I believe macro_cycles =0 in phenix.refine will give you only 2fo-fc. its in the section where one can ordered_solvent and simulated annealing. FR On Sep 9, 2009, at 1:22 PM, Maia Cherney wrote:
Hi,
I am trying to find the answer to a question that was discussed long time ago at this forum, but there is no mechanism to find old discussions.
You have to go through each month and figure out from the subjects where was a particular discussion.
Could you, the phenix team, make it easier to find answers to those questions that had been answered previously.
I remember, there was a question how to generate maps without refinement. I finished the refinement, but I need a map (in explor format) to show the 2fo-fc density in the publication.
Maia
Pavel Afonine wrote:
Hi Tirumala,
I agree, you are not the first who confused by this and an example right in the message would help.
First, your MTZ file contains the following data: (FP,SIGFP) and (Fav,SIGFav) and it is your choice to select the one that you want to use in refinement.
Second, once decided on the data - for example it is FP, then just add to your command line this:
refinement.input.xray_data.labels=FP
or, which is the same
xray_data.labels="FP,SIGFP"
Pavel.
On 9/9/09 11:10 AM, Tirumala Kumar Chowdary wrote:
Hi,
I am trying to run phenix.refine with a sharp output MTZ file (column labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav).
Phenix.refine stopped at
'Multiple equally suitable arrays of observed xray data found.
Possible choices: sharp_sad_se_eden.mtz:FP,SIGFP sharp_sad_se_eden.mtz:Fav,SIGFav
Please use refinement.input.xray_data.labels'
Can someone tell me on how to use this 'refinement.input.xray_data.labels' and how to specify which column labels to use. There is nothing written in the documentation about it.
Thanks Tirumal
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