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?

To add to what Nat said, yes, the MR.1.mtz is only used as map coefficients, the original data from scala is used as the data in autobuild.

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?

Autobuild produces an mtz file that has the same data as your original mtz, plus free R flags. This is overall_best_refine_data.mtz, it is identical also to exptl_fobs_freeR_flags.mtz


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?

I can't seem to make this happen on my computer. I just ran automr/autobuild and the phenix.refine ".eff" files used during autobuilding all say "ordered_solvent=False" and the models don't have any waters. I'm puzzled by your result on this.

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?

I think Pavel answered this one.

All the best,
Tom T

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"