Hi Marc,

I haven't seen a reply to you mail yet so I'll do my best - sorry it has
taken us a while to get back to you.

> So first :
> I would like to import an amino acid sequence from Ansig where two residues
> are unusual: one is an unsual cysteine and the other one is a kind of
> polyethylene glycol. These residues, as far as I know, are not defined in
> Analysis or in the MSD database.

The way to find out if these exist is by going to the MSDchem server:

http://www.ebi.ac.uk/msd-srv/chempdb/cgi-bin/cgi.pl

and typing in your search terms. For 'ethylene glycol' as 'Molecule name'
there's a number of matches - if the code you're looking for is in there
then go to:

http://www.ebi.ac.uk/msd-srv/docs/NMR/chemCompXml/main.html

If the code belongs to a 'Polymer' (i.e. DNA, RNA or protein) then get it
from there, otherwise (for ligands etc.) download the nonpolymer code.
Then put the .xml file in the relevant ccpnmr/data/ccp/chemComps/
directory (this is either 'DNA','RNA','protein' or 'nonpolymer').

> So my plan was to create these xml files and then put them in my own
> library. Is there a way to change the path for the library? (actually, I'm
> not the root and every time I need to add or delete an xml file, I might ask
> the root).

The way to do this would be:

1. Create the directory where you want to store the chemComp information
locally... e.g. in '<my local directory>/ccpnmr/data/ccp/chemComp'.  Also
create in there 'protein','DNA','RNA' and 'nonpolymer' directories (this
defines the 'molType'). Now you can either copy or symbolically link the
chemComp .xml files from the
<installation path>/ccpnmr/ccpnmr1.0/data/ccp/chemComp/
directories to the directories you just created. I would recommend using
symbolic links, as there will be additions and changes to the reference
information we provide.

2. Now you have to change the URL that defines where the chemComp
information for your project is stored. You can do this by starting up
your project with Analysis or the FormatConverter and accessing 'Save
as...' from the GUI. Open the 'Urls' table and edit the URL path for
chemComp (name 'chemCompData'). The 'Path' entry should be:

<the installation path>/ccpnmr/ccpnmr1.0/data/ccp/chemComp/

Change this to:

<my local directory>/ccpnmr/data/ccp/chemComp (or whatever you created).

3. Click 'Save'

4. You can now add your own chemComp .xml files to the local directory.

A couple of remarks though:

- Making a 'chemComp' is currently not straightforward - we will provide a
module that allows you to make them from the molmol or smiles
representation (so you can use standard chemistry packages to draw the
molecule, save it from there and then import it). If you cannot find the
chemComp you need right now then contact us again and we'll see what we
can do.

- If the correct chemComp is available you should be able to select it
when importing a sequence with the FormatConverter (the program should now
prompt the user to locate the correct chemComp when it encounters an
unknown code in a sequence file). We might in the future provide a direct
internet link to the central chemComp resource at the MSD.

- It is possible that we will be making a number of substantial changes to
the chemComp area soon. This will not affect you (we'll make sure there's
backward compatibility for your data files) but if you do venture into
defining you own chemComps at this stage there might very well be
difficulties later on. We'll provide an updated set of chemComp files with
the new version if there are changes, but old chemComp files (being
reference data files) might have problems with backward compatibility.

> Then:
> I also have a disulfide bridge between two cysteines. When I looked at the
> MSD database, I found the following residue CSS (mercapto cysteine) which is
> probably the one I want to use. Is this residue not defined by default in
> the Analysis library or am I in the wrong directory?
> (/ccpnmr/ccpnmr1.0/data/ccp/chemComp/protein/ on my computer)
>
> So downlaoding the CSS.xml file, where should I put it?

It is not part of the standard library, so just add it to your new <local
directory>/ccpnmr/data/ccp/chemComp/protein/ directory... . Again at one
stage you might want to download the newer version of the file (we'll let
everyone know when there's major changes in the reference data so you can
download non-standard files).

Hope this helps,

Wim

PS We will be writing comprehensive documentation on how to change data
storages and URLS, and on how to treat molecule creation... hopefully that
will be done within the next month!