Hello,
Several years ago Wayne and Wim helped me create a molecule with
nonstandard nucleotides. I'm having some issues repeating this
procedure with v2.1.5. There are two issues:
#1) In Molecules popup window, under the Add Sequence tab I can append
some of my nonstandard nucleotides (OMG, T11 and A2M, to be exact).
If I choose one and click the add sequence button I get a popup that
says
"Chemical Components OMG not available locally. OK to download to
project directory?"
I click OK and I eventually get a second popup that says:
"Residue code(s) OMG cannot be found for molecule type RNA."
The terminal gives the following output:
>>> No connection:
Cannot connect to download server
http://ccpforge.cse.rl.ac.uk/gf/project/ccpn-chemcomp/scmcvs/?action=browse&root=ccpn-chemcomp&pathrev=MAIN&path=/~checkout~/ccpn-chemcomp/data/pdbe/chemComp/archive/ChemComp/RNA,
or file does not exist...: [Errno socket error] [Errno 51] Network is
unreachable
I just updated analysis, so I should have the latest version.
#2) Unfortunately there are two nucleotides in my sequence that are
not in the list. I can find both at
http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl
(they are CFL and UMF). Last time I did made a molecule with these
nucleotides I had to get xml files from Wim and put these into a
directory in analysis, change the analysis code and recompile. I was
hoping there was a better way to do this in v2.1. If not, I would
appreciate it if someone could help me with getting the xml file for
UMF (I have the one for CFL) and hacking analysis to work with these.
Thanks,
Justin
|