[phenixbb] Rigid ligand placement into density map

Terwilliger, Thomas C terwilliger at lanl.gov
Thu Jun 19 14:58:42 PDT 2014

Hi Jason,

I have added an option in phenix.ligandfit to allow a fixed ligand. This should be available starting tomorrow.  For your purposes, the keywords will be:

fixed_ligand=True refine_ligand=False

Let me know if that doesn't do what you need!

All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Phan, Jason [jason.phan at vanderbilt.edu]
Sent: Tuesday, June 17, 2014 3:04 PM
To: phenixbb at phenix-online.org
Subject: [phenixbb] Rigid ligand placement into density map

Hi All,

Is there an option or flag in Phenix LigandFit to place the ligand rigidly with pre-generated conformations without torsional adjustments?

Would setting "conformers = 1" and "refine_ligand = false" work?

Coot Find Ligand with the "flexible" option unchecked seems to work but it won't tell you which original conformer (SD file)  the "fitted ligand" comes from since all
the conformers have the same residue name and number. Coot doesn't write out SD format either so any ID associated with the original conformer is lost.

phenixbb mailing list
phenixbb at phenix-online.org

More information about the phenixbb mailing list