From: Jan R. <jr...@im...> - 2004-07-20 10:49:43
|
SourceForge.net wrote: >Bugs item #977396, was opened at 2004-06-22 13:51 >Message generated for change (Comment added) made by migueljmol >You can respond by visiting: >https://sourceforge.net/tracker/?func=detail&atid=379133&aid=977396&group_id=23629 > >Category: None >Group: None >Status: Open >Resolution: None >Priority: 5 >Submitted By: JR (interessent) >Assigned to: Miguel (migueljmol) >Summary: protein failes if *.O is called *.O1 > >Initial Comment: >in 4thn >http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=4thn >the unusual amino acides are not recognized as protein, >because *.O is called *.O1 > >with 1amt (an other [AIB] containing structure) there is a >java.lang.ArrayIndexOutOfBoundsException: 1 > at >org.openscience.jmol.viewer.datamodel.AlphaPolymer.extendRuns(AlphaPolymer.java:184) > > >---------------------------------------------------------------------- > > > >>Comment By: Miguel (migueljmol) >> >> >Date: 2004-07-19 19:01 > >Message: >Logged In: YES >user_id=1050060 > >Jan, > >Are you just talking about the AIB groups 22 & 23 ? > >Do you think that we should allow O1 as an acceptable atom >name for the carbonyl oxygen? > > no, I suggest the combination of element type and connection pattern to determine an amino acid 0. Ala Arg Asp ... 1. *.CA only: within(4.2, *.CA) != (*.N, *.O, *.OXT, *.C) 2. default naming *.CA *.C *.N *.O 3. connection C?-[-N?-C?-C?=(-O?] -N?) only the CAlpha should branch within the same residue (and N ? case of Pro) >If we make this change, do you think that it will cause >other problems? > > if we include the connection that made an amino acid we should get amino acids? But there are ~1000 HETERO components with N?-C?-C?-O? connection (without checking branching e.g. Guanosine derivate: OMG N7 C5 C6 O6) http://www.imb-jena.de/~jr/Jmol/ Regards, Jan |