[phenixbb] some basic questions about phenix autobuild and phenix.refine

Niks nikdna at gmail.com
Wed Oct 24 00:37:51 PDT 2012

Dear All,

I have recently started using PHENIX so I am a beginer in PHENIX field. I
am getting better statistics (Rfactor/Rfree) as compared to REFMAC so
having strong inclination to continue with PHENIX but there are some
discripancies I found when comparing with CCP4 programs.Therefore i I have
some basic questions which I request you to throw some light and wisdom.

1) I have solved my structure using AutoMR and got two files MR.1.mtz and
MR.1.pdb as output with high LLG of 8236.889. When going for AutoBuild
afterwards it uses output pdb (MR.1.pdb) which is fine but uses MR.1.mtz as
map coefficient. Shouldnot it uses original mtz from scala?

2) Same in Phenix.refine when going after Autobuild finishes and it asks
for refining the model it uses same AutoMR output mtz (MR.1.mtz). As I was
suggested by many that we should use original mtz coming from scala for
Refinement to reduce model bias. shouldnot phenix.refine use Original mtz
file here too?

3) After going for AutoBuild after AutoMR, even when I unselect "Place
Waters" options in parameters for Refinement, I see output pdb file with
waters added to it. I do not want waters to be added till I refine my model
to the best , but Autobuild option comes out with waters added. Is there
anyway I can have autobuilt pdb without waters added?

4) Another question that troubling me most that  in Phenix.refine even if I
use original mtz which clearly specifies resoultion range from 127.488-2.5A
  my refined pdb files comes out with  Resolution range used for refinement
as 37.8-2.5A. I have tried to input low resolution range as 127.488 but
deafult is always 37.8 selected. My data may be very poor in lower
resolutions than 37.8A but my completeness is also going down (65.5% as
opposed  to 79.8% in REFMAC). Can I select my refinement using my specified
values of Resolution from mtz file coming out from SCALA?

Sorry for the lengthy mail and many questions.
Thanks and regards
PhD Student,
C/O Dr. C. G. Suresh,
National Chemical Laboratory,
Pune, India

"The most difficult phase of  life is not when No one understands you;It is
when you don't understand yourself"
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