PSI Website Information: If you see this message, then either your browser doesn't support Javascript or Javascript is disabled. You might want to enable it for this site?

Protein Crystallography Home Page

Updated:
12.02.2008

Software at the PX beamlines

Several software packages are available at the beamlines for

data processing
phase determination.

The packages are installed on a central Linux server. Templates for the most important packages can be found
under the directory /exchange/mx/templates.

X06SA: slspx1, slspx2, slsmpi1 to slsmpi4 serve as data processing and analysis computers.

X10SA: slspx3 and slspx4 serve as data processing and analysis computers.

Please note, that it is recommended to determine the centre coordinates via direct beam.

More software

It may be useful to have a look at the CCP4 user community wiki.

labelit indexing software

Usage: Put two testshots (preferably 90deg apart) in a directory and type > labelit.index at the prompt. This will index and integrate the testshots giving a list of the best/most probable solutions. To create a start up script for mosflm for one of these solutions type > labelit.mosflm_script X at the prompt. Where X is the number of the solution you want to look at.

The user guide is available here: labelit user guide.

imosflm

Usage: Cut and paste the following three lines into a shell. Typing imosflm should then start imosflm.
export MOSFLM_WISH=/exchange/mx/ActiveTcl8.4.12/bin/wish8.4
export MOSFLM_EXEC=/exchange/mx/imosflm-new/ipmosflm
alias imosflm='/exchange/mx/imosflm-new/src/imosflm'

The user guide is available here: imosflm user guide.
Note:
Direct beam images (image_000.img) WILL cause imosflm to crash. Give image 000 a different filename, ie image_DB_000.img, before loading image 001 and it *should* work.

Some useful scripts

ebind

Calculates electron binding energies, i.e., retrieves the energy for (atom)/(edge) OR
lists all possible edges that are within (margin) (default=100 eV) of (energy) as a triplet of (energy,atom,edge).

Usage: (type "ebind usage" to find out...)

ebind (atom) [(edge)]
ebind (energy) [(margin)]

pdbget

Downloads a PDB file in compressed format and uncompresses it afterwards so in the end you end up with 1zac.pdb.

Usage: pdbget 1zac