Re: [PyMOL] fetch biounits or NMR model

[Troels Emtekær Linnet]

Hi Michael.

Something similar has been made to show the "SITES" labels of a pdb file,
for quick referencing of a crystal structure.
http://pymolwiki.org/index.php/Select_sites

You could look into how that is written, and provide something similar for
an NMR structure?

Best
Troels


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2013/2/8 Zimmermann, Michael T., Ph.D. 

>  Dear PyMOL Users,
>
> ** **
>
> I’ve been using fetch and fetchlocal (from the wiki) for working with
> multiple datasets of structures, but have a nagging issue that I have not
> found an efficient way to solve. I typically download the first biological
> unit, which works for X-ray structures. The trouble is (for good reason),
> NMR structures don’t have a .pdb1 file. Does anyone have a script to do, or
> have a good idea about how to implement, the following? (It’s really my
> lack of familiarity with catching the value from functions like
> cmd.get_names (rather than it just being printed) in python that’s my
> barrier…)
>
> ** **
>
> Attempt to fetch 2yrq.pdb1
>
> If fetch fails, try fetching 2yrq.pdb
>
> If successful and we have >1 state, save the first state
>
> ** **
>
> Thanks!
>
> ** **
>
> *Michael T. Zimmermann*
>
> Ph. D. in Bioinformatics | Health Sciences Research | Division of
> Biomedical Statistics and Informatics
>
> *Mayo Clinic* | 200 First Street SW | Rochester, MN 55905 | 
> mayoclinic.org
> 
>
> ** **
>
>
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[PyMOL] fetch biounits or NMR model

[Zimmermann, Michael T., Ph.D.]

Dear PyMOL Users,

I've been using fetch and fetchlocal (from the wiki) for working with multiple 
datasets of structures, but have a nagging issue that I have not found an 
efficient way to solve. I typically download the first biological unit, which 
works for X-ray structures. The trouble is (for good reason), NMR structures 
don't have a .pdb1 file. Does anyone have a script to do, or have a good idea 
about how to implement, the following? (It's really my lack of familiarity with 
catching the value from functions like cmd.get_names (rather than it just being 
printed) in python that's my barrier...)

Attempt to fetch 2yrq.pdb1
If fetch fails, try fetching 2yrq.pdb
If successful and we have >1 state, save the first state

Thanks!

Michael T. Zimmermann
Ph. D. in Bioinformatics | Health Sciences Research | Division of Biomedical 
Statistics and Informatics
Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | 
mayoclinic.org

--
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013 
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb___
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