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

ucbccka ucbccka at ucl.ac.uk
Wed Feb 24 10:23:41 PST 2010

I am getting an error when trying to run phenix.ligandfit in the version

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
For lig_map_type=pre_calculated_map_coeffs supply F and PHI (optionally FOM)
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="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


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.


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