[phenixbb] ligand fitting

Tim Gruene tg at shelx.uni-ac.gwdg.de
Thu Oct 9 10:30:25 PDT 2014

Dear S,

a CC of 0.49 is quite strong, unless you mean 0.49% - did you take a
look at the resulting pdb-file?


On 10/09/2014 06:56 PM, Sneha Rangarajan 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 ☺
> S
> 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.
> -Nat
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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