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

• Dali Main Site

• Module Name: dali (see the modules page for more information)
• /singlethreaded and MPI
• Environment variables set
  • DALI_HOME
  • DALI_AF
• Example files in $DALI_HOME/example/
• Reference data in /pdb/ and $DALI_AF

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 ~]$

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

In certain circumstances, dali can be accelerated using MPI. To do so, include --NP $SLURM_NTASKS with the command, and submit the job using -n # -N 1 , where # is the number of MPI tasks requested. MPI only works on a single node, so # must be less than 56. If # is greater than 8, you must include -p multinode.

...
dali.pl --np $SLURM_NTASKS ...
...

Submit this job using the Slurm sbatch command.

sbatch -n 32 -N 1 -p multinode dali.sh

Running with the AlphaFold database:

#!/bin/bash
module load dali
dali.pl \
  --hierarchical \
  --oneway \
  --BLAST_DB ${DALI_AF}/Digest/AF.fasta \
  --pdbfile1 ${DALI_HOME}/example/my.pdb \
  --db ${DALI_AF}/Digest/HUMAN.list \
  --repset ${DALI_AF}/Digest/HUMAN_70.list \
  --dat1 ./ \
  --dat2 ${DALI_AF}/DAT/ \
  --title "my search" \
  --np ${SLURM_NTASKS}

Type ls ${DALI_AF}/Digest to see all the lists.