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

[alebus at pasteur.edu.uy]

Dear Jose,

thank you for your practical suggestion (although knowing how to input  
modified dictionaries in a proper way, still seems important to  
me...see below)

...unfortunately, after carefully modifying my pdb to match the one  
you point me to, refinement is even worse....! (I know it's very easy  
to mess up these pdb editing efforts by hand; I did go with extreme  
care though...)

bottom line : still needing help!

thanks a lot
alejandro


Quoting Jose Artur Brito <jbrito at itqb.unl.pt>:

> 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.
> Cheers,
> Jose
>
>
> 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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-- 
Alejandro Buschiazzo, PhD
Research Scientist
Unit of Protein Crystallography
Pasteur Institute of Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY

Phone: +5982 5220910 int. 120
Fax:   +5982 5224185