resfilter

	RESFILTER
[Top] [Crystallography] [Protein Structure] [Molecular Biology] [Other] [Personal] [Programs]

Applies a Resolution Cutoff to Reflection Data

resfilter Usage

The usage of resfilter is (as it should be) trivial for users of XtalView software. In addition to the reflection file, all that is required is an XtalView crystal file (see below):

Processing of a data file (say mydata.fin) can be done at the prompt:

resfilter mydata.fin res1 res2 > outdata.fin

Where res1 and res2 are the two resolution limits to be applied to the data.

Following the UNIX philosophy, the reflections outputted by the program go to the stdout so they can be written to a file or piped into other UNIX routines such as sort or awk or grep. The program can also accept files from stdin if the file is specified as "-". For example:

sort -n mydata.fin | resfilter - 20.0 4.0 > outdata.fin

The log of the step is reported to the stderr so it can be examined for errors. For example:

RESFILTER ******************************************************
                                          v 1.0   C. Putnam 1997

resfilter> Opening XtalView crystal file.

resfilter> Calculating crystal constants.

Crystal Volume:        1000000.000 Angstroms^3
Direct Space Cell:     100.000 100.000 100.000  90.000  90.000  90.000
Reciprocal Space Cell:   0.010   0.010   0.010  90.000  90.000  90.000

resfilter> Setting resolution limits:  minimum = 20.0  maximum = 4.0

resfilter> Opened file mydata.fin.

resfilter> Accepted 3454 reflections.
resfilter> Rejected 28344 reflections above high resolution.
resfilter> Rejected 5 reflections below low resolution.
resfilter> Rejected 0 reflections with incomplete lines.


****************************************************** RESFILTER

XtalView Reflection File Format

XtalView reflection files (*.fin, *.df, *.phs) are "unformatted". Space-deliminated columns contain h,k,l and 4-8 columns of values. .fin files are of the format H K L F1 SIGF1 F2 SIGF2 (unmeasured are marked with F=0.00 and SIGF=9999.00). .df, double-fin, are of the format H K L F1 SIGF1 F2 SIGF2 F3 SIGF3 F4 SIGF4. .phs files have the columns H K L FO FC PHS or H K L FO FOM PHS. For example the following is a exerpt of a .fin file:

   0   0   8  1084.88    50.04     0.00  9999.00
   0   0  12  2850.27   121.67     0.00  9999.00
   0   0  14  1675.91    67.00     0.00  9999.00

Setting up the Environment

This should be trivial for XtalView users...

In order to perform resolution-based rejection of data, the program needs to understand some crystallography. Specifically, the program needs the unit cell parameters that describe the crystal. The XtalView convention is to place the crystal information into a file located at the directory pointed to by the environment variable CRYSTALDATA. The file to be used is specified by the environment variable CRYSTAL. For example:

setenv CRYSTALDATA /home/cdputnam/crystals
setenv CRYSTAL testxtal

For this to work, a text file /home/cdputnam/crystals/testxtal must exist. The format for the crystal information file is fairly simple. An example should suffice:

name Test Crystal
cell 100.0 100.0 100.0   90.0 90.0 90.0
spgp p212121
symm  x,y,z; 1/2-x,-y,z+1/2; x+1/2,1/2-y,-z; -x,y+1/2,1/2-z.

A Final Word

As always, I've only extensively tested this program against many of the things that I do regularly so there are potentially a number of bugs that are creeping about. I've written the program to be very robust so that it should survive even fairly pathological cases, but I've only checked a finite number of these. If you run into any problems, feel free to e-mail me and depending on the problem (and my schedule) I might crack open the code and fix them.

Praise and requests for options that would be useful are also welcome.

Chris Putnam
cdputnam@scripps.edu
Graduate Student
The Scripps Research Institute

Last Updated: 4/21/99