Re: [ccp4bb] Refmac5 and dual conformation of a dual conformation

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

Previous message:
Subject: Refmac5 and dual conformation of a dual conformation
From: Andy Millston andymillston {- at -} YAHOO {- dot -} COM
Date: 2009-02-02

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From: Paul Langan langan_paul {- at -} LANL {- dot -} GOV
Date: 2009-02-02

Subject: Re: Refmac5 and dual conformation of a dual conformation
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2009-02-02

I have battled a similar piece of structure in a recent project. There
is no software in crystallography that can handle hierarchical alternative
conformations w/o tricks. I was refining in Shelxl but the same trick
will work elsewhere. I had to define a new residue type, with two heads.
The A conformation had atoms for both heads. The B conformation didn't
have atoms that couldn't be seen. I was missing the entire side chain
in that conformation so the SC had no atoms.

Besides creating the new geometry restraint library, you will have to
ensure that no bad contacts are flagged between the two heads.

In Shelxl you can tie all the occupancies together properly, with
a couple annoyances. In other programs you are on your own.

Another possibility is to create four conformations for the entire
stretch but then you'll have to have the program keep many pairs of
atoms superimposed. I don't know if Refmac has that feature.

You will, of course, have difficulties when you deposit this thing
with the PDB. There is no way to correctly represent your model in
a PDB file, nor I believe in mmCIF. It may be reasonable to switch
to the four conformation model for deposition, since you will not
have to worry about enforcing the superposition of atoms any longer.
That may be clearer to people who use the model at a later date.

Dale Tronrud

Andy Millston wrote:
> I am currently trying to refine a structure where a 5 residue stretch of
> a chain is in 2 conformations. Oddly enough, 1 of these 5 residues is in
> dual conformations in both the conformations! Is there a conventional
> nomenclature for defining such dual-dual conformations?
>
> Refmac5 does not accept the intuitive way of naming such an atom.
>
> For example: A normal dual conformer GLY would be named as AGLY and BGLY
> in PDB file and this is acceptable to Refmac5
>
> When I name a "dual-dual" GLY as AAGLY and BAGLY, Refmac5 fails! Any
> idea, WHY??
>
> Thank you!
>
> Here is the error log:
> ----------------
> Logical name: ATOMSF, Filename: /programs/ccp4-6.0.2/lib/data/atomsf.lib
>
> ***************************************************************************
> * Information from CCP4Interface script
> ***************************************************************************
> The program run with command: refmac5 XYZIN "/home/../myfile.pdb" XYZOUT
> "...tmp" HKLIN "....mtz" HKLOUT "....tmp" LIBOUT "..._56_lib.cif"
> has failed with error message
> fmt: read unexpected character
> apparent state: internal I/O
> last format: (I4)
> lately reading sequential formatted internal IO
> ***************************************************************************
>
>
> #CCP4I TERMINATION STATUS 0 fmt: read unexpected character apparent
> state: internal I/O last format: (I4) lately reading sequential
> formatted internal IO
> ----------------
>

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

Previous message:
Subject: Refmac5 and dual conformation of a dual conformation
From: Andy Millston andymillston {- at -} YAHOO {- dot -} COM
Date: 2009-02-02

Next message:
Subject: Neutron Protein Crystallography Call for Proposals
From: Paul Langan langan_paul {- at -} LANL {- dot -} GOV
Date: 2009-02-02