> Excuse me Miguel, > it was my mistake. Not completely your mistake ... Now I understand the problem.
[snip] >>There is no special treatment for HETATM. >>It is all based upon the atom name. >>It takes the first "N", the first "CA", the first "C" and the first "O" >>*All* of these must be present in the group, otherwise the group is not >>considered to be amino. >>They do not even have to be bonded together. Here is part of the problem. This is what is used internally, but it is *not* what is used for the predefined sets 'amino' and 'protein' ... maybe 'backbone' I need your help in figuring out what to do with the predefined sets. For RasMol/Chime compatibility, the predefined sets are generally much simpler. 'amino' is based upon the group name. >>I do not see any beta sheets. I see two alpha helices. In two different >>chains, one above the other. >> >> > the H-bonding pattern is long range like in beta-sheets wound up to form > a helix like structure and in pdb1nrm.ent: > SHEET 1 A 2 VAL B 1 TRP B 15 > 0 > SHEET 2 A 2 VAL A 1 TRP A 15 -1 O ALA A 5 N VAL B > 1 > but the sheet cartoon is not displayed I do not really understand. I will need to look at the file again. > ... with my script ... > > > >>The modified HETATM amino acids are part of the Polymer chain and render >>just fine. >> >>It looks like to me it is doing exactly what you want. The modified >> HETATM >>amino acids are part of the polymer chain. >> >> > what I want and what Jmol did is: > select sheet > cartoon > > but I did: > select protein > cartoon > but protein did not include the HET D-amino acids:-) > should I use > select amino This will not work either ... for compatiblity with RasMol > you wrote, a group would be considered amino if the backbone atoms are > present in one group? > but up to now, this failed, too. > > now I do: > select protein or ( not nucleic and (helix or turn or sheet)) > cartoon > and get the desired rendering I need a recommendation from you. I do not want to break existing RasMol/Chime scripts. Q: Should we change the definitions of 'amino', 'protein', 'backbone', etc so that modified residues are included? Q: Or should we create new sets for them? >>Q: What is it that I am not understanding? >> >> > Nothing, it was my fault, but you may consider defining a set e.g. amino > which are all the groups containing the amino backbone atoms. Let's think about this and try to come up with a good solution. But I need input from other people ... because these are things that I really don't understand. >>Unfortunately, I still do not understand. >> >>Q: It looks like to me that OXT must be a hydrogen or an OH group or >>something ... is that true? >> >> > that is right, but the pKa is about 5, though it may be 100% > deprotonated at "normal" pH 7 OK >>Q: I still do not understand what you want to do with the OXT? >> >> > you may include them into the set of backbone atoms, > is there a set including all "amino" backbone atoms N CA C O (OXT) in > one residue? So, you are saying that perhaps we should include OXT in the 'backbone' predefined set. Q: Do you also think that OXT should participate in backbone/trace/cartoon? Miguel ------------------------------------------------------- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
