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[Jmol-developers] [ jmol-Bugs-977396 ] protein failes if *.O is called *.O1
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From: SourceForge.net <no...@so...> - 2004-09-18 05:50:18
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Bugs item #977396, was opened at 2004-06-22 11:51 Message generated for change (Comment added) made by interessent You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=977396&group_id=23629 Category: None Group: None Status: Closed Resolution: Fixed 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: JR (interessent) Date: 2004-09-18 05:50 Message: Logged In: YES user_id=908382 with 4thn there are besides of ABI and DGL further amino acids, which are currently not detected as part of the protein set: CHG CYCLOHEXYL-GLYCINE HAC BETA-CYCLOHEXYL-ALANINE NAL BETA-(2-NAPHTHYL)-ALANINE these didn't contain *.CA named C-alpha atoms. ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-09-17 22:34 Message: Logged In: YES user_id=1050060 The names O and O1 are both acceptable now ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-07-19 17:01 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? If we make this change, do you think that it will cause other problems? Miguel ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=977396&group_id=23629 |