Dali on Biowulf
The three-dimensional co-ordinates of each protein are used to calculate residue - residue distance matrices.
References:
- Holm J. Using Dali for protein structure comparison. Methods Mol. Biol. 2112, 29-42
Documentation
Important Notes
- Module Name: dali (see the modules page for more information)
- /singlethreaded and MPI
- Environment variables set
- DALI_HOME
- Example files in $DALI_HOME/example/
- Reference data in /pdb/
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load dali [user@cn3144 ~]$ cp /pdb/pdb/pp/pdb1ppt.ent.gz . [user@cn3144 ~]$ cp /pdb/pdb/bb/pdb1bba.ent.gz . [user@cn3144 ~]$ import.pl --pdbfile pdb1ppt.ent.gz --pdbid 1ppt --dat ./ [user@cn3144 ~]$ import.pl --pdbfile pdb1bba.ent.gz --pdbid 1bba --dat ./ [user@cn3144 ~]$ dali.pl --pdbfile1 pdb1ppt.ent.gz --pdbfile2 pdb1bba.ent.gz --dat1 ./ --dat2 ./ --outfmt "summary,alignments" [user@cn3144 ~]$ cat mol1A.txt # Job: test # Query: mol1A # No: Chain Z rmsd lali nres %id PDB Description 1: mol2-A 3.6 1.8 33 36 39 MOLECULE: BOVINE PANCREATIC POLYPEPTIDE; # Pairwise alignments No 1: Query=mol1A Sbjct=mol2A Z-score=3.6 DSSP LLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHLLlll Query GPSQPTYPGDDAPVEDLIRFYDNLQQYLNVVTRhry 36 ident | | |||| | | | | | || Sbjct APLEPEYPGDNATPEQMAQYAAELRRYINMLTRpry 36 DSSP LLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHLLlll [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. dali.sh). For example:
#!/bin/bash set -e module load dali import.pl --pdbfile pdb1ppt.ent.gz --pdbid 1ppt --dat ./ import.pl --pdbfile pdb1bba.ent.gz --pdbid 1bba --dat ./ dali.pl --pdbfile1 pdb1ppt.ent.gz --pdbfile2 pdb1bba.ent.gz --dat1 ./ --dat2 ./ --outfmt "summary,alignments"
Submit this job using the Slurm sbatch command.
sbatch dali.sh
MPI batch job
In certain circumstances, dali can be accelerated using MPI. To do so, include --NP $SLURM_NTASKS with the command, and submit the job using --ntasks #, where # is the number of MPI tasks requested.
... dali.pl --np $SLURM_NTASKS ... ...
Submit this job using the Slurm sbatch command.
sbatch [--ntasks=#] dali.sh