ARCIMBOLDO-LITE installations at NSC


Directory list:

VersionDescription
1.0.10 ARCIMBOLDO-LITE v. 1.0.10

Level of support

Tier 3 NSC will not be able to help you much with this program, either because we lack the in-house experience, or because it is a test installation. In general, these types of installations are untested, and will not be updated unless you send a request to NSC.

Please see the page describing our software support categories for more information.
You can also contact support@nsc.liu.se for further information.

ARCIMBOLDO-LITE is a software for crystallographic ab initio protein solution. The LITE version runs on one compute node only.

Developer’s homepage: http://chango.ibmb.csic.es/arcimboldo_lite

The ARCIMBOLDO-LITE installations are generally maintained by Johan Raber or Torben Rasmussen. Please contact NSC Support if you have any questions or problems.

How to run

The easiest way to run ARCIMBOLDO-LITE is to create a small batch script and submit it to the queue.

Example batch script:

#!/bin/bash
#
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --exclusive
#SBATCH --account=snicxxx-yyy

module load arcimboldo_lite/1.0.10

job=jobname
ARCIMBOLDO_LITE ${job}.bor > ${job}.log

NOTE: You need to change jobname to the name of your .bor file.

The script is then submitted to the queue with:

$ sbatch name_of_script

NOTE: You need to change name_of_script to whatever name you have given your script.

Remember to change the account string, snicxxx-yyy, to the string for the project that you want to charge the job to. You can find the account string in NSC Express or using the projinfo command. If you are only included in one project, then you don’t need this line at all.

Example input file for ARCIMBOLDO_LITE (i.e. jobname.bor):

[ARCIMBOLDO]
shelxe_line = -m30 -v0 -a3 -t20 -q -s0.55
helix_length = 14
sigf_label = SIGF
molecular_weight = 22000
name_job = example
f_label = F
fragment_to_search = 2
number_of_component = 1
identity = 0.2

[LOCAL]
# Requires Phaser version 2.5.6
path_local_phaser: phenix.phaser
path_local_shelxe: shelxe

[GENERAL]
working_directory = path-to-work-dir
mtz_path = %(working_directory)s/data.mtz
hkl_path = %(working_directory)s/data.hkl

NOTE: You need to change example and data to whatever is suitable for your job. You also need to change path-to-work-dir to the name of the directory with your data files. If the input file (jobname.bor) and the data files are in the same directory, then path-to-work-dir can simply be . instead of an explicit directory name.

To get an overview of the available input parameters, do:

$ module load arcimboldo_lite/1.0.10
$ ARCIMBOLDO_LITE -b

You can also consult the ARCIMBOLDO manual.

Disclaimer

NSC takes no responsibility for the correctness of results produced with the binaries! Hence, always evaluate the binaries against known results for the systems and properties you are investigating before using the binaries for production jobs.