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

Oliver Clarke olibclarke at gmail.com
Fri Nov 20 11:35:28 PST 2015

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.

> 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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