[buster-discuss] Problem with Nterminal hydrogens

[Marion Boudes]

Thanks a lot Oliver, it worked well.
Regards,
Marion.


On 2 July 2013 22:02, Oliver Smart <osmart at globalphasing.com> wrote:

> On Tue, 2 Jul 2013, Marion Boudes wrote:
>
>  Hi all,
>>
>> I am working on a 1.8A structure with hydrogens. They are all fine,
>> except the 3 Nterminal ones: they drift (far) away from their initial
>> position upon refinement.
>>
>> As a workaround I froze these atoms during refinement (with a .Gelly file
>> mentioning CONSTANT XYZ A|1:H1 etc.), but I was wondering if there is a
>> more 'elegant' way to restraint them?
>>
>> Thanks a lot in advance.
>>
>> Kind regards,
>>
>> Dr Marion Boudes
>> Structural Virology
>> Department of Biochemistry & Molecular Biology
>> Building 76, Monash University
>> Clayton, VIC 3800, Australia
>>
>
>
> Marion,
>
> Apologies we have not (yet) got our protein dictionaries to treat the
> terminal hydrogen atoms properly. A better work around is to use Gelly
> utility distance and angle restraints to achieve good geometry. For
> the hydrogens attached to main chain A the following .Gelly works
> (I have tested this with PDB entry 3zo7):
>
> # Gelly file cludge to treat N terminal hydrogen atoms reasonably
> # here assume the N terminal residue is chain A residue number 1
> # restrain the "bond" distances to 1 Angs
> NOTE BUSTER_DISTANCE =1.0 0.01 A|1:N A|1:H1
> NOTE BUSTER_DISTANCE =1.0 0.01 A|1:N A|1:H2
> NOTE BUSTER_DISTANCE =1.0 0.01 A|1:N A|1:H3
> # keep the angles tetrahedal
> NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:CA A|1:N A|1:H1
> NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:CA A|1:N A|1:H2
> NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:CA A|1:N A|1:H3
> NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:H1 A|1:N A|1:H2
> NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:H1 A|1:N A|1:H3
> NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:H2 A|1:N A|1:H3
> # finally turn off the contacts between the hydrogen
> # atoms and the rest of the residue
> EXCLUDE A|1:H1 A|1
> EXCLUDE A|1:H2 A|1
> EXCLUDE A|1:H3 A|1
>
>
> If you have more than one chain then it will be necessary
> to duplicate all the NOTE and EXCLUDE lines and replace A| with
> B| etc.
>
> Hope this helps,
>
> Oliver (for buster-develop)
>
> | Dr Oliver Smart                             |
> | Global Phasing Ltd., Cambridge UK           |
> | http://www.globalphasing.com/**people/osmart/<http://www.globalphasing.com/people/osmart/>|
>
>
>
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