[phenixbb] input for specifying labin in phenix.find_ncs

Arka Chakraborty arko.chakraborty88 at gmail.com
Wed Nov 26 03:00:38 PST 2014

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> 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 [
> 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
> >
> > --
> >
> >
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*Arka Chakraborty*
*ibmb (Institut de Biologia Molecular de Barcelona)*
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