[phenixbb] ligand fitting

[Parthasarathy Sampathkumar]

Yes Sneha.., "apo" structure and the tweaked-peptide should be merged
(under the calculate pull-down menu in coot) before subsequent refinement
cycle(s).

Best Wishes,
Partha

On Thu, Oct 9, 2014 at 4:16 PM, Sneha Rangarajan <rsneha at umd.edu> wrote:

>  @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,
>
> Sneha
>
>
>
> *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,
>
>
>
> Partha
>
>
>
>
>
>
>
> On Thu, Oct 9, 2014 at 12:56 PM, Sneha Rangarajan <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?
>
>
>
> Thanks,
>
> S
>
>
>
>
>
> *From:* 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
> *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 J
>
>
>
> S
>
>
>
> *From:* Nathaniel Echols [mailto:nechols at lbl.gov <nechols at lbl.gov>]
> *Sent:* Friday, October 03, 2014 3:08 PM
> *To:* Sneha Rangarajan
> *Cc:* Pavel Afonine; 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> 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.
>
>
>
> -Nat
>
>
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>
>
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