[phenixbb] unwanted disulfids and geometry restraints

[Pavel Afonine]

Hi Ursula,

> 1)  I am using phenix.refine on the command line with a .eff file as 
> input that was modified from previous GUI phenix runs. My structure 
> has several Zn atoms and readyset creates a geometry_restraints file 
> for the Zn interactions. I am not sure if phenix.refine gets these 
> restraints when I run it from the command line. 

check *.geo file that lists all geometry restraints used in refinement. 
IF restraints in questions are not there then there is a problem.

> Do I need to read this file in some specific way?

No, just specify it in the command line along with all other files.

> 2) The other question is: phenix refines several of the Cysteine 
> neighbors in the Zn environment as disulfids, but they are not. How do 
> I prevent this from happening?

Hm.. this isn't easy.. phenix.refine automatically identifies disulfide 
bonds and creates restrains for them. This is controlled by 
disulfide_distance_cutoff=3 parameter. You can set it to some big 
number, so none desulfide bonds will be created automatically, but then 
you will need to specify those that you want to have using "Custom bonds":
http://www.phenix-online.org/documentation/refinement.htm#anch354
Sorry, not an easy solution but if desperate you can do it!

Pavel