input for specifying labin in phenix.find_ncs
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*
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
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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: [email protected] [[email protected]] on behalf of Gabor Bunkoczi [[email protected]] Sent: Tuesday, November 25, 2014 4:13 AM To: Arka Chakraborty Cc: [email protected] 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
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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, Arko On Wed, Nov 26, 2014 at 12:01 AM, Terwilliger, Thomas Charles < [email protected]> 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: [email protected] [ [email protected]] on behalf of Gabor Bunkoczi [ [email protected]] Sent: Tuesday, November 25, 2014 4:13 AM To: Arka Chakraborty Cc: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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-- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*
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,
Arko
On Wed, Nov 26, 2014 at 12:01 AM, Terwilliger, Thomas Charles
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 [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb -- Arka Chakraborty ibmb (Institut de Biologia Molecular de Barcelona) BARCELONA, SPAIN
participants (3)
-
Arka Chakraborty -
Gabor Bunkoczi -
Terwilliger, Thomas Charles