[phenixbb] PDF slides:

Pavel Afonine PAfonine at lbl.gov
Sun Mar 8 20:55:14 PDT 2009

Hi Mark,

thanks a lot for your positive and instructive feedback - it is very 
encouraging! Thank you!

Yes, the automation of structure refinement is "a work in progress", 
indeed. But I believe we are making a good progress with a positive 
gradient! And the progress we have right now highly encourages us to 
make further and further steps.

I honestly and, perhaps, naively believe that the complete automation in 
crystallographic structure refinement is possible and is subject of time 
and effort invested into it. I clearly understand and foresee how the 
next steps in automation look like and how they should be done, and we 
keep going towards achieving this goal. One of the things where I might 
fail is the time frame since all projected times for development should 
be multiplied by pi or, better, by pi**2, to be realistic -:)

For example, it took me a few weeks to work out the math and code the 
basic bricks for TLS refinement, but then I spent nearly 6 months making 
it rock solid reliable, robust and failure-proof (compared to the other 
software options).

Right now I'm working on real space refinement with the ultimate goal to 
have a dual-space refinement, where the refinement in reciprocal space 
(what we have right now) will be interleaved with the local refinement 
in real space. Hopefully, this will be an efficient tool for fixing 
local model imperfections that people used to do manually in graphics 
(putting side chains into density, etc...). Of course, it might be only 
possible with the power of torsion angle parameterization that Ralf is 
currently working on and is about to finish.
You are right, 100% correct handling of alternative conformations is 
another big project that is in out to-do list. We did some progress in 
this direction but had to switch to other pressing things. One day it 
will be covered.

And yes, sometime we need to write papers and make tutorial slides to 
make it clear what we are busy with (which takes a lot of "development 
time"), but it doesn't sound like a waste of time in the end! -:)

Thanks again for your feedback,

On 3/8/09 7:43 PM, Mayer, Mark (NIH/NICHD) [E] wrote:
> Hi Pavel,
> These are excellent tools for students and the working crystallographer;
> no need to apologize to sending to BB. For the 1st time I understood
> value of automation in refinement. But, its still a work in progress, good
> for everyone these days, and perhaps puts forward an ideal situation,  
> bit different from what some of us encounter in real life.
> What would be great in future would be examples and discussions about
> how/when to go anisotropic at resolutions where this is clearly warranted
> but not for the the whole chain, (e.g. we have current structures @ 1.6 Å
> which still have loops with almost no density) so advice on how to define
> boundaries for isotropic and anisotropic refinement in  single chain would
> be great.
> It was also interesting to see in your PDF that  building still plays a key role in
> structure solution; its obvious to anyone solving structures that
> manual intervention is still needed here. Definition for refinement
> of residues and solvent with coupled ACs still requires a lot of manual
> intervention after building and automation before refinement would be
> a real help!
> Thanks again for all your contributions.
> Mark Mayer
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