Monomers in COOT

From: Dr. STEPHEN SIN-YIN, CHUI
Dear All,

For all monomers (3 letter) used in COOT, where can i find the full names of the
whole library? Many thanks

stephen

--
Dr. Stephen Sin-Yin Chui (徐先賢)
Assistant Professor,
Department of Chemistry,
The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China.


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From: Jacqueline Vitali
try file > search monomer library.  Hit search without typing anything.  It will give you what it has.

Jackie Vitali

2011/10/12 Dr. STEPHEN SIN-YIN, CHUI <chuissy@hkucc.hku.hk>

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From: Paul Emsley
In the console, coot tells you which file it has read in, you can read
that file and look for _chem_comp.name

0.7 will have the function comp-id->name (it's in the pre-release already).
(comp-id->name "ATP")
->
"ADENOSINE-5'-TRIPHOSPHATE"

The names in the Refmac monomer library can be truncated sometimes - I
will work with Garib to address that.

Paul.

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From: Ed Pozharski
Assuming that you have ccp4 configured, you can use this one-liner

find $CCP4_LIB/data/monomers -name "ADP.cif"  -exec grep ADP {} + | sed
-n 1p;

just replace ADP with your three letter code.

Wait, do you mean the full chemical name of the entity or something else
by "full names of the whole library"?

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
                                               Julian, King of Lemurs

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From: Paul Emsley
The RCSB's Chemical Component Dictionary has full names of the monomers.
ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif

We need cifgrep

typically:
$ cifgrep --search _chem_comp.comp_id=ADP --out-type=_chem_comp.name $CCP4_LIB

and to answer this question (i.e. for all entries):
$ cifgrep --out_type=_chem_comp.name $CCP4_LIB

and while you're at it (with a bit more work) we need cifmerge
$ cifmerge first.cif second.cif > both.cif
which merges the catagories/entities/tags of second.cif into first.cif, writing a new file.

Paul