[phenixbb] feature enhanced maps

Schubert, Carsten [JRDUS] CSCHUBER at its.jnj.com
Tue Jul 23 12:54:09 PDT 2013

Hi Pavel,

I just used the FEM maps for the first time today. 3A dataset, marginal maps, some broken density of the main chain in disordered regions. The FEM maps are very impressive and pull out quite some features and waters from the noise, which were not visible before. The broken main chain density cleared up, some disordered side-chains were better defined as well as the inhibitor. It cannot do wonders in case of really disordered regions, as one of my colleagues found out on a pretty tough case, but it is certainly worth a try. Also real space refinement in coot against the FEM maps worked well. In general the maps do not look like a 3A map, but rather 2.5'ish or better, which makes correcting tracing mistakes much easier.

Again this is an N of one, so the feedback should be taken with a grain a salt for now, but I think this is a very good tool and worthwhile checking out. 

Thanks for the development



-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Pavel Afonine
Sent: Tuesday, July 23, 2013 2:08 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] feature enhanced maps

Hi Joseph,

>> Thanks Nat! I am trying out the new "Featured Enhanced Map" option.
>> Preliminary analysis says it really helps!
> Okay, that definitely isn't included in the GUI yet - I was waiting to 
> hear from Pavel before I added it.
> I am sure Pavel would be interested in seeing any cases where this 
> helps.  In general, although we obviously test new methods against 
> existing datasets, it is always more impressive to demonstrate that 
> they help solve new problems.

I'm glad it worked for you, and I'm very interested to hear any feedback or answer questions. This is still considered under development, though current implementation is stable and ready to use. There might be some changes to the algorithm in future (mostly to make it faster, so it can be routinely run after refinement, for example), but I don't think these changes will be major.

The only documentation at present is this set of slides:
which also provides usage instructions (using command line).

Nat: yes, it would great to have GUI for this! Thanks!


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