Re: [ccp4bb] Monomers in COOT

2011-10-13 Thread Paul Emsley 
On 13/10/11 04:25, Dr. STEPHEN SIN-YIN, CHUI wrote:
 Dear All,

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


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.

Re: [ccp4bb] Monomers in COOT

2011-10-13 Thread Ed Pozharski 
On Thu, 2011-10-13 at 11:25 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote:
 Dear All,
 
 For all monomers (3 letter) used in COOT, where can i find the full names of 
 the
 whole library? Many thanks
 
 stephen  
 


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

Re: [ccp4bb] Monomers in COOT

2011-10-13 Thread Paul Emsley 

On Thu, 2011-10-13 at 11:25 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote:

Dear All,

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

stephen



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?



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

Re: [ccp4bb] Monomers in COOT

2011-10-12 Thread 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 chui...@hkucc.hku.hk

 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.
 Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)