[Chimera-users] reasonable minimization times

David Belnap David_Belnap at byu.edu
Wed Aug 29 22:32:47 PDT 2012

Thank you, Elaine.  The Fc domain has 9 carbohydrate molecules that are unselected--as thus should be stationary.  The program seems to hang as it displays the following at the bottom of the Chimera window:


I used the command option you suggested and did "clear selection" before selecting the 10 residues to be minimized.  I am running this on a Mac Intel laptop (dual core machine, 2.4 GHz CPU) with 4GB RAM.  I have used Chimera version 1.7 (build 37003) 2012-07-26 and 1.7 (build 37262) 2012-08-29.  The process "sqm" is running at 100% when "top" is run from the command line.



On Aug 29, 2012, at 4:57 PM, Elaine Meng wrote:

> Hi David,
> All those parameters you mention are just for the hydrogen-addition and charge-addition steps prior to minimization and should have virtually no effect on the minimization time (assuming that is the part that takes so long).
> Minimization in Chimera can be very slow, in part because it does not use any distance cutoff.  However, your use of "spec sel fragment true" when only 8-10 residues are selected should limit the calculations significantly, to ignore all but the selected atoms.  I am surprised the calculation could take that long on such a small set of atoms.  How long it should take totally depends on the computer, of course, but for 8-10 residues I haven't seen it take that long. Make sure you have only those residues selected when issuing the command.
> In general, "conjugate gradient" steps are significantly slower than "steepest descent" steps, so you might try setting number of conjugate gradient steps to 0 ("cgsteps 0"), at least for your initial run.  There are additional parameters like step size that could have an effect, but how much of an effect or even whether increased or decreased time is not easily predictable.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Aug 29, 2012, at 3:32 PM, David Belnap wrote:
>> I am trying to link the crystal structure of an Fc domain with two Fab structures.  I am using the command "minimize spec sel fragment true" on the command line.  When various options come up, I've selected "if alternate locations, keep only highest occupancy", "add hydrogens", "add charges", "consider each model in isolation from all others", "also consider H-bonds", and AMBER ff12SB and ANTECHAMBER to assign charges.  I've had jobs run overnight that didn't finish.  What is a reasonable time for about 8-10 residues to be minimized? Can you suggest any ways to speed this up?
>> Thanks, David

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