Hi Niks,

I'll answer your question #4, and I hope Tom Terwilliger will answer the others.

If your input data are intensities (Iobs), then phenix.refine will convert then to amplitudes (Fobs) using French&Wilson method. This may result in a loss of some reflections. Also, phenix.refine applies some reflection outlier filtering of your data, which may result from 0 to a few (~10 or so) reflections removed.
This may explain the difference in number of reflections or completeness in specific resolution zones.

You can turn off rejection of outliers if you have strong reasons to do so.

Although it's not common practice and typically not recommended you can specify low and high resolution limits for the data to use in refinement.

Pavel

On 10/24/12 12:37 AM, Niks wrote:

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
Nishant
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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