[phenixbb] Phenix.ligandfit is not happy with my labels

Tom Terwilliger terwilliger at lanl.gov
Wed Feb 24 10:31:36 PST 2010

Hi! I'm sorry for the problem.
Can you try adding this:

> lig_map_type=pre_calculated_map_coeffs

Let me know if that still doesn't do it. Perhaps if you could send me  
(not the list) the input files I can check it out if so.

All the best,
Tom T

On Feb 24, 2010, at 11:23 AM, ucbccka wrote:

> I am getting an error when trying to run phenix.ligandfit in the  
> version
> phenix-1.6-289.
> I am trying to get it to use an mtz generated via refmac <recoils at  
> the
> chorus of booooo's> and fit the ligand into the difference map.
> If I run
> phenix.ligandfit data=phaser_1.1_refmac1.mtz
> model=phaser_1.1_refmac1.pdb ligand=ATP.pdb
> It complains about my labels, saying..
> *********************************
> Sorry, input labels or map type unclear for
>      phaser_1.1_refmac1.mtz
> For lig_map_type=pre_calculated_map_coeffs supply F and PHI  
> (optionally FOM)
> (or 2FOFCWT and PH2FOFCWT)
> For lig_map_type=fo-fc_difference_map supply one column label for FP
> For lig_map_type=fobs_map supply one column label for FP
> Please specify which lig_map_type above you would like and also  
> specify the
> necessary input column labels for your map like one of these samples:
> input_labels="FP"
> input_labels="2FOFCWT PH2FOFCWT"
> input_labels="FP PHIB FOM"
> *************************************
> Looking at the documentation I tried getting PHENIX to tell me what  
> labels
> it could see by running that autosol query and it kindly told me  
> that my
> mtz file contained
> ************************
> 'FreeR_flag'
> 'F_New'
> 'SIGF_New'
> 'FC'
> 'PHIC'
> 'FC_ALL'
> 'FWT'
> 'PHWT'
> 'FOM'
> **************************
> so, I ran
> phenix.ligandfit data=phaser_1.1_refmac1.mtz
> model=phaser_1.1_refmac1.pdb ligand=ATP.pdb input_labels="DELFWT
> and got the original message complaining that my labels are unclear.
> I even used the GUI, it recognises all the pairs of labels giving me  
> the
> options to look at each map if I want and then..... complains that my
> labels are unclear.
> Clearly my labels are unclear, but I am now unclear how to proceed.
> If anyone could suggest something please then I would be most
> appreciative.  Clearly.
> cheers
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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