[phenixbb] ligand fitting

Sneha Rangarajan rsneha at umd.edu
Mon Oct 13 14:22:29 PDT 2014

Thank you all. 
Yes, it has improved the geometry and the score slightly without much effect on the Rfactors.


-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Tim Gruene
Sent: Monday, October 13, 2014 2:23 PM
To: phenixbb at phenix-online.org
Subject: Re: [phenixbb] ligand fitting

Dear Sneha,

the impact of hydrogens to the scattering is not very great, as the link provided by Pavel also illustrates. Their meaning for the geometry is much more important and - if properly implemented - the use of hydrogen atoms in refinement should give you a better molprobity score than not using them.

I recommend to always use hydrogen atoms at any stage of refinement, although you won't notice it much in R-factors and such. They don't cost data, nor do they add to the number of parameters, so you don't loose anything, but you most likely gain better geometry.

In my experience the rise in run time of the refinement program is negligible.


On 10/13/2014 06:31 PM, Sneha Rangarajan wrote:
> Thanks everyone for your suggestions.
> I have managed to fit my peptide into the density.
> My Rfactors are now 25/30 and geometry looks good too.
> One more question- When does one use "add hydrogens" in refinement? Does it help in the final stages of refinement?
> Thanks a lot,
> Sneha
> From: Nathaniel Echols [mailto:nechols at lbl.gov]
> Sent: Thursday, October 09, 2014 5:21 PM
> To: Sneha Rangarajan
> Cc: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] ligand fitting
> On Thu, Oct 9, 2014 at 1:16 PM, Sneha Rangarajan <rsneha at umd.edu<mailto:rsneha at umd.edu>> wrote:
> @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?
> No, in AutoBuild terminology, "ligands" means "atoms I want AutoBuild to leave alone (but include in refinement)", which would mean your apo model.  You wouldn't supply peptide.pdb at all, because AutoBuild isn't going to move it into the correct place; ideally you want it to just build new residues into the appropriate density.
> To be honest I think I would be tempted to simply build the peptide by hand, which shouldn't be too difficult at this resolution. I'm normally a big fan of letting the program do all of the heavy lifting, but this is one of those corner cases where the manual approach might be more efficient.  (This is a point for future improvement in Phenix, of course.)  Your own opinion of how easy it will be may be different than mine, however.
> -Nat
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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