[phenixbb] real space correlation
Pavel Afonine
pafonine at lbl.gov
Wed Aug 22 13:48:09 PDT 2012
Hi,
the problem is fixed. You can get it now from svn or next nightly build
will have it.
Also, I changed (hopefully improved and simplified the interface). To
illustrate, here are a few examples:
- compute map CC and 2mFo-DFc and mFo-DFc density values:
-- overall and per residue or per atom (programs makes the choice):
phenix.real_space_correlation m.pdb d.mtz
-- overall and per atom:
phenix.real_space_correlation m.pdb d.mtz detail=atom
-- overall and per residue:
phenix.real_space_correlation m.pdb d.mtz detail=residue
-- you can specify which data from input file to use:
phenix.real_space_correlation m.pdb d.mtz data_labels=FOBS
-- you can choose to use neutron scattering table:
phenix.real_space_correlation m.pdb d.mtz scattering_table=neutron
-- force program to show cc and map values for H atoms (decision is
made automatically otherwise):
phenix.real_space_correlation m.pdb d.mtz detail=atom
use_hydrogens=true
-- you can specify maps to use, for example:
phenix.real_space_correlation m.pdb d.mtz map_1.type=Fc
map_2.type="2mFo-DFc"
phenix.real_space_correlation m.pdb d.mtz map_1.type="12Fo -
9.75Fcalc" map_2.type="2mFo-DFc"
Pavel
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
More information about the phenixbb
mailing list