Petr wrote: > Jmol reads the indices of amino acid residues from pdb file - here is the > line, the N of ARG in chain A will have index 103 because of "ARG A 103" > > ATOM 1 N ARG A 103 -15.318 8.439 62.436 1.00 25.84 > RADA N > > The renumber x in Rasmol allows you to change that read index to another > that starts from x (even negative values are sometimes necessary). > Everything else remains the same.
OK. Q: Does it renumber all groups in all chains, or just the selected set? > Why it is useful: > > A. Protein X for which the structure is stored in pdb file is a sub-domain > of larger one Y. Y has e.g. 567 residues, domain X that was crystallized > (independently) only 70. Crystallographers retained Y- numbering of > residues in X. Now because X is molecule by its own, you analyze its 70-aa > sequence and have 5 tables of results indexed 1-70,because the analyzing > programs would index it based on the 70 aa sequence you input. To see what > the results mean means to add 103 to everything you want to see - source > of errors if you do not want to write a script to do that. OK, I think I understand that > B. There is "conventional" numbering of proteins, based upon some > alignment etc. and again, that generates problem above. OK > C. Most difficult problem is to have "gaps" in the sequence data, which > happens if crystallography cannot provide coordinates for certain > residues. > It can be identified by non-sequential "103's" in the "ARG A 103" segments > of the read line(s). That is not suitable for renumber command, with other > programs then RASMOL I usually correct for that by text-editing the pdb > file by filing the gaps by inserting lines with identifiable nonsense > coordinates, but that requires that the rest of the software recognizes > that. I did not really understand what you meant by 'non-sequential "103's" ' Q: Are you saying that there may be some sequence numbers missing? as in 101,102,103,110,111,112 ? Q: So, in this case are you saying that you would like to renumber a chain, but retain any 'gaps' that might exist? Jmol has some recognition of polymers. So if two residues are too far apart to bond then Jmol can recognize that ... even if they are in the same chain. Q: Would that be useful in trying to calculate whether or not the sequence should retain the previous 'gap'? Q: Should there be any type of 'renumbering' based upon polymer chains? The complicated scenarios are probably more than I can handle Q: Should 'renumber' only work on the selected set of atoms. Then you can select the subsets that you want and renumber them as you like them. Q: Please confirm that after 'renumber', all insertion codes are set set to space/null. One minor problem that occurs to me is this ... If the user has previously turned on labels that contain the residue number then those labels will continue to hold the previous values. To correct this one would have to reexecute the 'label' command. Miguel ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
