Hello Bachar, On Fri, 2013-05-10 14:29 EDT, Bachar Cheaib <cheaib.bac...@gmail.com> wrote:
> Dear pymol users, > > I have wondered whether someone know how to know if a such structure in > pdb file is multi-mer or mono-mer biologically speaking? Somehow in the > related publication of structure this information is present in > occurrence and in pdb also is not nonintuitive to catch without the > BIOMT transformations. A monomer could be deposited with multiple copies > (or chains) of the same protein, but strikingly a biological (in vivo) > homo-tetrameter (ex.1xiu ) it seems to be represented as a dimeric (two > chains) and missing the two others in the pdb file > > This record "REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC" > does not tell us if a structure is really multi or monomeric in the pdb > file. This does tell you that the protein is thought to exist as a tetramer. What is determined by crystallography and therefore what is present in a PDB file is the structure that exists in the asymmetric unit, in other words the unique part of the structure. That could be a portion of the structure if it has internal symmetry, but it could also be two or more copies of the biological unit. If the asymmetric unit is not a tetramer (as in your case), then you do need to use the BIOMT information to generate the tetramer. That is why that information is there. Just in the answers to a previous question that you included in your message, you could load the structure with the "type=pdb1" option: fetch 1xiu, type=pdb1, async=0 set all_states which will fetch the biological assembly for that structure. The extra monomers that were generated by the crystallographic symmetry will be visible when you set all_states. Or you could split the states out into separate objects. > I would like just like to know how to conclude multimeric states > informations from the pdb file without doing transformations ? just this > information Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
