maps in X-plor 3.8
Axel T. Brunger
brunger at LAPLACE.CSB.YALE.EDU
Thu Sep 26 18:57:38 EST 1996
My previous comments need further explanation.
1. The difference in grid size arises from the new internal map
data structure in X-PLOR(online) 3.8xx. An asymmetric unit is stored
as opposed to the whole unit cell. This required a change in the routine
to determine the grid dimensions such that the grid lattice is
compatible with space group symmetry. In X-PLOR 3.1, all maps were computed
in P1, and, thus, the grid could be anything.
Note, that the map write command allows the user to write maps regardless
of the asymmetric unit, i.e, the asymmetric unit of maps is just for internal
storage and the user doesn't have to be concerned with it at all.
2. The additional line contains debugging information consisting
of the map average value and the scale factor that was applied when
the map was written. I'm inclined to leave this information in the file
even though it means that format has changed. However, the additional
lines doesn't seem to cause any problems with most programs.
> we still have X-plor version 3.80. We notice that map generation is somewhat
> different from 3.1, despite the promises of complete compatibility.
> 1) while trying to generate a small map for testing we find that slightly
> different map grid regions are generated when either specifying coverage
> of a set of residues, or when specifying the map limits in Angstroms.
> This is not creating any serious problems for us; I assume there was a bug
> fix at some time. It just complicated debugging of the next point.
> 2) The map format seems to have changed. Formerly the last line of the file
> read: "-9999". Now this line is followed by an additional line containing
> 2 numbers; e.g.:
> 0.1488E-11 0.1524E-01
> This does create a problem for us, because program Setor, a fine and highly
> reccomended viewing program, is unable to read the altered format.
> Does this line contain scaling information or what?
> and where can I read about
> the change in format? Is documentation for the new version available either
> on-line or somewhere in the ftp distribution? I picked up the regular
> distribution, but not the complete (and huge) tutorial file. The only thing I
> could find was a directory /tutorial/manual which contained some .tex and .aux
> files; nothing in any format I could read.
| Axel T. Brunger Dept. Molecular Biophysics and Biochemistry|
| Professor/Investigator Bass Center, 266 Whitney Avenue |
| Office: 203-432-6143 Howard Hughes Medical Institute/Yale Univ. |
| FAX: 203-432-6946 New Haven, CT 06520, USA. |
| http://xplor.csb.yale.edu/~brunger |
| mailto://firstname.lastname@example.org |
More information about the X-plor