[phenixbb] Non bonded contacts

Pavel Afonine pafonine at lbl.gov
Wed May 14 01:00:51 PDT 2014

Hi Mark,

I suggested to assign them different altlocs, which should work.

Another option I can think of is: if atoms in question make some kind of 
interaction (bond) you can define a pseudo-bond in phenix.refine using 
Custom Bonds machinery (with any bond distance and esd of your choice). 
Defining such bond will automatically turn off the repulsion bethween 
these atoms.


On 5/13/14, 6:34 AM, Mark A Saper wrote:
> Pavel,
> Your suggestion of setting the alt-loc the same for the two residues in order to avoid the non-bonded contact restraint is not working yet.  Do the residues need to be in the same chain
> Thanks,
> Mark
> On May 12, 2014, at 12:23 PM, Mark A Saper <saper at umich.edu> wrote:
>> Hi Pavel,
>> I'll try that.  I have a PLP cofactor and a lysine.  I refined with them forming a Schiff base but the maps had large delta F indicating that the PLP ring was being pulled out of density.  So now I am modeling it as PLP and Lys.  But there is some bridging density.  I want to see how close the Lys would extend if it didn't see the PLP.
>> Thanks,
>> Mark
>> On May 9, 2014, at 8:25 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
>>> Hi Mark,
>>>> Is there a straightforward way to turn off non-bonded restraints between 2 residues? I see the restraints in the .geo file.  Thanks.
>>> you can asigne them diferent altloc identifiers and then they will not see each other via non-bonded interactions.
>>> If these two residues in question are symmetry mates then there is a keyword for this: custom_nonbonded_symmetry_exclusions .
>>> Also, I wonder why you want to do this?
>>> Pavel

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