i read and see that autobuild finds ncs automatically and uses it. i have one .pdb with one copy of the model for segid's A and B, and chainid's A and B. however, i notice sometimes in density modification that ncs has "NO" flags as to its use, and the output .pdb's have a single chain in them. refinement has sensible .eff's and such for ncs, there's find_ncs_* output, but some .log's suggest it is not specified or used. so just generally, how is ncs used - e.g. is it strict, which would explain a single chain the output .pdb? -bryan
Hi Bryan, Autobuild looks at the sequences of the chains in the PDB file to see if there are duplications. If so, it checks to see if any parts of the structures of with the duplicated sequences are similar. If so, it will use the NCS relating those segments in (1) density modification and (2) refinement. The NCS is not "strict" in the sense of "constraints", rather it is used as a restraint in refinement (but by default with very tight restraints). The identification NCS in autobuild (and in phenix.refine) is done by phenix.simple_ncs_from_pdb, so you can see (or modify) how this is done by running phenix.simple_ncs_from_pdb my_model.pdb (or equivalently, phenix.find_ncs my_model.pdb). The single chain output from autobuild suggests that you are running with "rebuild_in_place=False", and then autobuild puts all the parts of the model that match one copy of your sequence from the sequence file as "chain A". I hope that helps! -Tom T On Sep 22, 2010, at 10:01 AM, Lepore, Bryan wrote:
i read and see that autobuild finds ncs automatically and uses it. i have one .pdb with one copy of the model for segid's A and B, and chainid's A and B.
however, i notice sometimes in density modification that ncs has "NO" flags as to its use, and the output .pdb's have a single chain in them. refinement has sensible .eff's and such for ncs, there's find_ncs_* output, but some .log's suggest it is not specified or used.
so just generally, how is ncs used - e.g. is it strict, which would explain a single chain the output .pdb?
-bryan _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
The single chain output from autobuild suggests that you are running with "rebuild_in_place=False", and then autobuild puts all the parts of the model that > >match one copy of your sequence from the sequence file as "chain A".
so if e.g. user thinks 2-fold NCS, and there is a protomer plus its copy in a .pdb (segid A and B) related by that 2-fold, can the input sequence file has just one string of residues for the protomer? i.e. not one string and its copy? -bryan
Hi Bryan, Yes, one copy of each unique sequence is all that is necessary in the sequence file (in fact all other copies are ignored). All the best, Tom T On Sep 22, 2010, at 11:37 AM, Lepore, Bryan wrote:
The single chain output from autobuild suggests that you are running with "rebuild_in_place=False", and then autobuild puts all the parts of the model that > >match one copy of your sequence from the sequence file as "chain A".
so if e.g. user thinks 2-fold NCS, and there is a protomer plus its copy in a .pdb (segid A and B) related by that 2-fold, can the input sequence file has just one string of residues for the protomer?
i.e. not one string and its copy?
-bryan _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
participants (2)
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Lepore, Bryan -
Tom Terwilliger