Re: [ccp4bb] problem in coot

- Protein crystallography

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- Protein purification
- Crystallisation

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

Previous message:
Subject: problem in coot
From: Jayashankar s {- dot -} jayashankar {- at -} GMAIL {- dot -} COM
Date: 2008-04-28

Next message:
Subject: balbes with space group checks
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-04-28

Subject: Re: problem in coot
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-04-28

Jayashankar wrote:
> Dear ccp4bb and Paul emsley,
>
> I have a problem in coot,
> I could clearly see the density for some small molecule that was
> present in the sample buffer. when I generate .cif from monomer sketch
> library from ccp4 and use same .cif
> in coot for real space refinement, the small molecule goes back and
> sit into the nearby protein density rather than to stay in the
> speculated density for that molecule.
>
> i can very well regularize the zone but could not do any real space
> refinement of that small molecule.
>
> What might be the problem?

Dear Jayashankar,

First you need to check that the map against which you are refining is
the correct one.
(Model/Fit/Refine -> Select Map).

If that doesn't work, try masking out the protein. (Let's presume that
the surrounding protein atoms are in the A chain and the small molecule
is not in the A chain):
Extensions -> Mask Map by Atom Selection
with selection "//A/"
Now change the refinement map to "Generic Masked Map" using Select Map.
Now refine again.
That should work.

HTH,

Paul.

CCP4bb navigation

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

Previous message:
Subject: problem in coot
From: Jayashankar s {- dot -} jayashankar {- at -} GMAIL {- dot -} COM
Date: 2008-04-28

Next message:
Subject: balbes with space group checks
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-04-28