[phenixbb] input for specifying labin in phenix.find_ncs

Terwilliger, Thomas Charles terwilliger at lanl.gov
Tue Nov 25 15:01:53 PST 2014


Hi Arko,

To add to what Gabor mentioned, if you are lucky you can also skip the labin keyword and the columns with phase and amplitude (preferentially FWT PHWT) will be guessed.

If you supply both heavy-atom file and mtz, it will look for ncs in the heavy atoms and check it against the map.  If no clear ncs is found, it will try again just using the map alone.

All the best,
Tom T

________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Gabor Bunkoczi [gb360 at cam.ac.uk]
Sent: Tuesday, November 25, 2014 4:13 AM
To: Arka Chakraborty
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] input for specifying labin in phenix.find_ncs

Hi Arko,

the following works for me:
phenix.find_ncs yy.mtz labin="FP=F PHIB=PHI FOM=FOM"

I am not sure that find_ncs will use multiple sources of information,
i.e. it will either use the PDB file (either heavy atom positions or MR
structure), or the MTZ-file (using density). I do not know what happens
if you specify both.

BW, Gabor

On 2014-11-25 10:29, Arka Chakraborty wrote:
> Dear Phenix BBers,
>
> I have a seemingly trivial problem in specifying column labels in
> phenix.find_ncs. Following the manual, on entering labels as :
> phenix.find_ncs xx.pdb yy.mtz params.ncs.labin = "labin FP=F PHIB=PHI
> FOM=FOM"
> , phenix returns the error :  'Sorry, cannot interpret the keyword:
> params.ncs.labin=labin FP=F PHIB=PHI FOM=FOM'. Any clues on what
> mistake I might be making will be greatly appreciated.
>
> Thanks a lot,
>
> Regards,
>
> Arko
>
> --
>
> ARKA CHAKRABORTY
> IBMB (INSTITUT DE BIOLOGIA MOLECULAR DE BARCELONA)
> BARCELONA, SPAIN
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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