Thanks for the info! I was just worried that the added hydrogen atoms would not be in the minimal position. They do move a little from the minimization. Do you think that is significant? Alex Gawronski On Tue, Aug 4, 2009 at 11:38 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Alex, I would never recommend minimization as part of a pipeline to prepare structures for DelPhi calculations. Is there some reason you expect these structures to be particularly bad? The minimization is intended for when you have done some manual building, or mutation, or docking, and want to clear up some local bad contacts or highly strained geometries. It is only a local minimization, and will not "refine" the structure if that requires crossing any energy barriers.

I don't know what the issue with "spec" and "freeze" are, but they worked fine when I tried them today. There must be a selection for "freeze" to have any effect. "spec" only controls which models are minimized, so if you only have one model open at a time there is no reason to use it. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>

For preparing structures for DelPhi, you might want to look at the Dock Prep tool (under Tools... Structure Editing). It has several structure "regularization" options such as changing selenomethionine to methionine, removing solvent, removing alternate locations of atoms, and rebuilding missing sidechains (although not backbone), as well as hydrogen addition. However, don't bother with the charge addition since that will be irrelevant to the DelPhi calculation --- DelPhi looks up charges from a separate parameter file. < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.h...

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Actually "minimize" calls Dock Prep to fix up the structure beforehand. I say just use Dock Prep directly and don't bother with charge addition and don't minimize, unless there is some reason to think the structures are particularly warped.

The main thing to worry about for an accurate DelPhi calculation is getting the charges and radii assigned correctly from the DelPhi parameter files. You should check the DelPhi log file. That is a DelPhi issue, fairly separate from Chimera.

I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

On Aug 3, 2009, at 1:32 PM, Alex Gawronski wrote:

Hello,

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I'm preparing proteins for Delphi analysis using Chimera's minimize function (from a script). However this process is very time consuming. Is using minimize necessary to get accurate results from Delphi? If not, what is necessary? I've played around with the "spec" and "freeze" parameters and they either seem to have no affect or throw an error (which I submitted as a bug). What do you suggest I do?

Thanks, Alex Gawronski Carleton University