[phenixbb] Non bonded contacts

Mark A Saper saper at umich.edu
Tue May 13 06:34:02 PDT 2014


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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