You might want to try using Modeller instead.
http://www.salilab.org/modeller/wiki/Mutate%20model
It does higher level modelling.

Jed

Martin Hediger wrote:
> Dear List
> I'm trying to automate the following sequence of steps in a PyMOL python 
> script:
> 1. Start the mutagenesis wizard
> 2. Mutate a reside according to an input from the script (some integer 
> to specify the id)
> 3. "Apply" and close the mutagenesis wizard
> 4. Start the Sculpt Wizard
> 5. Fix all coordinates but the residue just mutated
> 6. Start the sculpt algorithm to get a rough optimization of the side chain
> 7. End the sculpt algorithm and close the sculpt wizard.
> 8. Save the structure to a new file.
>
> I have the steps up to 3. ready in a script for generation of variants.
> However, when running a log file while performing steps 4. onwards, 
> there are no commands written into the log file for the sculpting 
> functions. Pressing the "Sculpt" button in the PyMOLX11Hybrid does not 
> lead to a command I can see in the log file.
> What would be the Python code to start the sculpt process?
>
> Any hints are welcome.
>
> Thanks a lot.
>
>
>
> ------------------------------------------------------------------------------
> Enable your software for Intel(R) Active Management Technology to meet the
> growing manageability and security demands of your customers. Businesses
> are taking advantage of Intel(R) vPro (TM) technology - will your software 
> be a part of the solution? Download the Intel(R) Manageability Checker 
> today! http://p.sf.net/sfu/intel-dev2devmar
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>   

------------------------------------------------------------------------------
Enable your software for Intel(R) Active Management Technology to meet the
growing manageability and security demands of your customers. Businesses
are taking advantage of Intel(R) vPro (TM) technology - will your software 
be a part of the solution? Download the Intel(R) Manageability Checker 
today! http://p.sf.net/sfu/intel-dev2devmar
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Reply via email to