On 20/11/2021 11:31, Weiergräber, Oliver H. wrote:
Dear Paul,
>From my experience, I agree that an option to inactivate the anti-bumping
restraints in RSR would be very useful.
To be honest, my impression is that it tends to be a hindrance rather than
helping, at least in cases where extensive rebuilding is required.
Best regards
Oliver
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Paul Emsley
[pems...@mrc-lmb.cam.ac.uk]
Sent: 20 November 2021 11:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] COOT RSR
On 20/11/2021 09:42, Matthew Snee wrote:
I had a bit of trouble getting used to the new COOT real space refine... it
took me an embarrassingly long time to work out that there is nothing wrong
with the fitting/restraints..
You are not alone in finding Coot's RSR unintuitive (at least initially).
it just doesn't seem to allow clashes with parts of the model that aren't in
the selected RSR zone even when the fit would be perfect.
That's right.
To help out, I have added dynamic interaction analysis: use CURLEW to download the
Refinement Tools and then use Refine -> Contact Dots On. Now when you use RSR
you can see what's bumping into what (I usually have this feature turned on).
Is there a quick way to toggle this feature on/off?
No.
It seems like a nice addition, but it can cause problems where one incorrect
part of a partially built model prevents me building another, or for cases
where two different residues/ligands occupy the same space at partial occupancy.
The solution is to move the wrong parts of the model out of the way first - or
include them in the set of refining residues.
Paul.
Hello Oliver,
I am willing to change the real space refinement if I see a reason to do
so. If you can show me an example where the old method is easier then
I'd be interested to watch it.
Paul.
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