Re: [Jmol-developers] [ jmol-Bugs-977396 ] protein failes if *.O is called *.O1

Tue, 20 Jul 2004 03:50:28 -0700 

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


-------------------------------------------------------
This SF.Net email is sponsored by BEA Weblogic Workshop
FREE Java Enterprise J2EE developer tools!
Get your free copy of BEA WebLogic Workshop 8.1 today.
http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
_______________________________________________
Jmol-developers mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-developers

Reply via email to