[phenixbb] phenix.maps: a command line tool to compute various maps
PAfonine at lbl.gov
Thu Feb 4 21:21:55 PST 2010
Starting PHENIX nightly build version 1.6-295 (or whatever next
version), the new command line tool
is available. As the name suggests, this is the tool for map
calculation: regular (p*Fobs-q*Fcalc) or maximum-likelihood
(p*mFobs-q*DFcalc), with any user-defined coefficients p and q, as many
For example, 2mFo-DFc, 3Fo-2Fc, mFo-DFc, Fc, Fo, Anomalous difference
maps can be all computed at once. Also, a user has a full control over
various map calculation parameters, such as filling missing Fobs with
DFc, computing kick maps, etc. Maps can be output in X-plor formatted
files or as Fourier map coefficients in MTZ formatted file. X-plor
formatted maps can be computed for the whole molecule/unit cell or any
selected part of the structure.
This new tool is meant to be a replacement for current practice of
computing the maps using phenix.refine (although, phenix.refine still
output maps as before).
For more information and usage examples simply run phenix.maps .
This is available from PHENIX GUI too (thanks Nathaniel Echols).
For usage instructions and quick manual type phenix.maps and hit Enter.
Please let me know should any questions or problems related to using
this tool arise.
P.S. Below is the result of running phenix.maps:
phenix.maps: a command line tool to compute various maps.
How to run:
1. Run phenix.maps without any arguments: just type phenix.maps in the
line and hit Enter. This will create a parameter file called
which can be renamed if desired.
2. Edit maps.params file to specify input/output files and the desired
It is possible to request as many maps as desired.
3. Run this command to compute requested maps: phenix.maps maps.params
- The scope of parameters 'map_coefficients' defines the map that will be
output as Fourier map coefficients. The scope of parameters 'map'
the map that will be output as X-plor formatted map.
- To create several maps: duplicate either 'map_coefficients' or 'map'
scopes of parameters as many times as many maps is desired. Then
of them to define the maps.
- A map is defined by specifying a map type using 'map_type' keyword
within each scope of parameters: 'map_coefficients' or 'map'. The
supported format for 'map_type' is: [p][m]Fo+[q][D]Fc[kick][filled]. For
example: 2Fo-Fc, 2mFobs-DFcalc, 3Fobs-2Fmodel, Fo-Fc, mfobs-Dfcalc,
The 'map_type' parser will automatically recognize which map is
- The program creates as many files with X-plor formatted maps as many
formatted maps is requested, and it creates only one MTZ formatted
all Fourier map coefficients in it.
- The X-plor formatted map can be computed in the entire unit cell or
selected atoms only.
- Kick maps and missing Fobs filling is done (if requested) as
Adams et al. (2010). Acta Cryst. D66, 213-221.
- Twinning (if detected) will be accounted for automatically.
- All arrays used in map calculation, for example: Fobs, Fmodel,
m, D, etc., can be output into a CNS or MTZ formatted reflection file.
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