Jan wrote: > modified and amino acids should be part of a set e.g. 'proteinogenic' > (but if future RasMol versions follow 'protein' will it be OK, too) > otherwise using 'proteinogenic' I may be able to define > define proteinogenic (protein or helix or sheet or turn) and not nucleic > in RasMol to approximate the effect
Jan, Tim and I made the decision to modify 'protein'. Please test it and let us know what you think. 'amino' is left as it was ... the base 20 amino acids + the 2 ambiguous ones. > for scripting, an access to the terminal residues of a polypeptide would > be great e.g. > select proteinogenic and bound(*C, *.N)==0 > the N-terminal *.N or > select residue(proteinogenic and bound(*C, *.N)==0) > the N-terminal group > or > select proteinogenic and count(*.CA and within(4.2, *.CA))==2 > both terminal *.CA This sounds interesting. We will consider new operators in the future. I have filed a bug report so we don't lose this. >>>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. > me too, I agree. OXT and the special backbone hydrogens are now part of the 'backbone' set. But this selection is still dependant upon the atom name 'OXT'. No connectivity checking is currently implemented. At the time that the groups are constructed the bonding has not yet been run ... this is a problem. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: Oracle 10g Get certified on the hottest thing ever to hit the market... Oracle 10g. Take an Oracle 10g class now, and we'll give you the exam FREE. http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
