Re: [PyMOL] How to view electron densities from the PDB

[Roger R. <rro...@ma...>]

Robert Campbell wrote:
> Hi,
>
> On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner <mgl...@gm...>
> wrote:
>
>   
>> This is probably a fairly basic question, but I'm stumped. I want to
>> visualize electron densities along with my PDB file. So, say I'm interested
>> in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL
>> doesn't seem to read the CIF file (?), so I downloaded and installed the
>> PDB's tool sf-convert (http://sw-tools.pdb.org/apps/SF-CONVERT/index.html).
>> I tried
>>
>> sf-convert -i CIF -o Xplor -sf 2djx-sf.cif
>>
>> but got some errors about the input format.
>>
>> sf-convert -i mmCIF -o Xplor -sf 2djx-sf.cif
>>
>> seemed to work (it produced a .Xplor file with what looks like data to me).
>> However, PyMOL gives me errors when I try to load the resulting .xplor file.
>>     
>
> The "sf" file that you have is not electron density but structure factors.
> You need to calculate electron density from the data in that file and phases,
> which you would have to calculate from the structure.  Fortunately someone
> else is already doing that for you.  Try the Electron Density Server
> (http://eds.bmc.uu.se/eds/).
>
> Simply enter the PDB code and you'll find ... oh dear ... that 2djx is not
> entered yet. :(
>
> I see that it is a fairly new structure (released yesterday) and EDS is
> updated weekly.  So either wait a week or so, or find a crystallographer to
> run the coordinates and structure factors through a single refmac cycle to
> calculate a map for you.
>
> Cheers,
> Rob
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University,
> Kingston, ON K7L 3N6  Canada
> Tel: 613-533-6821            Fax: 613-533-2497
> <rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc
>
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>   
Instructions for creating and displaying CCP4 maps in pymol can be found 
at http://www.pymolwiki.org/index.php/Display_CCP4_Maps. However, 
displaying a model with maps in pymol is perhaps not the most 
straightforward way to inspect models and maps. Even here, you will have 
to use the fft utility in CCP4 to generate the maps. (You will probably 
want to display a simple map.) To generate a CCP4 map, you will have to 
convert your mmCIF file to an appropriate MTZ file using another CCP4 
utility. It might be more straightforward to read in the PDB file and 
the appropriate MTZ file into Coot instead of pymol.

Cheers,


-- 
------------------------------------------------------------------------
Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
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email: rro...@ma...