[phenixbb] accept MR solution even if the number of clashes is above the threshold

Roger Rowlett rrowlett at colgate.edu
Thu Jul 2 06:51:39 PDT 2015

Increase the number of allowed clashes in Phaser, and examine the 
resulting solution in Coot to see if (1) electron density is reasonable, 
and (2) molecular packing is reasonable. It is very common that a search 
model has some surface loops in alternate locations compared to your 
target that generate the clashes. These loops can be deleted in your 
search model if desired, or, if you have sufficient data quality, you 
can try using the initial phases obtained to autobuild the target.

Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowlett at colgate.edu

On 7/2/2015 8:55 AM, Almudena Ponce Salvatierra wrote:
> Hi everyone,
> I am running Phaser (from Phenix) and while checking the .log file (it 
> is still running) I realize that it found some solutions with a TFZ 
> score over 7, but it won't take them I guess because the number of 
> clashes is higher than allowed (>12, I guess they're not so many either).
> My models are poor and for so I would like to check these solutions 
> that for now Phaser will reject. However in the input I don't want to 
> increase the allowed number of clashes because this will then affect 
> all the other solutions and this will take forever...
> So my question is: can I tell phaser somehow to write down/save the 
> solutions for which the TFZ score will be higher than 7? Even though 
> the clashes
> Thanks a lot in advance
> All the best,
> Almu
> -- 
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
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