[phenixbb] how to extend R-free set

[Francis E Reyes]

If it's not implemented already, I'd love to see a command line  
utility to do this.


F

On May 19, 2010, at 10:13 AM, Pavel Afonine wrote:

> Hi Bob,
>
> you can use "Reflection file editor" for this. It is available from  
> PHENIX GUI. I'm not sure if the corresponding command line option  
> exists, Nat knows this better.
>
> Pavel.
>
>
> On 5/19/10 9:09 AM, Robert Immormino wrote:
>> Hi,
>>
>> Hopefully I'm just missing something obvious....
>>
>> I'm trying to copy the Rfree set from an old set of data, to a new
>> mutant structure....and extend to higher resolution.
>>
>> I've tried:
>>
>> phenix.reflection_file_converter old.mtz --label="R-free-flags"
>> new.sca --label="i_obs,sigma" --mtz new.mtz
>>
>> and several other combination, but I am still failing to get phenix  
>> to
>> read multiple data files and output the desired mtz.  I can get just
>> the Rfree flags or the I and SigI, but not both.
>>
>> I also tried with phenix.refine
>>
>> phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif
>> refinement.input.xray_data.labels="i_obs,sigma"
>> refinement.input.xray_data.r_free_flags.label="R-free-flags"
>>
>> This seems closer, but I get the error:
>>
>> Sorry: R-free flags not compatible with F-obs array: missing flag for
>> 492 F-obs selected for refinement:
>>
>> Thanks,
>> -bob
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D