[phenixbb] simulated annealing composite omit map or iterative build composite omit map at 2.7A resolution

Xiao Lei xiaoleiusc at gmail.com
Wed Jul 15 11:37:47 PDT 2015

Dear Phenixbb members,

I am thinking of generating a composite omit map for my whole structure
model (the model is solved by phaser MR in CCP4 and refined by
phenix.refine program, results of phenix.refine shows Rfree/Rwork is 27% /
20%. The resolution of data is 2.7A). From previous phenix posts and
information from internet, I know there are four composite omit map types
in Phenix: "simple"; "refine"; "simulated annealing" and "iterative build"
composite omit map. Because I want to get rid of model bias as much as
possible, I am thinking of choosing either "simulated annealing" or
"iterative build" method, though I know it needs much longer time to run. I
know "iterative build" composite map option is more powerful to get rid of
model bias as I found in phenix manual that "A more powerful approach is to
generate an "iterative-build" omit map (Terwilliger et al. 2008), which
rebuilds the structure instead of annealing." But at the
"autobuild-iterative guild omit map" manual it also said "The AutoBuild
Wizard produces a refined model that can be nearly complete if the data are
strong and the resolution is about 2.5 A or better. At lower resolutions
(2.5 - 3 A) the model may be less complete and at resolutions > 3A the
model may be quite incomplete and not well refined."

My questions are: 1. As the resolution of my data is 2.7A, does this mean
Simulated annealing composite map option is better for me in this case?

2. Inside phenix panel, there are two map tools for generating composite
omit map, one is "Composite omit map" tool and the other is
"Autobuild-iterative build omit map" tool. I tried the "composite omit map"
tool with simulated annealing option with my refined model and original
x-ray data, in the output file I only get 2mFo-DFc map (I know this is by
default) but no pdb output, I am guessing this is because in this
"composite omit map" tool my model is not modified (or refined) by the
program,  just the composite omit map is generated, am I right?   If I am
right, does this mean the following step is to open the output map in coot
with my model, and do manual adjustment of the model in the regions which
does not fit the map?

3. In the "autobuild-iterative build omit map" tool, there is also an
option of "simulated annealing" composite omit map, is this option the same
as the "simulated annealing" option in the "composite omit map" tool and
will give the same output (just the 2mFo-DFc map by default, not modifying
my model) ?

4. If I use iterative-build composite map with this 2.7A resolution, I'm
guessing I will get a modified or refined pdb model output and a composite
2mFo-DFc map, but my model may not be complete because of the resolution,
does this mean I have to manually add the missing part of model in the
following step?

5. Is there an option to generate composite omit mFo-DFc map along with
composite 2mFo-Fc map at the same time?

Thanks ahead.

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