[phenixbb] ligand fitting

Sneha Rangarajan rsneha at umd.edu
Thu Oct 9 13:16:25 PDT 2014

@Partha: My peptide is 13 residues long. I don’t see the density for all of it (just few of them). Pardon me for the naïve question but once I superimpose it in coot and adjust its position should I merge it with my “apo” structure (make it part of my model) and refine it to make it fit the density better or something like that?

@Nat: If I want to run autobuild to fit the ligand into the density, should I give it my “apo” model as ‘starting model’ and peptide.pdb as ‘ligands’ alongwith the mtz?
And yes, the peptide was never part of any model or sequence file right from the start since I wanted to avoid any bias. While I see positive density, autobuild has not built any peptide into it.

Thanks a lot,

From: Parthasarathy Sampathkumar [mailto:spartha2 at gmail.com]
Sent: Thursday, October 09, 2014 2:06 PM
To: Sneha Rangarajan
Cc: Nathaniel Echols; phenixbb at phenix-online.org
Subject: Re: [phenixbb] ligand fitting

Hi Sneha,

Easier option would be to superpose homolog-protein+peptide coordinates onto your "apo" structure (using SSM for example within coot), which might get the peptide closer to the binding-site of your protein, and then tweak it for better fit.

OR if the peptide is not too long, and its electron density is clear one might be able to build it manually from scratch.

Hope this helps,


On Thu, Oct 9, 2014 at 12:56 PM, Sneha Rangarajan <rsneha at umd.edu<mailto:rsneha at umd.edu>> wrote:
Hello everyone,

I have a question about ligand fitting into density.
At this point my maps look quite good with decent density for the peptide (ligand)[Rfactprs 26/31].

I tried using ligandfit by giving it the pdb and mtz of the ligand free model along with peptide.pdb (peptide stripped from a pdb where it was complexed with a homologous protein).
However the output was a ligand.pdb file with a CC of 0.49. I am not sure how to interpret this. Does this mean it could not find the density for the ligand?

Is there a better way to fit the peptide into density?


From: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> [mailto:phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>] On Behalf Of Sneha Rangarajan
Sent: Wednesday, October 08, 2014 10:30 AM
To: Nathaniel Echols
Cc: phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Subject: Re: [phenixbb] (no subject)

This was a great idea. My Rfactors after a second round of autobuild are now 25/32. I think it might be getting there afterall ☺


From: Nathaniel Echols [mailto:nechols at lbl.gov]
Sent: Friday, October 03, 2014 3:08 PM
To: Sneha Rangarajan
Cc: Pavel Afonine; phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Subject: Re: [phenixbb] (no subject)

On Fri, Oct 3, 2014 at 11:58 AM, Sneha Rangarajan <rsneha at umd.edu<mailto:rsneha at umd.edu>> wrote:
I did another round of refinement with default settings (XYZ,realsp, IndB and occ) with and without weight optimization.
Without weight opt, the Rfactors are 23/36 with RMSbonds-0.0108 and RMSangles-1.750

One idea would be to run AutoBuild again.  I've seen cases before where it didn't converge using the default settings, and feeding a previous result back into the program for a second run produced significantly better models.  It might help get rid of the overfitting.


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