Last modified: 8-oct-2010

Electron density map calculations

Map update

To update maps after refinement or model building steps, go to the "MAPS" depp page and click on MAIN_MENU:map_calc.html menu items.

Density modification

For applying density modification including averaging see the MAIN_MENU:dens_mod.html.

Initial setup

If you follow some of MAIN standard procedures MAIN_DOC:1mol/1mol.html or MAIN_DOC:nmol/nmol.html then there is probably not much to say. Initial maps have been calculated and loaded already.

Syntax quides

To understand the MAIN syntax (commands MAIN_DOC:com/make.html, MAIN_DOC:com/reflect.html, MAIN_DOC:com/fourier.html. For exploring the syntax see also the macro "generate_map.cmds" created with "CAL_MAP" from the menu block MAIN_MENU:map_atom.html macros.

Insight into syntax of structure factors manipulation

This subsection explains several possibilities how to merge PHASE and AMPLITUDE information from FCALCULATE and FOBSERVED into FWORKSET in order to BACK transform an electron density map.

In order to combine amplitudes of FCALC with FOBS these two arrays need to be scaled to each other. Scaling constants are obtained with an R-VALUE calculation. MAIN calculates scale constants for each resolution shell independently. This resolution shell independent scaling allows to use all measured reflections including the low resolution terms. Simultaneously an overall reciprocal space B-value, is also calculated. R-VALUE and with it scaling constants and overall B-value depend upon the number of resolution shell divisions applied. This then of course effects also refinement of your model. Only defined reflections with FOBS and FCALC> 0 and reflections for which I/sigma is more than the specified threshold value (2.0 is the default) are accepted into the R-VALUE calculation.

> reflection shells 10 select defined .a sigma 2.0 end r-values

Here you may wish to write the Fobs, Fcalc and the phase information of the selected reflections (defined reflections are those with Fobs> 0 )

> write over file cb-inh-p21.phase refl fobs fcalc phase select defined end

Now the desired AMPLITUDE and PHASE information should be transferred into the FWORKSET array that will later fill the complex map MAP_ONE that will be transformed into electron density with a Fourier back-transformation.

Here it is decided what kind of map will be calculated. For a 2Fobs - Fcalc map calculation the Fcalc should be scaled to Fobs in using scaling constants from the last R-VALUE calculation. First the PHASES and AMPLITUDES are copied from FCALC to FWORK. Essentially only the PHASE information should be brought to FWORK, but since FWORKSET is an array of complex numbers, their phase can not exist without a certain nonzero amplitude. SCALE FCALC means that FCALC should be scaled in accordance with the last R-VALUE calculation.

> reflect set ampl phase fwork = fcalc * 1.
> reflect set ampl scale fcalc   fwork = fobs * 2. - fcalc * 1.

For an Fobs - Fcalc map calculation the scales of FOBS and FCALC amplitudes need to be set to one. Also here SCALE FCALC means that FCALC should be scaled in accordance with the last R-VALUE calculation.

> reflect set ampl phase fwork = fcalc * 1.
> reflect set ampl scale fcalc     fwork = fobs * 1. - fcalc * 1.

A Patterson Fobs map requires only a square of FOBS with zero phase. (You need to read appropriate Patterson symmetry operators.)

> refl set ampl phase fwork = fobs ^ 2

An Fcalc map with all reflection (P1 cell) needs only the FCALC information.

> refl set ampl phase fwork = fcalc * 1.

In addition to these you can also scale Fcalc resolution dependent with your own TEMPERATURE factor and a resolution shell independent constant.

> refl set temp 20. const 1.0 ampl phase scale fcalc   fwork = fcalc * 1.

For a translation function (or a correlation calculation) you need to transform the first FCALC set into FWORK, then perform another FCALC calculation and then multiply FCALC with FWORK and store results in FWORK:

> refl set ampl phase fwork = fcalc * 1.0 * fwork * 1.0