Hi Arti,
> Hi all,
> I am having problems understanding how to add my own monomer to the
> ccp4
> monomer library.
> 1. Can it be done.
Yes it can be done.
> 2. How can I convert minimum description of a monomer to a complete
> one (
> libcheck fails when it tries to create the cartesian coordinates
> for this
> monomer (COM_COM)) from the library.
There is something wrong with COM (actually I do not understand why
it is COM_COM rather than COM?
Alexei? Garib?)
Anyway, I have created you ligand COM (1-THIOETHANESULFONIC ACID)
interactively using Sketcher and generated a complete ligand description
for you (exactly as described in Paragraph 5.1 of the paper you
mention).
PDB (COM_libcheck.pdb) and Library (COM_mon_lib.cif) files attached.
Now, it should work.
Best regards,
Roberto
> 3.If I ask Refmac to use the lib that I created for this monomer,
> it runs
> but the atoms in the pdb are either ripped apart or have links
> where they
> shouldnt be, this is when viewed in Coot. Refmac run without restrains
> doesnt show this, so the file is OK.
>
> 4. An excerpt
>
> "The dictionary can be extended easily by users. Users can
> create and organize personal monomer entries as well as
> modifications and links. In case of conflict, a user's definitions
> always override those stored within the distributed dictionary."
>
>
> from
>
> REFMAC5 dictionary: organization of prior chemical knowledge and
> guidelines for its use
> Acta Crystallographica Section D
> Biological Crystallography
> ISSN 0907-4449
> Acta Cryst. (2004). D60, 2184-2195
> Can a user use the default lib as well as the new ones.
>
> I am using ccp4-6.0.2. I would appreciate any help.
> Thank you.
>
>
>
> Arti S. Pandey
> Graduate Student
> Chemistry and Biochemistry
> Montana State University
> Bozeman,MT 59717
---
Dr. Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax +44 (0)20-7848-6435
e-mail [log in to unmask]
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