Dear Justin,
I would recommend the procedure given on the CCPN WIKI
(http://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-analysis/howtos-1/create-a-sequence-with-unusual-amino-acids-or-nucleotides
Follow the links Homeý > ýDocumentationýon > ýCcpNmr Analysisý > ýHowTosýos > ý
Then look under the Molecules subheading for the HowTo you want. I
recommend the variant under the heading 'The intuitive way'
Incidentally, the WIKI is now up to date and actually quite good. That was
not always so, but now it is definitely worth looking at if you are stuck.
I checked that OMG, A2M and T11 are all present. You are getting problems
because OMG and A2M are not classed as RNA, but as 'other'. Hence you can
not add it under 'Add Sequence' which assumes that everything you add is
RNA. The method from the link above should solve your problems.
Additional comments:
1) The molecules popup is confusing. We are considering ways of improving
it for coming versions.
2) ChemComps are a bit disorganised. We shall be discussing what we can do
about it soon.
3) There is a bug in the {Sequences} tab, so you can not use [Add
Compound] on an empty molecule. It is being dealt with.
Yours,
Rasmus
---------------------------------------------------------------------------
Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
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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