Hello,
On the download issue, it looks to me like the entire CcpForge website is
down right now. Hopefully that will be temporary.
In v2, once you have a ChemComp, you can put in the standard directory
(data/ccp/molecule/ChemComp/) and it should be picked up automatically.
(I can't remember if the download code sticks it there or elsewhere.)
Hopefully someone can address point 2 below (Tim is designing a graphical
ChemComp builder but it's not quite ready yet).
Wayne
On Fri, 10 Dec 2010, Justin Douglas wrote:
> 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
>
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