Dear Justin,
What happened when you just copied the molecule directory to the new
location? If the new project is virgin that might actually work, so I am
curious how it failed.
My best guess of the problem is that the new ChemComps are in the project
directory of the old project - that is the default location for new
ChemComps. The new project therefore cannot find them. The simplest
solution would be to copy the new ChemComps to ccp/molecule/ChemComp in
the new project before you run the datShifter. ALternatively, but less
recommended, you could copy the ChemCOmps with the dataShifer first. In
the long term one could set up a separate repository at individual, group,
or department level and make sure all nwe ChemComps go there. You would
then have to tell your projects to look in that repository as well. This
last is a better solution, but it is slightly more work to set up, and I
do not know how well our GUI supports these operations.
Yours,
Rasmus
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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 Mon, 9 Feb 2009, Justin Douglas wrote:
> Hi Wayne,
>
> Unfortunately this molecule has 4 strange chemComp. I tried to copy the
> folder project1/ccp/molecule to project2/ccp. That didn't work
> automagically.
>
> I guess this leads to a general question. Is there a general way to
> transfer a molecular system from one project to another? This molecule in
> question is used in the lab a lot and I made this molecule in one project.
> Unfortunately I don't remember how I did it (I should check the mailing
> list because I enlisted a lot of help from you and Wim). The gist is that
> it is an modified RNA with all U & C bases having a Fluorine in the 2'
> position and all A and G bases but 2 have O-methyl groups in the 2'
> position. These chemComp are A2m, CFL, Omg and Umf. I had to download them
> from the EBI website.
>
> Thanks,
>
> Justin
>
>
> Unfortunately what the code is doing there is generic enough that it's not
> > obvious what is going wrong. But it looks like (at a guess) that the
> > funny chemComp is not being found. But why it is not being found I don't
> > know. Is its XML file located in the project-specific directory for the
> > first project and not in a similar location in the second project? That
> > might cause a problem like this (but I don't know the details of how this
> > stuff is being copied over by the dataShifter so I could be wrong). If
> > that's the problem then it's possible that just copying the XML file over
> > from the first project to the second one before you run the dataShifter
> > would work. (Or it might need some more finessing, because it might not
> > just pick this up automagically.)
> >
>
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