[phenixbb] ligand fitting

[Pavel Afonine]

Hello,

just to point out  that CC alone may not be adequate measure, as we show 
here:

Acta Cryst. (2014). D70, 2593-2606.
Metrics for comparison of crystallographic maps

In addition, a histogram of per-atom correlations along with a histogram 
of actual map values per-atom may be useful.

Pavel

On 10/9/14 10:30 AM, Tim Gruene wrote:
> 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?
>
> Best,
> Tim
>
> 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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>
>
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