Hi Hermi,
What does the map look like when you load it up in coot after ligandfit? Is the map clear, and the ligand not fitting, or the map bad?
If the map is bad, then probably ligandfit has not guessed your input data file information correctly. You have two basic choices:
1. supply FP PHI [FOM] and specify "pre_calculated_map_coeffs"
or
2. supply FP only and specify "fo-fc_difference_map"
If the map is good and the ligand is not fitting at all...that is surprising and I would be very interested to see the data and ligand (send to
[email protected] not the list if you wish to do this).
You can adjust other ligandfit parameters such as delta_phi_ligand, fit_phi_inc, n_group_search, n_indiv_tries_max, but it is not so likely that these will help.
I hope that helps!
All the best,
Tom T
On Jul 27, 2010, at 8:47 AM, Hermella Woldemdihin wrote:
Hi,
I am using LigandFit on the GUI version of Phenix. In my electron density map there is a good density for my ligand.
And I have my ligand in pdb format. As an input to LigandFit I gave my ligand file(pdb), an MTZ file from my data processing
and my protein at some stage of refinement (@ a good R-values). I used the default settings (Resolution=0, Minimum CC of ligand to map=0.75
and Ligand map shape=Fo-Fc) and I got a bad result. My overall CC=0.33 and Score=68.68). What shall I do to get the best solution???
Thanks all!
Hermi
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