Re: [ccp4bb] Coot real space refine and clusters

- Protein crystallography

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

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Subject: Coot real space refine and clusters
From: kaiser {- at -} CALTECH {- dot -} EDU kaiser {- at -} CALTECH {- dot -} EDU
Date: 2009-12-08

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From: Vandana Kukshal v_kukshal {- at -} CDRI {- dot -} RES {- dot -} IN
Date: 2009-12-09

Subject: Re: Coot real space refine and clusters
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-12-09

kaiser@CALTECH.EDU wrote:
> first cudos to Paul&Kevin for the incredible speed that coot gets more and more useable as an allround building tool -thanks!
>

Appreciated.

> I've had a 'problem' several times now with coot and proteins containing metal clusters. Is there a way to make the real space refinement aware of the existence of atoms not included in the actual refinement? Like for example in MAIN where you can define 'active' the atoms to be refined and 'passive' the atoms to be included in the energy calculation?

I don't know about MAIN. This is what happens in Coot, actually, the
"passive" atoms are defined on the fly.

> The problem is that everything close to metal clusters gets refined into the cluster density and there is no way including the ligand in the refinement as the selection requires consecutively numbered AAs.
>

You no longer need consecutively numbered AAs. This should "just work"
with Sphere Refinement [1] if you have defined the geometry of you link
(c.f. TRANS link in mon-lib-list.cif, if indeed you have a link, it is
not clear to me). If you do not have a link NBCs will be applied,
which may be what you want.

You can also fix/anchor atoms for refinement - using the anchor
toolbutton on the right.

Paul.

[1] If you haven't already done so, pick up the Sphere Refinement key
binding in the Wiki (shift-R):

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Pauls-key-bindings-for-coot
or

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Bernhards_key_bindings_for_coot.py

CCP4bb navigation

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

Previous message:
Subject: Coot real space refine and clusters
From: kaiser {- at -} CALTECH {- dot -} EDU kaiser {- at -} CALTECH {- dot -} EDU
Date: 2009-12-08

Next message:
Subject:
From: Vandana Kukshal v_kukshal {- at -} CDRI {- dot -} RES {- dot -} IN
Date: 2009-12-09