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

Eric Pettersen pett at cgl.ucsf.edu
Fri Nov 20 17:27:36 PST 2015

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 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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