> Hi all, > > Jmol 10.00.33 and 10.00.18 seem to be unable to select any protein residue > range > in the PDB structure "1TON" from the PDB database (e.g.: 53-58). In > contrast > version 10.00.00 is able to do this.
Yes, I see the behavior. select 53 # works ... select residue number 53 + HOH group 53 select 54 # also works select 53-54 # only selects the two HOH groups. So, the range selection *is* selecting groups 53 & 54, but it is selecting the HOH groups, not the residuce groups. > When I looked at the PDB file I noticed that it contains no chain > identifier and > that the "HOH" residue numbering starts at 1, overlapping with the protein > residue numbering. It looks like this could cause the problem. With > "113I", a > similar structure without this kind of overlap, Jmol 10.00.33 doesn't show > any > selection problems. Yes ... the problem is that there are two groups with the same number in the same chain. > I don't know if "1TON" is still within the PDB format specifications and > how > many other PDB structures also have this kind of overlap. So maybe this > isn't a > bug but just a reduced error tolerance. Yes, the file may well be out of spec. I do not know. I do not recall specifically, but I am quite sure that any changes made in the range selection code since 10.00 were made in order to address problems with other files. Probably something related to alternate conformations. We can consider changing the range selection behavior, but we need to be careful not to break anything. In this particular case, it seems that the range selection should pick up both ranges. As an example, let us assume that we have a chain with the following 10 residue sequence numbers. 1 2 3 4 5 1 2 3 4 5 Q: If I say 'select 1-5' should all 10 residues be selected? Q: If I say 'select 2-3' should 4 residues be selected? Q: If I say 'select 3-2' how many residues get selected? The RasMol documentation for 'select' is not clear as to whether or not the order of the the order of the residue numbers in the range must be the same order that the residues are found in the file. Q: Do you think that Jmol should require that the order of the range expression be the same as in the pdb file? Example: 1 2 3 4 5 If I say 'select 2-3' then two residues should be selected. Q: What happens if I say 'select 3-2'? Miguel ------------------------------------------------------- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
