December 2011 - phenixbb - phenix-online.org

pdb hierarchy
by Bradley Hintze 04 Dec '11

04 Dec '11

Hi Phenix, I have a hierarchy question. I was using the hierarchy and got something that I did not expect. when running this: pdb_io = pdb.input(pdbfile) hierarchy = pdb_io.construct_hierarchy() for model in hierarchy.models(): print model.id for chain in model.chains(): print ' ' + chain.id When I do this I expect the chains in pdbfile to be printed once for each model in pdbfile. However, when I ran this I got, for example, chain 'A' printed four times under the same model. Why is this? Thanks, Bradley

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Writing PDB
by Bradley Hintze 04 Dec '11

04 Dec '11

Hi again, I am trying to take a pdb and write out a new pdb with just a specified chain. I am trying to do this with the hierarchy but am unfamiliar with its functions How do I do this? Thanks, Bradley

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the Ming dial
by Dialing Pretty 04 Dec '11

04 Dec '11

Dear All, In the Ming dial, there is a occupancy (%), which indication of excellent , good, etc. Does it mean if I choose the "occupancy" of excellent, the rotamer outlier ratio will be lowered? My crystal has a resolution of 2.8, and I find no matter how I turn the dial, the original fits the map best. Currently my rotamer outlier is 8%, thus I need the way to have it solved. In addition, for Coot and Ming, which is much convenient to reduce rotamer outlier? I am looking forward to getting your reply. Cheers, Fenghui

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on the rotamer optimization
by Dialing Pretty 03 Dec '11

03 Dec '11

Dear All, Besides Coot and Ming, is any software or server which could further optimize the side chain outliers? I am looking forward to getting your reply. Cheers, Dialing

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solvent model in phenix.refine
by Weiergräber, Oliver H. 01 Dec '11

01 Dec '11

Hello, the ordered_solvent option in phenix.refine apparently uses these parameters by default: min_model_peak_dist = 1.8 max_model_peak_dist = 6.0 min_peak_peak_dist = 1.8 I was wondering about the justification for this (extremely relaxed) set of limits. As far as I know, the shortest hydrogen bonds (if defined as donor-acceptor distance) are about 2 A, and even these are considered exceptional and rare. Similarly, anything in excess of 3.5 A is quite unlikely to be significant energetically, so why use 6 A as an upper limit? Even if max_model_peak_dist was only meant to limit the extent of the outer solvent shell, there is no such thing as max_peak_peak_dist to avoid unreasonably long individual bonds. My personal suggestion would be a range of about 2.3 - 3.2 A for a significant hydrogen bond, with the lower limit exemplified by charged interactions (carboxyl-water or oxonium-water), which tend to be shorter - and stronger - than average. On the other hand, I do frequently observe elongated densities which, in accordance with the default parameters, are typically interpreted by phenix.refine as two water molecules about 2 A apart. So the question arises whether this is a realistic assumption, compared to a "sliding water" model in which the position of a single molecule is just ill-defined in a certain direction (due to a competition of adjacent binding sites for example)? Best regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Clashing alternative conformations
by Sozanne Solmaz 01 Dec '11

01 Dec '11

Dear all, I have the following problem: I have a homodimer of two protein chains A and B, which I refine in Phenix, and one residue has 2 alternate conformations (a and b) for each chain. If the residues of both chains A and B are in the alternative conformation b, they clash. However, I would expect that never both residues are in conformation b, and therefore only the combinations aa, ab and ba of alternative conformations exist. My problem is, that during the refinement, the two b conformations of the residues clash, which drives the clash-score of the overall structure to a very high value and repulsion pushes the two b-conformations apart during refinement, therefore I cannot model them properly. Is it possible in Phenix to define these two conformations as non-clashing and non-repulsive? Thank you, best regards, Sozanne Solmaz.

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