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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Pavel,<br>
<br>
I'm aiming to restrain residues adjacent to alternate conformers, such that the alternate conformers are not able to significantly drift from initial positions within the refinement cycle.<br>
<br>
i.e Residue with two alternate conformers/altlocs A and B <br>
<br>
All-All-A/B-All-All<br>
<br>
becomes<br>
<br>
All-<b>A</b>-A-<b>A</b>-All<br>
All-<b>B</b>-B-<b>B</b>-All<br>
<br>
with the bold residues restrained to one another. Hope this makes sense.<br>
<br>
Thanks<br>
<br>
Elliot<br>
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<div style="direction: ltr;" id="divRpF244741"><font face="Tahoma" size="2" color="#000000"><b>From:</b> Pavel Afonine [pafonine@lbl.gov]<br>
<b>Sent:</b> 18 January 2017 18:28<br>
<b>To:</b> Elliot Nelson; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Phenix.refine Restraints: replicating refmac external restaints<br>
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<div>Hi Elliot,<br>
<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Looking to generate restraints for phenix.refine that are similiar/equivalent to external restraints in REFMAC. From over viewing the documentation i feel the correct way to do this
is to generate bond restraints, i.e:<br>
<br>
Equivalent of:<br>
<br>
exte dist first chain A resi 38 atom C alte A second chain A resi 38 atom C alte B value 0.0 sigma 0.02 type 1<br>
<br>
would be :<br>
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<br>
I don't know how restraints function in Refmac.<br>
<br>
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bond {<br>
action = *add <br>
atom_selection_1 = chain A and resid 38 and altloc A and name C<br>
atom_selection_2 = chain A and resid 38 and altloc B and name C<br>
symmetry_operation = None <br>
distance_ideal = 0.0<br>
sigma = 0.02<br>
slack = None<br>
}<br>
}<br>
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<br>
This will define a bond between these two atoms by adding a term to the restraints:<br>
<br>
(1/sigma**2)*(distance_model - distance_ideal)**2<br>
<br>
Note, you can add as many of such bonds as you with. Also, using similar syntax you can add angles, planes, torsions, etc.<br>
<br>
Just out curiosity and if it's not a secret: what are you trying to achieve?<br>
<br>
Pavel<br>
<br>
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