[phenixbb] LigandFit parameters?

Tom Terwilliger terwilliger at lanl.gov
Tue Jul 27 08:05:42 PDT 2010

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"


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 terwilliger at lanl.gov 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
> _______________________________________________
> 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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