[phenixbb] input for specifying labin in phenix.find_ncs

Terwilliger, Thomas Charles terwilliger at lanl.gov
Wed Nov 26 08:00:36 PST 2014

Hi Arko,

Yes, I suppose you could change the labels in the mtz file...but using the labin line as Gabor mentioned is supposed to do the job as well!

And yes, find_ncs does normally require a map coeffs file if you are looking for ncs from a pdb file.  If you want to work around this you can supply any mtz file and specify "force_ncs=True" and it should ignore what is in the mtz file.

All the best,
Tom T

On Nov 26, 2014, at 4:00 AM, Arka Chakraborty wrote:

Dear Dr. Terwilliger,

Its a pleasure writing to you. I have good memories of the EMBO workshop in Grenoble last year.
As you commented, I have used combinations of HA plus mtz, mtz alone, model alone, model and mtz. When the map coefficients come from a 2DFo-mFc synthesis generated by phenix.refine there is no problem as phenix.find_ncs readily detects the labels. The problem arises when I try to use an mtz from CCP4 coming from density modification in DM or directly from phasing as the column labels are not what the program wants. I suppose changing the labels should do it?.
With the heavy atom and mtz case another peculiarity is that it finds operators with cc of 0.64 from the ha sites and then moves to the map for searching operators giving a cc above 0.8 and finally reports operators with a cc of 0.54 ( presumably from the map). Unfortunately the ha sites require a mtz with map coefficients to work. I was wondering if there is a way to use the ha sites alone in phenix.find_ncs?( apart from getting the matrix from superposition in coot or the programs in CCP4 suite)?. I was unable to find a way from the manual. The present case is a bit tricky because of presence of a tNCS.

Best regards,


On Wed, Nov 26, 2014 at 12:01 AM, Terwilliger, Thomas Charles <terwilliger at lanl.gov<mailto:terwilliger at lanl.gov>> wrote:
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<mailto:phenixbb-bounces at phenix-online.org> [phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>] on behalf of Gabor Bunkoczi [gb360 at cam.ac.uk<mailto:gb360 at cam.ac.uk>]
Sent: Tuesday, November 25, 2014 4:13 AM
To: Arka Chakraborty
Cc: phenixbb at phenix-online.org<mailto: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
> , 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
> --
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> phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
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Arka Chakraborty
ibmb (Institut de Biologia Molecular de Barcelona)

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