[PyMOL] Header records in pdb files

[Björn Kauppi]

Hi all,

Is there a way to display the header record from a pdb file after reading it in 
to PyMOL? Or is that lost?
Preferentially I would like to be able to keep the whole header whilst working 
and be able to write it out together with the coordinates, perhaps with an 
extra remark saying something like PyMOL was here!


If it is difficult to implement, at a minimum I would like to see in the 
PyMOL-log the HEADER and TITLE cards, after reading a pdb-file, (to be I sure 
typed in the correct pdb-code in that nice pdb-loader plug-in, for example...)

Just a thought...



Björn Kauppi

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Re: [PyMOL] surface/grid questions

[Robert Campbell]

Dear Marcelo,

* castilho casti...@if.sc.usp.br [2004-08-23 17:02] wrote:
 My name is Marcelo and I am a basic-level pymol user. I work with docking
 programs and I am trying to make pymol our default program for analysing
 docking results...this brings me to some questions:
 
 Is it possible to colour protein surface according to Hydrogen
 donor/acceptor properties in pymol ?

I guess that depends on whether you can define what constitutes a donor
or acceptor easily enough.  I think with sufficient logical operations
you could.  For example:

  select donor, name N or (resn ASN and elem N) or (resn GLN and elem N)
  etc.

Then you could colour the donor selection as you like.

 Does Pymol computes a ligand-protein interface (for example just the contact
 area between the ligand and the protein)? is it possible to see just this
 surface area according to the previous question schema ?

If you have the ligand and protein in separate objects, let's call them
ligand and protein, you can do this:

  show surf, ligand within 3. of protein
  show surf, protein within 3. of ligand

where it will show the surface only for atoms within 3 Angstroms of the
other molecule.  You could also include the byres keyword which might
remove some holes in the surface if desired:

  show surf, byres ligand within 3. of protein

If the structure file you read in contains both, then you can create
separate objects from the single initial object:
 
  create protein, initial and chain A
  create ligand, initial and chain B

where I'm assuming that the protein has the A chain identifier and the
ligand has the B chain identifier and the initial object was called
initial.

 Does pymol read grid (Goodford's grids) ? in case not, how can I convert
 GRID maps into something pymol can read ?

It appears that you can convert Goodfords grid format to other map
formats (e.g. Brix and CCP4) using the Bsoft program package:

http://www.niams.nih.gov/rcn/labbranch/lsbr/software/bsoft/bsoft.html

The software contains the code for reading and writing GRID files, so
perhaps that could be incorporated into PyMOL.  (I couldn't find any
license file, though I suppose the author could be contacted directly.)

Hope this helps.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D. r...@post.queensu.ca
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6  Canada   http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2