[phenixbb] Issues with ligandfit.

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Thu Sep 17 11:24:47 PDT 2020

Hi Vatsal,

I'm sorry for the trouble! You can check to see if ligand fitting is
generally working on your computer with a test that comes with your phenix
installation.  You can type in a command window:

    phenix_regression.list LigandFit_std

This will print out something like this:

Listing of available Phenix regression tests
Total of 1705 tests available.
Listing 1 tests matching of the following strings: LigandFit_std


Try running the test that is printed out...it should run and say "OK" when
it is done. If not...let me know!

Then to address your question more directly...by "recently", do you mean
that you have a new version of Phenix, or new data, or both?

If new data, best thing to try is rerun with old data, then change things
until you are running with new data and see when something fails. If that
doesn't show what the problem is, I'm happy to help (if you send the data
and log file I can debug it here)

If you have a new version of Phenix and the same data that worked with an
old version does not work any more, let me know as above.

If you have a new version of Phenix and new data, can you run with old
data, old version, then old/new, then new/old, then new/new and see which
one causes the problem.

-Tom T

On Thu, Sep 17, 2020 at 9:38 AM Vatsal Purohit <vpurohi at purdue.edu> wrote:

> Hi,
> I’ve been using the Ligandfit function to location ligand binding sites
> using electron density obtained without any ligands in the structure model.
> However, recently, the program has been giving me the following error while
> trying to open the resolve maps:
> Sorry: None of the resolve versions worked
> Is there something I can do to try and fix this?
> Any advice would be appreciated.
> Regards,
> Vatsal
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
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Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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