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

Pavel Afonine pafonine at lbl.gov
Wed Oct 24 08:27:39 PDT 2012

Hi Niks,

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

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.


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"
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20121024/372a0af3/attachment.htm>

More information about the phenixbb mailing list