[buster-discuss] Problem with Nterminal hydrogens

[Oliver Smart]

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/ |