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CCP4BB  December 2008

CCP4BB December 2008

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Subject:

Re: Summary - torsion angle restraints in REFMAC

From:

Eckhard Hofmann <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Sat, 6 Dec 2008 10:26:18 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (108 lines)

Hi Huiying,
I would be very careful to play around with the overall weights for your 
purpose. Keep in mind that the overall weights will affect the full 
model. Usually the weights on proteins will be well balanced between the 
different types of restraints, and you will be meddling with this 
balance. While it will probably not be "visible" in the structure, it 
nevertheless is not the appropriate way to do this and will lead to 
small, but systematical deviations. You definitely should be using the 
sigmas in the cif to adjust the weight for the individual torsion you 
are worried about.

I expect you always do a dry run with the isolated ligand in refmac 
"structure idealization" mode after fiddling with the cif, as this is 
most important to make sure you don't do something wrong there (maybe a 
typo or similar)? Especially with ligand cifs the golden rule "garbage 
in, garbage out" applies, as can be found in many pdb structures.

This would be the point to urge all depositors to also put the 
additional restraint files into the database as auxiliary files to their 
structures.

Cheers,
Eckhard



Huiying Li schrieb:
> 
> 
> The keyword script Eckhard mentioned did the job I wanted to achieve. I 
> created the cif file for my ligand through the Monomer Library Stetcher 
> and then edited torsion angle part to include the restraint for the OH 
> tiling angle. I am running the CCP4 Suite 6.0.2 and CCP4i 1.4.4.2. but I 
> still have to include an external keyword script
> restr tors include resi XXX
> to impose torsion angle restraint on the ligand. With the script read in 
> I can further adjust the Overall wt for Torsion under Geometric 
> parameters menu to achieve a geometry that best fits to the density.
> 
> I have tried weighting term 0.05 or 0.08 for this case. The smaller 
> weight at 0.05 gave me better planarity for the aromatic residues 
> without sacrifying too much in R/R-free (only 0.1% lower with 0.08 weight).
> 
> Thanks again for suggestions from many others.
> 
> Huiying
> 
>  On Fri, 5 Dec 2008, Eckhard Hofmann wrote:
> 
>> Hi Huiying,
>> could you tell us which version of refmac you are using?
>> There has been an issue with torsion definitions in ligands NEVER 
>> included in the refinement, even if they were in the cif (at least up 
>> to Refmac_5.2.0019). I did have the same effect you had and wondered 
>> why. (See list in October 2007)
>>
>> Garib modified the code in a later version of 5.4 to allow you to 
>> include all torsions from one residues by applying the following line:
>>
>> restr tors include resi XXX
>> or to include only one specific definition in refinement
>> restr tors include resi XXX name var_1
>>
>> In CCP4i you'll have to include this with the Developers Option to 
>> include an external keyword-file. NOTE: Without doing anything, the 
>> torsion definitions are still NOT used, which would explain the 
>> behaviour you observe. This is a feature, not a bug ....
>>
>> I'am not sure what the situation is in the current version, maybe 
>> Garib should answer this?
>>
>> Hope that helps,
>> Eckhard
>>
>>
>>
>> Huiying Li schrieb:
>>> I want to impose restraints during REFMAC refinement on the tortion 
>>> angles that control the tilting of an OH group from a plane in a 
>>> ligand bound to the protein. A few things that confused me:
>>>
>>> 1. In library cif file, should I just increase or decrease the 
>>> tor.value_angle_esd if I want to loosen or tighten the restraits?
>>>
>>> 2. What is the meaning of the last column in torsion angle 
>>> parameters: _chem_comp_tor.period, in cif file? In the PDB output 
>>> file REFMAC also lists the RMS and WEIGHT for the torsion angles, 
>>> period 1 through 4.
>>>
>>> 3. In REFMAC gui under Geometric parameters, there is only one user 
>>> controlled weight for torsion. By changing the weight here, does it 
>>> change the torsion weight for all 4 periods?
>>>
>>> Thanks in advance for the help.
>>>
>>> Huiying
>>
>>
>>
> 


-- 
Eckhard Hofmann <[log in to unmask]>
Ruhr-Uni Bochum
AG Proteinkristallographie, LS Biophysik, ND04/316
44780 Bochum
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762

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