[buster-discuss] FAD dictionary issues

alebus at pasteur.edu.uy alebus at pasteur.edu.uy
Wed Jun 16 23:16:54 CEST 2010


Thanks Clemens!

indeed these pdb version formats seem to play tricky games!  now it  
seems to work properly

I'll see if I really get this working and let you (all) know - better  
if I actually end up understanding the whole way of doing it (I  
believe reading a bit on the syntax and possibilities of TNT  
dictionaries, has helped me a bit: the number just after the PLANE  
keyword in the restraints dictionary, has to include the total number  
of desired atoms included in that particular plane restraint, no  
matter how many are actually named afterwards to the right of the sd  
figure...)

best regards,
alejandro


Quoting Clemens Vonrhein <vonrhein at globalphasing.com>:

> Dear Alejandro,
>
> we have a FAD dictionary in
>
>   $BDG_home/tnt/data/cofactor_geo.dat
>
> whihc usually BUSTER should pick up automatically. This dictionary
> should be fairly good for refining FAD.
>
> However, there is the possibility of a mix-up between PDB v3 and v2
> atom naming. What happens if you run
>
>   % pdbvconv -p your.pdb -o tmp.pdb
>
> This should detect the PDB version in your PDB file (and convert from
> that version into the other, so it can go v2->v3 as well as v3->v2).
>
> The important thing is that you don't have a mixture of the two
> formats. And since at the moment BUSTER still uses (internally) v2
> atom naming, I would recommend getting your FAD atom names into v2
> format.
>
> I attach the two version of FAD you would get for residue A1001 from
> Jose's 3h8i entry.
>
>   FAD_3h8i_A1001_v3.pdb   (as in PDB entry/file)
>   FAD_3h8i_A1001_v2.pdb   (after running pdbvconv on it)
>
> Cheers
>
> Clemens
>
> On Wed, Jun 16, 2010 at 12:37:23PM -0300, alebus at pasteur.edu.uy wrote:
>> 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
>> >
>> > _______________________________________________
>> > buster-discuss mailing list
>> > buster-discuss at globalphasing.com
>> > https://www.globalphasing.com/mailman/listinfo/buster-discuss
>>
>>
>>
>> --
>> 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
>> _______________________________________________
>> buster-discuss mailing list
>> buster-discuss at globalphasing.com
>> https://www.globalphasing.com/mailman/listinfo/buster-discuss
> --
>
> ***************************************************************
> * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
> *
> *  Global Phasing Ltd.
> *  Sheraton House, Castle Park
> *  Cambridge CB3 0AX, UK
> *--------------------------------------------------------------
> * BUSTER Development Group      (http://www.globalphasing.com)
> ***************************************************************
>



-- 
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


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