[phenixbb] real space correlation

Pavel Afonine pafonine at lbl.gov
Tue Aug 21 09:18:42 PDT 2012

Hi Bradley,

it's a bug due to insufficient amount of tests exercising this tool. I'm 
working on the fix.
The second bug here is that when you run

phenix.fetch_pdb --mtz 1eao

it outputs

Model saved to /net/chevy/raid1/afonine/work/tmp/1eao.pdb
Sequence saved to /net/chevy/raid1/afonine/work/tmp/1eao.fa
Structure factors saved to /net/chevy/raid1/afonine/work/tmp/1eao-sf.cif

while the actual output is


Meanwhile type

phenix.model_vs_data 1eao.{pdb,mtz} comprehensive=true

which will give you CC(2mFo-DFc, Fc) per atom or per residue (depending 
on resolution).


On 8/20/12 11:42 AM, Bradley Hintze wrote:
> Hey Phenix team,
> I am trying to get real space correlation measurements for 1eao and 
> ran into a problem.
> $ phenix.fetch_pdb --mtz 1eao
> $ phenix.real_space_correlation 1eao.pdb 1eao.mtz
> Multiple equally suitable arrays of observed xray data found.
> Possible choices:
>   1eao.mtz:FOBS,SIGFOBS
>   1eao.mtz:F(+),SIGF(+),F(-),SIGF(-)
> Please use .labels
> to specify an unambiguous substring of the target label.
> Looking in the options for phenix.real_space_correlation it is unclear 
> how to specify the labels for the reflection file. Any assistance on 
> this would greatly be appreciated.
> Thanks,
> Bradley
> -- 
> Bradley J. Hintze
> Duke University
> PhD Candidate
> Department of Biochemistry
> Please help me raise money for my ride to assist children 
> with disabilities!
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