pymol-users

Re: [PyMOL] chempy documentation

[<but...@ya...>]

My preference would be for something implemented in
Python/C. The project could start with a clean,
extensible (it should be easy to add new molecules)
and modular Python library and then start replacing
some functions with C equivalents. I would like a
library that doesn't use inheritance, or use it at
less as possible (it makes too difficult to read code)
which could only
contain descriptions of molecules and maybe perform
some basic operations (functions could be and are
implemented in other libraries) Even when the library
wolud be in Python, It should be easy to "plug" C
functions into it so we would not loose in
performance. It should also be as similar to chempy as
possible so pymol  could be easily ported to it.
I don't know how well chempy fits with the avobe
description, because, due of the lack of
documentation, I only use it in a very basic way.
Maybe It only needs minor changes and documentation to
become the standar in chemical objects for Python.

It sounds an interesting project. I would probably
join if something comes out

Cheers

Raúl 


>CDK is too Java-centric in my view, and I'll be the
>first to admit that
>Python is much too slow for cheminformatics.
>
>My preference would be for a fast, clean, back-end
>cheminformatics 
>library
>with a simple C API that could be exposed to and
>interporate with 
>Java, C, C++, SQL, and .NET.  Several proprietary
>examples of this 
>design
>exist, and they are all quite successful.  

>We need an open-source equivalent!

>Cheers,
>Warren
>DeLano Scientific LLC



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Re: [PyMOL] segmentation fault after switching mainwindow between visualisation and commandline

[Christian S. <cse...@bp...>]

$PYTHONPATH is not set on my machine.



You wrote:

      Re: segmentation fault after switching mainwindow between visualisation 
and commandline
      From: Martin <martin.hoefling@gm...> - 2006-11-13 05:15

       ... i had a similar Problem this morning. What is your PYTHONPATH? For 
me, 
       unsetting it solved the problems.
       
       Cheers	
       	Martin
       


segmentation fault after switching mainwindow between visualisation and 
commandline
From: Christian Seifert <cseifert@bp...> - 2006-11-13 02:07

 Hi,
 
 I found a critical and reproducible bug using the 0.99rc6-binarys on my
 machine.
 
 Stepps:
 - starting pymol from a kde terminal with user-rights
 - loading a pdb-file (e.g. 1K5D from pdb-database)
 - rotate the molecule with the mouse in any direction
 - hitting "Esc" to get to the commandline-mode
 - hitting "Esc" again to get back to the visualisation-mode
 - trying to rotate the molecule again with the mouse
 
 The programm crashes, the two windows of pymol disappear and my
 terminal-window show the following error:
 
 >./pymol: line 14:  7110 Speicherzugriffsfehler  $PYMOL_PATH/pymol.exe "$@"
 
 "Speicherzugriffsfehler" is the german word for segmentation fault.
 
 There is nothing in dmseg.
 
 The full output:
 >cseifert@lexx ~/pymol $ ./pymol
 >
 > PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.
 >
 > A current PyMOL Maintenance and/or Support Subscription may be required
 > for legal use of this Build beyond a finite honor-system evaluation period.
 > Please visit http://www.pymol.org/funding.html for more information.
 >
 > This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6.
 > OpenGL graphics engine:
 >  GL_VENDOR: ATI Technologies Inc.
 >  GL_RENDERER: ATI MOBILITY FireGL V5200 Pentium 4 (SSE2) (FireGL) (GNU_ICD)
 >  GL_VERSION: 2.0.5946 (8.27.10)
 > Detected 2 CPUs.  Enabled multithreaded rendering.
 >HEADER    SIGNALING PROTEIN/SIGNALING ACTIVATOR   10-OCT-01   1K5D
 >TITLE     CRYSTAL STRUCTURE OF RAN-GPPNHP-RANBP1-RANGAP COMPLEX
 >COMPND    MOL_ID: 1;
 >COMPND   2 MOLECULE: GTP-BINDING NUCLEAR PROTEIN RAN;
 >COMPND   3 CHAIN: A, D, G, J;
 >COMPND   4 SYNONYM: RAN, TC4, RAN GTPASE, ANDROGEN RECEPTOR-
 >COMPND   5 ASSOCIATED PROTEIN 24;
 >COMPND   6 ENGINEERED: YES;
 >COMPND   7 MOL_ID: 2;
 >COMPND   8 MOLECULE: RAN-SPECIFIC GTPASE-ACTIVATING PROTEIN;
 >COMPND   9 CHAIN: B, E, H, K;
 >COMPND  10 SYNONYM: RANBP1, RAN BINDING PROTEIN 1;
 >COMPND  11 ENGINEERED: YES;
 >COMPND  12 MUTATION: YES;
 >COMPND  13 MOL_ID: 3;
 >COMPND  14 MOLECULE: RAN GTPASE ACTIVATING PROTEIN 1;
 >COMPND  15 CHAIN: C, F, I, L;
 >COMPND  16 SYNONYM: RANGAP, PROTEIN RNA1;
 >COMPND  17 ENGINEERED: YES
 > ObjectMolecule: Read secondary structure assignments.
 > ObjectMolecule: Read crystal symmetry information.
 > Symmetry: Found 1 symmetry operators.
 > CmdLoad: "/home/cseifert/Desktop/1K5D.pdb" loaded as "1K5D".
 >./pymol: line 14:  7110 Speicherzugriffsfehler  $PYMOL_PATH/pymol.exe "$@"
 
 Thanks,
 
 Christian Seifert.

Re: [PyMOL] segmentation fault after switching mainwindow between visualisation and commandline

[Martin <mar...@gm...>]

Am Dienstag, 21. November 2006 15:58 schrieb Christian Seifert:
> $PYTHONPATH is not set on my machine.
>
>
>
> You wrote:
>
>       Re: segmentation fault after switching mainwindow between
> visualisation and commandline
>       From: Martin <martin.hoefling@gm...> - 2006-11-13 05:15
>
>        ... i had a similar Problem this morning. What is your PYTHONPATH?
> For me,
>        unsetting it solved the problems.

Pythonpath is still set. Found "the solution" just right now: Killing the 
x-server and restarting it solved the issue for me. No idea why it did.

Cheers.
	Martin