[ccp4bb] packing diagrammes

- Protein crystallography

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: anisotropic temp for H2O
From: Elad Binshtien eladbi {- at -} BGU {- dot -} AC {- dot -} IL
Date: 2009-08-27

Next message:
Subject: curved cylindrical helices in PyMOL?
From: Susanne Ressl susanne {- dot -} ressl {- at -} MPIBP-FRANKFURT {- dot -} MPG {- dot -} DE
Date: 2009-08-27

Subject: packing diagrammes
From: Anita Lewit-Bentley alewit {- at -} PASTEUR {- dot -} FR
Date: 2009-08-27

Dear all,

thanks to everybody who offered their experience and hints.

The most convenient way of preparing a packing diagramme, at least for
me, was via PyMol as suggested by Michael Klein (see below).

One can do something similar with the CCP4 graphics package, but for
some reason the protocol suggested by the manual slows down the
computer too much to be practical.

Anyway, the challenge is out there: a programme for preparing a
packing diagramme with the protein represented by a reasonable
approximation of its real shape. It would make a good teaching tool as
well.

Thanks again,

Anita

>
> I have made a few figures like the one you describe. I calculate
> the center of mass of the domain using ccp4 program pdbset with the
> command COM
>
> #! /bin/csh -f
>
> ################### Take output from O into a form suitable for
> refinement
>
> pdbset xyzin domain.pdb xyzout junk.pdb << eof-1
> #cell 132.02 115.21 96.20 90.00 90.00 90.00
> NCODE 1
> # New cell in junk.pdb, it is recommended that a spgrp is also given
> #spacegroup P212121
> COM
> eof-1
> #
>
> then run pdbset.csh > pdbset.log
>
> the center of mass is then listed in the pdbset.log
> I then make a fake atom out of the center of mass X,Y,Z coordinates
> using a pdb style format, name the atom O or whaterver. I then use
> pymol to display the atom as a sphere.
>
> Example:
> ATOM 2 O TYR A 59 4.198 22.414 35.783 1.00
> 24.65 A O
>
> replace 4.198 22.414 35.783 with the center of mass coordinates
> from pdbset..
>
>
> In pymol use command:
> show spheres,
> set sphere_scale=1.5
>
> change the number to adjust the size
> if the spheres do not show up try to ray the image..
>
> if you want to show the symmetry of the atom/spere in pymol
>
> symexp s,nameofyourobject,(all),50
> change the number to adjust how big the symm operators are..
>
> sorry if it seems complex, it really is'nt too bad and will work!
>
> HTH,
> michael
>
>
>
>
>
> --
> Michael G. Klein Ph.D.
> Project Research Scientist
> Structural Genomics
> DOE Joint Genome Institute
> 2800 Mitchell Drive
> Walnut Creek, CA 94598
> Phone: (925) 927-2556
> MGKlein@lbl.gov
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: anisotropic temp for H2O
From: Elad Binshtien eladbi {- at -} BGU {- dot -} AC {- dot -} IL
Date: 2009-08-27

Next message:
Subject: curved cylindrical helices in PyMOL?
From: Susanne Ressl susanne {- dot -} ressl {- at -} MPIBP-FRANKFURT {- dot -} MPG {- dot -} DE
Date: 2009-08-27