[phenixbb] How to use phenix for SAD data

Erik Mckee emckee at cs.tamu.edu
Mon Jul 10 21:47:40 PDT 2006

here is my suggestion:
mosflm data needs to be scaled (use scala in ccp4) (make sure anomalous is
turned on) (this should give you a mtz file with anomalous data)
then in the phenix gui under wizards, choose AutoSol
the first screen will ask you to choose your mtz and experiment type (sad)
the next screen will ask the file name again, but will be already filled
in, leave it
the next screen will ask what columns to output, you can remove all but
the anomalous I's (either the +/- or the DANO/SIGDANO format) (will be
written as a sca file after this step)
the next screen will look like the first, and should just have a single
sca file on it (output from the previous screen)
the next few screens allow you to set the experiment parameters
if all goes well, auto sol should start running after 3 or 4 more screens

On Tue, 11 Jul 2006 pramod at cdfd.org.in wrote:

> Hi all
> i am using the Phenix-GUI first time ,for solving the sad data. I processed
> my raw data with the mosflm.Further output of the mosflm were used for
> getting other information or working through this data.so, i started with
> the strteiges of solve through mad. after setinmg up all the anamolous
> parameters ,this is always displaying red in the very first in the setup
> anamolous data gui with the information that format error.i used the format
> ccp4 unmerged i.e the direct output of the mosflm after integration.i also
> used the conversion of mtz file into hkl through ccp4 scaling and merging
> intensities-in which one option i used is the get output as unmerged intensities
>     but, that also didnot worked.
>     suggestions will be appreciated
> and also i want the deatiled information about how to use the phenix gui
>     properly.
>     with regards
> Pramod Kumar
> Junior Research Fellow
> c/o-Dr.Shekher C Mande
> Center for DNA Fingerprinting and Diognostics
> ECIL road
> Nacharam
> Hyderabad-76
> -
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> phenixbb at phenix-online.org
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