On Tue, 16 Nov 2004, timothy driscoll wrote: >On 2004-11-15 (16:44) Miguel wrote: > >>Rebecca wrote: >> >>> I've got a molecule that has a propeptide but there are no chain >>> designations in the file to distinguish this part of the molecule >>> from the rest. So, when selecting a region (I'm trying to select >>> only the first 62 amino acids that consistitute the propiece) PE >>> selects the first 62 and also the next 62 (because the residue >>> numbering system begins again from '1' at the '63rd' amino acid). >>> Any ideas on how to get around this when no chain designations are >>> provided? >> >>I don't know what a propeptide is but ... >> >>you could try: >> >> select amino & 1-62 >> >>OR >> >>you could try selecting by atom numbers instead of by residue numbers: >> >> select atomno >= 1 & atomno < 999 # or whatever your atom numbers are >> > > >hi, > >answered this offlist. turns out the easiest way was by atomno range. > >a propeptide is a part of the protein that is cleaved during >post-translational modification to give the active form of the enzyme >(where it might be problematic to have the enzyme active before it is in >the proper cellular location). > >the residue numbers for this propeptide (file 3PBH) are 1P-62P; the rest >of the protein starts at residue 1. note that the propiece residue >numbers include the 'P'; this is not a chain designation. but >unfortunately, we could not even select these residues using 1P, 2P, >etc., nor using resno=1P, etc. :-( I guess this is a PDB which breaks the PDB format definition? (using 'alternate location' indicator when an explicit chain id would be better... or perhaps not?). Would anyone consider setting up a PDBug site - i.e. a Bugzilla (or similar) bug tracking system for PDB files which need attention in various ways? This would be a great 'check first' resource to help with this kind of problem. > > >regards, > >tim >