[Chimera-users] Dock prep with multiple structures - endless loop?

Oliver Clarke olibclarke at gmail.com
Fri Nov 20 18:55:23 PST 2015

Hi Eric, thanks! I think that is indeed the issue - subsequent to my
initial post I found that running each structure individually was much
faster (although still slow enough that I would rather run several
structures overnight), so the alterations you've made ought to fix it.

I think for ChimeraX the use of progress bars or ETA timers for any process
that might run longer than say a minute or two might be worth considering -
helps the user know whether killing the process and adjusting parameters is


On Fri, Nov 20, 2015 at 8:27 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Oliver,
> The tremendous slowness is due to Chimera considering hydrogen bonding
> interactions for choosing which rotamer to use.  So this means a
> donor/acceptor calculation for each *possible* rotamer at each position.
> I don’t think this can be avoided without a significant hit to the quality
> of the rotamer choice.  However, it *is* doing something inefficient in
> your case.  It isn’t ignoring other models when looking at rotameric
> hydrogen bonding interactions.  Therefore the fact that that you have
> several models open at once is slowing you down.  I’ve just changed the
> code so that when Dock Prep calls the rotamer code it tells it to consider
> each model in isolation.  I’ve done the same for Dock Prep calling the
> add-hydrogen code (only matters in nogui mode since the GUI dialog offers
> explicit control over that setting).  I don’t know that it would help
> enough in your case (or similar cases since you’ve already dealt with your
> structures) but it’s something.
> I hope to move the H-bond finding code from Python to C++ for ChimeraX,
> but the code is complicated and relies on some underlying chemical
> group-finding code, so it’s not 100% settled if the code will move or not.
> —Eric
> Eric Pettersen
> UCSF Computer Graphics Lab
> On Nov 20, 2015, at 11:35 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> As an addendum to this for anyone who encounters the same situation - I
> gave up and used SCWRL4 instead, with the -v flag for increased speed.
> Perhaps not as good, but for multiple large structures it might be the only
> time-efficient way of filling partial rotamers in a sensible way.
> Cheers,
> Oliver.
> On Nov 20, 2015, at 7:54 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> Hi,
> Would it be possible to add a progress bar (with ETA) for Dock prep at
> some point? I ran it overnight to fill partial sidechains on six structures
> (each ~6000aas), and it still isn’t finished, but I can’t tell whether it
> is just taking a really long time or whether something has gone wrong. The
> status bar is still updating with “Matching donors”, “finding acceptors”
> and “building search tree” messages, but it seems to be giving these
> messages multiple times for each structure - is that normal?
> Cheers,
> Oliver.
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