Jan wrote: > Hi Miguel, > I had some problems posting to the jmol list using two different SMTP > relays.
I am also having many email problems today. I am having trouble posting messages to the pdb-l mailing list. > It is a modified peptide but not at the position where the (lacking) *.O > should be, but at the *.N as you may see with the LINK record > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_48.html > LINK CB PYL C1005 N GLY C 5 > > and there are missing atoms. REMARK 470 may be considered when the > monomer class is determined. > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_31.html I think that it will be much to difficult to parse the REMARK records. >>> Q: Are there lots of things that can hook on where the carbonyl oxygen >>> should be? >>> >>> >> The phenylethane group is not "where the oxygen should be" but, >> rather, attached to the N atom of [gly]5:C. OK >>> Q: Do we need to rethink the critera for determing whether or not >>> something is an AminoMonomer? >>> > No, but consider REMARK 470 > or, quick and dirty, we may rethink the criteria where schematic > rendering could be applied, e.g. where > select protein or amino > is true ('protein' are the determined amino acids and 'amino' the set of > the standard amino acids) The only way that we can allow an incomplete residue to participate in a Polymer is if we relax the requirements for being a Monomer. But, in this case we need to have the =O because the vector of the carbonyl group is necessary in order to calculate the plane of the residue backbone. >>> Q: What other structures could plug themselves into a protein backbone? >>> >>> >> The question is, to what extent does Jmol have to represent non-real >> (or extremely exotic) protein-like structures? > > no, but as you stated, how to deal with missing atoms and schematic > rendering. OK. For now we are going to consider this issue closed. If someone has a set of specific examples and a recommendation on how to handle them then we will reopen the issue. Miguel ------------------------------------------------------- This SF.Net email is sponsored by The 2004 JavaOne(SM) Conference Learn from the experts at JavaOne(SM), Sun's Worldwide Java Developer Conference, June 28 - July 1 at the Moscone Center in San Francisco, CA REGISTER AND SAVE! http://java.sun.com/javaone/sf Priority Code NWMGYKND _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
