Re: [phenixbb] Non bonded contacts

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. Pavel 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 wrote:

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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 wrote:

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Hi Mark,

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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