On Wed, Oct 24, 2012 at 12:37 AM, Niks wrote:

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?

It should use the original MTZ file for the experimental data - but since Phaser already calculates a weighted map, it is most convenient to use that to start the building process. Which version of Phenix are you using? Can you send me a screenshot of the input window?

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?

Unless AutoBuild used MR.1.mtz as the data file too, that sounds like it could be a bug. I will check it out.

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?

Did you remove the waters from the input file before running MR? If so, this also sounds like a bug.

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 the discrepancy is due to Phenix reporting the resolution for reflections which are actually measured. The MTZ file might claim that it goes from 127.5 Å down, but it probably has HKL indices (and maybe R-free flags) for those reflections between 127-38Å but no actual amplitudes or intensities. Once the data are extracted into Phenix it discards the reflections for which no data are available, and reports only the resolution it sees. The discrepancy in completeness statistic could happen if you're using anomalous data in Phenix but merged data in Refmac; Phenix will report the completeness keeping F+ and F- separate. I'm more worried about the low completeness in general, however; unless you just have very incomplete high-resolution shells, this much missing data tends to result in map artifacts and other difficulties during refinement, especially if it's a systematic chunk of reciprocal space that's missing (as is usually the case). The "3D data viewer" under "Reflection tools" will let you visualize which data are missing - it might be worth checking this out. -Nat

Dear Nishant, 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"