[phenixbb] phenix/ccp4 monomer library compatibility

[Nigel Moriarty]

Ralf curated the Monomer Library (in about 2005) for suitable
restraints. Garib has updated/improved the library greatly since then
so substituting the current library is a fine idea. As Pavel said, the
GeoStd has a number of entries including the standard amino acids
which contain the rotamer information. PHENIX programs will be
supplied with the restraints from the GeoStd library if it exists,
otherwise its taken from the "Monomer Library" which ever one is in
place.

Cheers

Nigel

On Wed, Sep 5, 2012 at 9:15 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
> To clarify:
>
> CCP4 Monomer Library is a great resource. However it contains a lot of
> entries are not suitable (to say the least) to use in refinement. Therefore,
> what's phenix.refine is using is a subset of Monomer Library, that contains
> only usable (for refinement) entries, plus Nigel's geo standard that
> contains curated entries plus those complimented with some new infromation
> (such as R-lab rotamer library torsions).
>
> Nigel may probably provide more information about geo-standard and libraries
> used in Phenix in general.
>
> Pavel
>
>
> On 9/5/12 7:50 AM, Dmitry Rodionov wrote:
>>
>> Speaking of dictionaries...
>>
>> It seems that latest Phenix is distributed with dictionaries from 2005:
>>
>> /usr/local/phenix-dev-1148/chem_data/mon_lib/list % head mon_lib_list.cif
>>
>> global_
>> _lib_name         mon_lib
>> _lib_version      4.11
>> _lib_update       15/04/05
>> # ------------------------------------------------
>> #
>> # ---   LIST OF MONOMERS ---
>> #
>> data_comp_list
>> loop_
>>
>> We had a problem similar to yours with some ligands.
>>
>> What we did about it:
>>
>> get latest dictionary from Garib Murshudov's group page
>> http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
>>
>> unpack
>>
>> rename resulting folder monomers to mon_lib
>>
>> fix up the beginning of mon_lib/list/mon_lib_list.cif:
>> Line 1: underscore missing after "global"
>> Line 6: number sign missing
>>
>> overwrite the existing mon_lib folder of Phenix.
>>
>> It seems to work.
>>
>> Dmitry
>>
>> On 2012-09-04, at 7:55 AM, Paul Emsley wrote:
>>
>> On 04/09/12 12:34, Wulf Blankenfeldt wrote:
>>
>>
>> this may have been asked a thousand times, but: are the ccp4 standard
>> monomer libraries incompatible with phenix.refine, and if yes, is there an
>> easy way to resolve this?
>>
>> I am refining a structure with an FMN, which I build with the "get
>> monomer" option in coot. Unfortunately, phenix.refine doesn't like it and
>> throws it out. Using a cif generated with elbow, on the other hand, has
>> chirality errors (which I can fix...) and isn't liked by coot (0.6.2), which
>> refuses to refine the ligand.
>>
>> :-(
>>
>> Hi Wulf,
>>
>> It seem that somehow you have an inconsistency between the model and the
>> dictionary.
>>
>> The correct atom names are defined by the PDB. e.g.
>>
>> ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/mmcif/FMN.cif
>>
>> When I use "Get Monomer" I get a FMN monomer this is consistent with this
>> (well, except for phosphate hydrogens). In particular, there are primed atom
>> names (not starred).  If you are using - or referencing an old CCP4
>> distribution you may be picking up an old dictionary when using "Get
>> Monomer" - coot should tell you in the console (at least) the file names
>> that it reads.  If you want to reference the Phenix copy of the monomer
>> library, you can use use COOT_REFMAC_LIB_DIR to point to it.
>>
>> If you use the model (pdb file) and dictionary cif from elbow (and call it
>> FMN) then coot should be happy no matter what the PDB says. And I would
>> imagine that that would be so for phenix.refine also.
>>
>> Paul.
>>
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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov