Re: [ccp4bb] ANIS and SHELXL

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

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Subject: Removal of bacterial Hsp70 contaminant from recombinant protein
From: Yong Tang liutang19 {- at -} GMAIL {- dot -} COM
Date: 2007-03-09

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From: Robert Esnouf robert {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-03-09

Subject: Re: ANIS and SHELXL
From: Artem Lyubimov lyubimov {- at -} CALMAIL {- dot -} BERKELEY {- dot -} EDU
Date: 2007-03-09

Hi Sam,

The ISOR command restrains the anisotropic temperature factor
parameters to (roughly) approximate isotropic temperature factors,
and is by default specified for all your water molecules when you
generate your initial SHELX script. Usually, you can use ANIS
without parameters (i.e. generate anisotropic parameters for all
atoms) and restrain the anisotropic Us of waters with ISOR, that
works very well.

Once you've modified your structure, make sure that the anisotropic
parameters are indeed gone from the residues you've modified. If I
recall correctly, some actions will remove anisotropic parameters,
and some won't. In COOT, for example, I find it useful to re-set the
B-factor every time I modify a residue. When you run SHELX with ANIS
(again, without parameters), it'll automatically add anisotropic
parameters to the atoms that lack them.

And of course you can always remove the anisotropic parameters
manually from atoms that do not benefit from them, though it's a bit
tedious to do. Depends on how obsessive you are about your structure.

The SHELX manual is rather useful, look up ISOR and ANIS for very
helpful description of these commands. Also, look up a section
called "Restraints on anisotropic displacement parameters", which
discusses, well, restraints on anisotropic displacement parameters,
which is also very useful.

Hope this helps,
Art

On Mar 9, 2007, at 7:47 AM, U Sam wrote:

> Hi
> I am trying to refine my structure anisotropically by shelxl.
> When I use, "ANIS", all the atoms including water becomes anisotropic.
> (a) If I want to make only protein residues and ions (SO4 and
> Acetate) and not the waters, how should I declare ANIS in the .ins
> file.
> (b) If I modify or add any residues/ions, then in the next step how
> ANIS should be declared to make only modified residues/ions
> anisotropic after few cycle of isotropic refinement.
>
> Thanks for the suggestion/comments.
> Sam
>
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CCP4bb navigation

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

Previous message:
Subject: Removal of bacterial Hsp70 contaminant from recombinant protein
From: Yong Tang liutang19 {- at -} GMAIL {- dot -} COM
Date: 2007-03-09