Miguel sent (2004.05.19 at 3.09p [+0200gmt]) : >[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 find the 'amino' set somewhat confusing, so I never use it. ;-)
>>> >>>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? > I believe this is an area where Jmol can do it 'better' than Chime. modified residues that are part of a protein chain should be included in the defined set 'protein'. >>>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. > I don't understand amino either - it could be interpreted in so many different ways. amino ..acids? amino..groups? amines? etc. but to me, a protein is still 'protein' even if it has chemically modified residues integral to its backbone. therefore, modified residues that contribute to the continuity of the backbone should be included in the 'protein' set even if they are identified as HETATM in the file. > >>>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? >>> yes - although the hydrogen may be absent if it is a crystal structure. OXT can be separated from other backbone oxygens by its bonding pattern. keep in mind too that many structures do not have OXT (e.g., termini are sometimes cleaved during the protein prep, or do not crystallize well because they can be disordered, etc.). > >>>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? > yes to both. you can consider it a 'special' member of the backbone group, but definitely backbone. regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- 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%62&alloc_ida84&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
