> Hi Miguel, > here are the files. I had them for a long time, so I cannot reconstruct > where they come from. > Many thanks for your help.
Adriano, The files which you sent me off-list do not meet the .pdb file format specification because the atoms within the amino residues are not ordered correctly. Therefore, they are not recognized as proteins. On page http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html the pdb format specification says: * ATOM records for proteins are listed from amino to carboxyl terminus. In the files which you sent me the atoms are not listed in this order. The carboxyl carbon is listed first, followed by the alpha carbon. The amino nitrogen and the carboxyl oxygen come later. ATOM 1 C ASP N 16 5.368 52.748 17.884 1.00108.97 C ATOM 2 CA ASP N 16 5.097 51.451 17.123 1.00109.52 C ATOM 3 CB ASP N 16 4.074 51.501 15.983 1.00110.44 C ATOM 4 CG ASP N 16 3.935 50.198 15.212 0.01110.94 C ATOM 5 N ASP N 16 4.774 50.334 18.074 1.00108.81 N ATOM 6 O ASP N 16 6.432 53.359 17.679 1.00109.04 O ATOM 7 OD1 ASP N 16 4.935 49.454 15.112 0.01111.17 O ATOM 8 OD2 ASP N 16 2.827 49.913 14.703 0.01111.16 O Below is the conventional ordering that complies with the pdb specification. ATOM 1 N THR 1 17.047 14.099 3.625 1.00 13.79 1CRN 70 ATOM 2 CA THR 1 16.967 12.784 4.338 1.00 10.80 1CRN 71 ATOM 3 C THR 1 15.685 12.755 5.133 1.00 9.19 1CRN 72 ATOM 4 O THR 1 15.268 13.825 5.594 1.00 9.85 1CRN 73 A In this case, I suggest that you use 'select amino' instead of 'select protein' In Jmol the 'amino' set is defined only using the names of the groups, independent of the atoms/data/contents The 'protein' set is defined using only the contents of the groups, independent of the group names. However, depending upon what you are trying to accomplish. This may not be adequate. Polymer shapes are based upon proteins, not aminos. Therefore, cartoons will not work on this model. Let me know what you are thinking. Miguel ----- Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] ----- ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
