[buster-discuss] buster-discuss Digest, Vol 22, Issue 3

Jose Artur Brito jbrito at itqb.unl.pt
Wed Jun 16 16:13:03 CEST 2010

Dear Alejandro,
please take a look at entry 3H8I of the PDB. It has a covalently bound 
FAD and it was refined with BUSTER so the atom names should be correct 
and recognized by BUSTER and CCP4 libraries.

On 06/16/2010 11:00 AM, buster-discuss-request at globalphasing.com wrote:
> ----------------------------------------------------------------------
> Message: 1
> Date: Wed, 16 Jun 2010 06:33:16 -0300
> From: alebus at pasteur.edu.uy
> Subject: [buster-discuss] how to handle user defined stereochemical
> 	dictionaries
> To: buster-discuss at globalphasing.com
> Message-ID:<20100616063316.xhyu4mlwk84cc4go at www.pasteur.edu.uy>
> Content-Type: text/plain;	charset=ISO-8859-1;	DelSp="Yes";
> 	format="flowed"
> Dear BUSTER community,
> I am having some problems refining a protein that contains FAD.
> Some of the 'available' dictionaries (such as ccp4) seem to have some
> errors (adenine N6 is not included in the corresponding planarity
> restraint, etc)
> in the end, I'm obtaining some distorted geometries (res 2.8?, SG 18)
> So, two questions:
> 1. What is the proper way to use a user-defined dictionary?
> I tried including the -l option for the autobuster refine command,
> immediately followed by the name of the dictionary (both a .cif,
> refmac style; or one .dic derived from that one using MakeTNT).
> Autobuster refine will tell me in the beginning "Dictionary versions
> picked up from NOTE BUSTER_RESTRAINT_DICT cards as: ... ------
> restraints FAD by MakeTNT_2.4.0 from REFMAC dictionary...". (although
> I actually do not find the name of my dictionary anywhere...probably
> not reading it I guess)
> But then, a few lines lower it will invariably say "Have no dictionary
> entry giving ccp4 atom types for residue types:  FAD SO4
>          will use default ccp4 atom types CUNK  NUNK OUNK PUNK SUNK
> .... where possible."
> (by the way, SO4 is actually in the 'regular' dictionaries: why can't
> it find it? I saw this question from Miguel Ortiz, but then no follow
> up on that...)
> 2. What is the procedure to look at this "fast"?
> I mean, without actually running a full refinement protocol, just look
> at if buster actually read and kept the desired dictionary, and to
> which idealized model those restraints would actually be pointing to
> in further buster refinement cycles.
> Thanks a lot for any advice!
> Alejandro

José Artur Brito, B.Sc. (Eng.), PhD Student

Membrane Protein Crystallography Lab
Instituto de Tecnologia Química e Biológica
Oeiras - Portugal

Tel.: +351.21.446.97.61
Fax:  +351.21.443.36.44

E-mail: jbrito at itqb.unl.pt
URL: http://xtal.itqb.unl.pt

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