[buster-discuss] abasic refinement.

[Laurent Maveyraud]

Hi,

as far as I understand the error message, the problem does not seem to 
result from missing atoms. Buster complains that it doesn't recognise 
the name of the atoms you have in your residues.
Missing atoms are usually treated properly, at least for proteins (eg 
missing side chain atoms for lysine).
 From the example PDB file ou provide, the residue name should be DG, 
with the chain ID being C. The error message complains that residue "C" 
has wrong atom names.
Does the PDB example corresponds to the run that generated the error ?

There was a message on the buster discussion list about DNA in 2010 
(Nicolas, it was yours !). The names of the sugar atoms should be with 
*, not with ' :
O5* instead of O5' (for residue name  C G A T U, not DG...)
Could this be the reason of the problem ?

hope this helps

laurent
Le 12/06/2014 10:39, FOOS Nicolas a écrit :
> Just to be sure of what Buster did,
> Did it complain about something at the begining of the refinement ?
> Maybe you can check if the problem come from missing atoms, or if it come from the misundestanding DNA.
> You can also generate your own restraint for your molecules and give this resraint to Buster.
>
> Hope to help.
> ________________________________________
> De : buster-discuss [buster-discuss-bounces at globalphasing.com] de la part de Ed Pozharski [ccp4pozharski at gmail.com]
> Envoyé : mercredi 11 juin 2014 20:04
> À : Francis Reyes; buster-discuss at globalphasing.com
> Objet : Re: [buster-discuss] abasic refinement.
>
> Ok, how about polyA with side chain occupancies set to zero?
>
>
> Sent on a Sprint Samsung Galaxy S® III
>
>
> -------- Original message --------
> From: Francis Reyes
> Date:06/11/2014 1:59 PM (GMT-05:00)
> To: Ed Pozharski , buster-discuss at globalphasing.com
> Subject: Re: [buster-discuss] abasic refinement.
>
> Ed,
>
> The problem is not in making the PDB. I've made it.
>
> For example,
>
> ATOM   1216  P    DG C   9      24.074 -29.421  24.416  1.00 20.00           P
> ATOM   1217  OP1  DG C   9      22.922 -29.968  23.666  1.00 20.00           O
> ATOM   1218  OP2  DG C   9      23.858 -28.739  25.711  1.00 20.00           O
> ATOM   1219  O5'  DG C   9      25.147 -30.586  24.645  1.00 20.00           O
> ATOM   1220  O3'  DG C   9      28.318 -32.882  25.868  1.00 20.00           O
> ATOM   1221  C1'  DG C   9      28.671 -30.101  25.829  1.00 20.00           C
> ATOM   1222  C2'  DG C   9      27.497 -30.719  26.571  1.00 20.00           C
> ATOM   1223  C3'  DG C   9      27.286 -31.929  25.672  1.00 20.00           C
> ATOM   1224  C4'  DG C   9      27.428 -31.312  24.285  1.00 20.00           C
> ATOM   1225  C5'  DG C   9      26.129 -30.850  23.651  1.00 20.00           C
> ATOM   1226  O4'  DG C   9      28.312 -30.175  24.464  1.00 20.00           O
> and no base atoms.
>
> BUSTER just has issues with obtaining the restraints for it and tries to automatically generate its own restraints .
>
> Is it possible to increase the number of atoms missing before triggering automatic restraint generation?
>
> I tried a combination of NeverGenerateDictionary="yes" but it gets shuttle to PDB2TNT which doesn't know about the connectivity between the residues. (it treats each base as a monomer and will break the interresidue bond in refinement).
>
>
>
>
> F
>
> On Jun 11, 2014, at 1:53 PM, Ed Pozharski <ccp4pozharski at gmail.com> wrote:
>
>> You can make polyA and then delete "side chains" (in coot or with a grep one liner).  This way it will also be easier to build them back in (although you may need format conversion post-buster to get coot to work and I vaguely remember coot having some problems with truncation).
>>
>>
>> Sent on a Sprint Samsung Galaxy S® III
>>
>>
>> -------- Original message --------
>> From: Francis Reyes
>> Date:06/11/2014 1:39 PM (GMT-05:00)
>> To: buster-discuss at globalphasing.com
>> Subject: [buster-discuss] abasic refinement.
>>
>> Hi all,
>>
>> I'm refining a protein:dna complex, and I'm yet uncertain to the sequence identity of the bases. Instead I'd like to to just simply place the phosphate backbone of the double stranded DNA and removed the bases (abasic DNA).
>>
>> I receive the following error:
>>
>>     >>> ab_pdb2tnt >>>
>>     >>> ab_pdb2tnt >>> Extracted from file 06/01-BUSTER/Rigid-1/ab_pdb2tnt.log :
>>     >>> ab_pdb2tnt >>>
>>     >>> ab_pdb2tnt >>> WARNING : 10 atoms (out of 11) for residue "C" in PDB file
>>     >>> ab_pdb2tnt >>>           have names that are not present in the suggested
>>     >>> ab_pdb2tnt >>>           dictionary
>>     >>> ab_pdb2tnt >>>           /groups/gonen/home/reyesf/xtal/buster/tnt/data/nuclgeo.dat.
>>     >>> ab_pdb2tnt >>>           Therefore we will force the generation of a new
>>     >>> ab_pdb2tnt >>>           dictionary based on the current coordinates! For
>>     >>> ab_pdb2tnt >>>           details see below:
>>
>>
>> and then restraint generation by grade ends with error.
>>
>>
>> Is it possible to refine abasic DNA?
>>
>> Thanks,
>>
>> F
>>
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>> buster-discuss at globalphasing.com
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>
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-- 
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Laurent Maveyraud         laurent.maveyraud AT ipbs DOT fr
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