Yes, "Save Symmetry Coordinates" in COOT is a very easy way. To avoid text editing, you can first reload the pdb and use the "Copy Fragment ..." under Extensions/Modeling to get the desired chains. Then use the "Merge Molecules" under Calculate to assemble.
Yong
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Mark J van Raaij
Sent: Friday, May 22, 2015 10:09 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Easy way to generate symmetry-related protein chains? (summary)
It seems the easiest way is to "Save Symmetry Coordinates" in COOT and then assemble the desired chains in a text editor.
> Extensions -> Modelling -> Symm Shift Reference Chain Here.
is present if you build COOT yourself, but is not in the pre-built releases (for now).
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 22 May 2015, at 14:24, Mark J van Raaij wrote:
> Just wondering if there is an easy way to generate symmetry-related chains, necessary for instance to join protein chains into the biologically relevant multimers.
> What I do now is look up the correct symmetry and translation operator in COOT or PYMOL and input that in PDBSET, but there may be easier ways.
>
> in the CCP4bb archive I found the following tip for COOT:
>
> Extensions -> Modelling -> Symm Shift Reference Chain Here.
>
> but that does not appear to be available in COOT, or not anymore.
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC c/Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://www.cnb.csic.es/~mjvanraaij
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