Difference maps with local fitting

[olibclarke@…]

Begin forwarded message:

From: Oliver Clarke
Subject: Re: ChimeraX with Phenix
Date: February 12, 2016 at 1:56:42 PM PST
To: Tom Goddard

Weird - still leaves it as center of view in my hands.

With regards to maps, we've already talked about a lot of the things that could be enhanced - dealing with symmetry, and applying map modifications like B-factor sharpening and low pass filtering in fourier space. One of the other map-related tasks that I use chimera for a lot, but which I think could maybe be improved, is to create difference maps to identify bound ligands in cryoEM maps. Obviously if there is no conformational change vop substract works fine, but when the domain that binds the ligand moves slightly, I have found it very useful to make a "locally aligned" difference map - basically, fit the structure of the domain to both maps, extract out density with a 5 or 10Å buffer in both cases, align the resultant density fragments and then use vop subtract to create the difference map. I've wrapped this up in the following alias:

#Calculates a local difference map by extracting density around a selection (5A buffer) aligned to the two maps, aligning the extracted densities and subtracting one from the other.
#Usage: local_diff_map sel #map_id1 #map_id2
alias ^{local_diff_map savepos tmp; close #1001,​1002,​1003,​1004; fitmap $1 $2; vop zone $2 $1 5 modelid 1000 minimalbounds true; fitmap $1 $3; vop zone $3 $1 5 modelid 1001 minimalbounds true; fitmap #1001 #1000; vop resample #1001 ongrid #1000 modelid 1002; vop subtract #1000 #1002 modelid 1003 minrms true; volume #1003 step 1 ; split_diff_map #1003 #1004 ; close #1000,​1001,​1002,​1003 ; reset tmp}

I feel like something like this functionality might be useful to more people if it was an official function rather than a hacked together script. Also, I wonder whether the "minRMS" option could be extended to try different B-factors, as well as different scalings, so that one can create clean difference maps between say a 3Å map and a 5Å map without too much fiddling - or between maps that have just had different levels of sharpening applied prior to import into chimera.

Cheers,
Oli.