Re: [phenixbb] how to fix a side chain not to be refined?

Yep, this is not too surprising since the current phenix.refine implementation of rotamer fitting does not use the new residue/rotamer fitting machinery (the one I showed at past WCPCW), which will be in place in a few coming months. Stay tuned! Pavel On 4/19/13 7:27 PM, Rongjin wrote:

Hi Nat,

You are right. By turning off the "fix rotamers" the Arg does not move any more.

Best

Rongjin

------------------ Original ------------------ *From: * "Nathaniel Echols"; *Date: * Apr 20, 2013 *To: * "PHENIX user mailing list"; *Subject: * Re: [phenixbb] how to fix a side chain not to be refined?

On Fri, Apr 19, 2013 at 2:14 PM, Rongjin wrote:

...

I have an Arg with flexible side chain, close to an iodide ion. Every time I refine it, the side chain of Arg will push the iodide ion away, even I selected

The syntax below looks correct to me, although you should probably do the same thing for the ADP selection, but it's a little disturbing that it's doing this. Do you have rotamer correction turned on? That may be the problem, if it is trying to fit to the difference density (I don't think it's very aware of nearby atoms).

-Nat

...

the Arg not to be refined:

refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous sites { individual = "not (chain A and resid 40)" } }

The residue 40 in Chain A is that Arg close to the Iodide. Is this selection correct? How to fix the side chain of Arg in refinement?

I attached two pictures, one before and one after refinement, the local area of the Arg and the iodide. The iodide is bound to an Asn residue of one symmetric molecule.

Thank you Rongjin Guan

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