[phenixbb] how to easily find old subjects

[Francis E Reyes]

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

---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D