has passed away.  We are trying to >move toward a permanent way to honor Warren's memory and what >he stood for: Open Source Computational Biosciences and molecular >visualization. To do this, Jim Wells and I put together a mis

[PyMOL] save sequence

Dear all, apologies for the stupid question, but I was wondering if it is possible to save the sequence (one letter AA codes) of the structure(s) open in PyMol? Many thanks, Thomas

Re: [PyMOL] Sequence alignment and Structure alignment

You can save the "alignment" object resulting from an align command to an aln file: align sele1, sele2, object=aln_obj save alignment.aln, aln_obj Cheers. Thomas On Sun, Sep 28, 2008 at 21:14, Praveen Madala wrote: > Hi, > Can I able to save sequence alignment got .. after performing the >

[PyMOL] APBS error

Dear all, when trying to use the APBS plugin I experience the following problem The first time I tried to run it it the error message was simply "ObjectMapLoadDXFile-Error: Unable to open file!" Now the second time it pops up an error log: Error: 1 WindowsError Exception in Tk callback Functi