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 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' 'PHIC_ALL' 'FWT' 'PHWT' 'DELFWT' 'PHDELWT' 'FOM' **************************

so, I ran

phenix.ligandfit data=phaser_1.1_refmac1.mtz model=phaser_1.1_refmac1.pdb ligand=ATP.pdb input_labels="DELFWT PHDELWT"

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 [email protected] 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: [email protected] 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