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Re: [ccp4bb] Refining alternate ligand/autoinhibition |
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CCP4bb navigationCCP4bb <-- 2007 <-- May 2007 <-- 08 May 2007Subject: Re: Refining alternate ligand/autoinhibition From: Stefan Arold s {- dot -} arold {- at -} CBS {- dot -} CNRS {- dot -} FR Date: 2007-05-08 Here some additional infos: I am using ccp4 6.0; Refmac_5.2.0019 version 5.2.0019 and the data are only to about 2.8 A I have tried to leave out the alternate flags - still the same: the repulsion persists... I have also tried to use the same chain label for the peptide and the protein (to simulate two conformations of a pseudo-hybrid unit), but this didn't help either... best wishes Stefan Eleanor Dodson a écrit : > Well - A and B are meant to be flags to show there are 2 conformations > of a particular unit. sp they arent appropriate here and may be > muddling things up. > > On the other hand you shouldnt get any repulsion between pairs of > atoms whose added occupancy is <= to 1.0 > > Is that always the case for your 2 scenarios? > > Try removing the A and B flags and see if that is better. > Eleanor > > > Stefan Arold wrote: > >> Dear All, >> >> I am having trouble refining a difficult case of alternate structures >> in REFMAC. In the crystal, two states superimpose: >> 1) Apo-protein with its own auto-inhibitory tail fixed into the >> ligand binding site >> and >> 2) Peptide-bound protein, where the peptide has displaced the >> auto-inhibitory tail. >> this also includes alternate side-chains of the protein ligand >> binding site, according to the apo state or peptide-bound state >> >> I was hoping that assigning 'A' and 'B' alternate states (for 'apo' >> and 'peptide-bound') to the protein chain (chain A) >> [ex: >> ATOM 62 C ATYR A 17 20.856 42.150 21.476 0.60 >> 75.23 C] >> >> and state 'B' to the peptide >> [ex: >> ATOM 87 N BALA D 513 9.910 69.145 50.780 0.40 >> 20.00 N] >> >> would do the job - but unfortunately, even though refmac refines this >> structure, the two states 'sense' each other, and refmac refinement >> applies repulsive forces, pulling the apo-auto-inhibitory tail and >> the peptide away from each other... >> >> Neither the refmac manual, nor the ccp4bb archives helped, so I >> thought one of you might... >> >> many thanks >> >> Stefan >> >> >> > -- ================================================== Stefan T. Arold, PhD Centre de Biochimie Structurale CNRS UMR 5048 - UM 1 - INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex - France email: S.Arold@cbs.cnrs.fr Phone: +33 (0)4.67.41.77.02 Fax: +33 (0)4.67.41.79.13 ================================================== CCP4bb navigationCCP4bb <-- 2007 <-- May 2007 <-- 08 May 2007 |
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