[PyMOL] How to view electron densities from the PDB

2008-06-27 Thread Michael Lerner 
Hi,

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.

This may not be directly related to PyMOL, but I'm hoping it's a common
enough task that someone can point me in the right direction.

Thanks,

-michael

-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909
Rockville, MD 20852
http://www.umich.edu/~mlerner

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

2008-06-27 Thread Robert Campbell 
Hi,

On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner mgler...@gmail.com
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: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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

2008-06-27 Thread Roger Rowlett 

Robert Campbell wrote:

Hi,

On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner mgler...@gmail.com
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: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://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
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@mail.colgate.edu