[buster-discuss] ions & ccp4 dictionary

[Thomas Womack]

On 9 May 2011, at 22:22, Karolina Michalska wrote:

> Hello,
> 
> Can someone explain how to deal with ions in Buster? I have
> zinc and chloride modeled and I get the following info: No ccp4 atom
> type ZN+2UN so will use TNT bad contact term. The same for chloride.
> Interestingly, the charges have been assigned correctly and Buster
> reports that contact.dat and idealdist_contact.dat are being used. The
> final pdb reports: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE
> TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL ZN.

autoBUSTER should behave correctly; we have two processes for handling short contacts between atoms, and the messages simply indicate that the contacts involving chloride and zinc ions are being handled by one of them and not the other.

(I presume you are using a reasonably new version of the BUSTER suite, and running with the 'refine' command)

If your refinement isn't starting up, please give us more details of the error messages you see at the end; if you are seeing serious problems in the final refinement output, there are various things that can be done with additional distance restraints.  But the messages you see at the moment do not indicate a problem.

Yours sincerely,

Thomas Womack (Global Phasing)