FFT map coefficients only for certain chains

From: zhang yu
Date: 19 February 2012 22:46


Dear CCP4ers,

Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The "isomesh" command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. 

In the interface of "FFT" tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that "If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region" . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A.

Thanks.

Yu

 

--
Yu Zhang




----------
From: <Herman.Schreuder

Dear Yu,

 

You seem to be mixing up map coefficients and map files. Map coefficients are modified reflections, e.g. 2*Fobs-Fcalc multiplied by a weighting factor with h,k,l indices and are stored in a .mtz file. From these map coefficients, you can calculate a map file with an FFT program. A map is an array with local values of the electron density spaced say 1Å apart with extentions like .map. If you provide Coot with just map coefficients, it will calculate on the fly the map around your centering atom so it does not need a map file.

 

Since every part of real space (the contents of the unit cell) contributes to every reflection, it is not possible to generate "observed" map coefficients for one chain alone. I do not know what options you exactly tried, but normally, if you select a certain chain, it will calculate a map based on all chains, but only output the map around the selected chain.

 

To get map (coefficients) of only one chain, there are two options:

1) a straight Fcalc map. Only input a pdb file with the chain you want to select. Do not use observed F's. You will get calculated density for that chain only and the rest of the map will be empty (zeroes).

2) a (vector difference) Fo-Fc omit map. Input a pdb file without the chain you want to select and calculate an Fo-Fc map. All chains will be subtracted from Fo with the exception of the chain you left out from the Fc calculation. This map will contain density of the omitted chain plus noise due to the fact that your model is imperfect (the famous 20% Rfactor of well-refined structures). The generate a vector difference map, you should use phases calculated for the complete model for Fo, and omit-phases for Fc.

 

I hope this clarified things a bit,

Herman

----------
From: Paul Emsley

Like Herman, it was not apparent to me what exactly you want wanted.

If you want a map that covers only [1] or excludes [2] a particular atom selection then you can do that in Coot. 

Extensions -> Maps... -> Mask Map by Atom Selection,

e.g. to show only the "A" chain, use an atom selection of "//A".

You can then export the map using:

Extensions -> Maps... -> Export Map  
or
Extensions -> Maps... -> Export Local Map Fragment...

If you really want structure factors from that then you can use sfall (MODE SFCALC MAPIN).

Paul.

[1] use mask inversion
[2] don't use mask inversion

----------
From: zhang yu

Herman,

Thanks for clarifying the difference between map coefficients and map files for me. What I really need are only map files, and I could generate those masked maps by following Paul's suggestion.

Yu