Miguel wrote:
... Turns out it is saying something slightly different.It is saying: * I see a group * It has an atom named CA * It has an atom named N * It has an atom named C * It should have an atom named O, but it does not. However, that does not tell you whether or not it was accepted as an 'AminoMonomer'. Here is a snippet of code from AminoMonomer.java: if (specialAtomIndexes[JmolConstants.ATOMID_CARBONYL_OXYGEN] < 0) { int carbonylOxygenIndex = specialAtomIndexes[JmolConstants.ATOMID_O1]; System.out.println("I see someone who does not have a carbonyl oxygen"); if (carbonylOxygenIndex < 0) return null; offsets[1] = (byte)(carbonylOxygenIndex - firstAtomIndex); } The net effect is that if the atom 'O1' is present then it *will* be accepted as an amino group, even though the message "I see someone who does not have a carbonyl oxygen" is printed out. I am sure that I went back in and added this code for 'O1' support because someone asked for it. So, the code does not print any informative message to tell you whether or not the group was accepted as an AminoMonomer. Q: What information do you think would be useful?
the label information %U
Q: What should the messages say?
%U may be interpreted as carbonyl oxygen Regards, Jan ------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
