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Questions and answers > DNA/RNA-protein interactions (SNAP)
--cleanup option doesn't work
jms89:
Hello, when using the linux binary, the --cleanup option doesn't work. Instead of outputting the -output='filename' file, and removing all the generated .pdb files, no output is produced at all. Surely this is not the intended behavior.
Thanks.
xiangjun:
I don't quite understand your point. The --cleanup option is indeed intended to clean up output files with common names. What's wrong? Please provide a minimal reproducible example so I can understand your point better.
Best regards,
Xiang-Jun
jms89:
I see - two things were unclear.
First, I thought you could run x3dna-snap in the following way:
`x3dna-snap -i=[inputfile] -o=[outputfile] --cleanup`
which, *I assumed* would produce the output files, minus whatever --cleanup removed. From your response it seems that the intended use would instead be,
`x3dna-snap -i=[inputfile] -o=[outputfile]`
`x3dna-snap --cleanup`
I was hoping that the --cleanup option would also remove ALL the generated .pdb files, including the ones which show the specific residue-nucleotide interactions. Maybe this could be considered for a future release?
Thanks for the response.
xiangjun:
The --cleanup option in SNAP should have already done what you suggested, as shown below:
--- Code: ---tmp [536] mkdir snap-cleanup
tmp [537] cd snap-cleanup/
/Users/xiangjun/tmp/snap-cleanup
snap-cleanup [538] ls
snap-cleanup [539] cp ../1oct.pdb .
snap-cleanup [540] ls
1oct.pdb
snap-cleanup [541] x3dna-snap -i=1oct.pdb -o=1oct-snap.out
Processing file '1oct.pdb' [1oct]
total number of base pairs: 14
total number of helices: 1
Time used: 00:00:00:00
snap-cleanup [542] ls
1oct-snap.out A-gln.pdb AT-arg.pdb AT-leu.pdb C-arg.pdb G-thr.pdb T-arg.pdb T-ser.pdb snap-dssp.txt snap-pseudoPairs.pdb
1oct.pdb A-ser.pdb AT-asn.pdb AT-ser.pdb C-thr.pdb GC-arg.pdb T-cys.pdb T-thr.pdb snap-helices.pdb snap-pseudoStacks.pdb
A-arg.pdb A-thr.pdb AT-cys.pdb AT-thr.pdb G-arg.pdb GC-ser.pdb T-gln.pdb T-val.pdb snap-pairs.pdb snap-sugarAA.pdb
A-asn.pdb A-val.pdb AT-gln.pdb AT-val.pdb G-ser.pdb GC-thr.pdb T-leu.pdb snap-baseAA.pdb snap-po4AA.pdb
snap-cleanup [543] x3dna-snap --cleanup
done with cleaning up files.
Time used: 00:00:00:00
snap-cleanup [544] ls
1oct-snap.out 1oct.pdb
--- End code ---
What version of SNAP are you using? Please repeat my above step, and report back if you can reproduce what I got.
Thanks for trying out SNAP!
Xiang-Jun
jms89:
Here's the exact output and behaviour I get.
--- Code: ---$ ls
1jgg.pdb
$ x3dna-snap -i=1jgg.pdb -o=1jgg-snap.out
Processing file '1jgg.pdb' [1jgg]
total number of base pairs: 10
total number of helices: 1
Time used: 00:00:00:00
$ ls
1jgg.pdb AT-asn.pdb A-val.pdb snap-dssp.txt T-asn.pdb
1jgg-snap.out AT-gln.pdb C-tyr.pdb snap-helices.pdb T-gln.pdb
A-arg.pdb AT-lys.pdb G-arg.pdb snap-pairs.pdb T-lys.pdb
A-asn.pdb AT-met.pdb GC-arg.pdb snap-po4AA.pdb T-met.pdb
A-gln.pdb AT-tyr.pdb GC-tyr.pdb snap-pseudoPairs.pdb T-tyr.pdb
A-met.pdb AT-val.pdb G-tyr.pdb snap-sugarAA.pdb T-val.pdb
AT-arg.pdb A-tyr.pdb snap-baseAA.pdb T-arg.pdb
$ x3dna-snap --cleanup
done with cleaning up files.
Time used: 00:00:00:00
$ ls
1jgg.pdb A-met.pdb AT-met.pdb C-tyr.pdb T-arg.pdb T-tyr.pdb
1jgg-snap.out AT-arg.pdb AT-tyr.pdb G-arg.pdb T-asn.pdb T-val.pdb
A-arg.pdb AT-asn.pdb AT-val.pdb GC-arg.pdb T-gln.pdb
A-asn.pdb AT-gln.pdb A-tyr.pdb GC-tyr.pdb T-lys.pdb
A-gln.pdb AT-lys.pdb A-val.pdb G-tyr.pdb T-met.pdb
$ x3dna-snap --version
SNAp: a program for the characterization of three-dimensional
Structures of Nucleic Acid-Protein complexes
beta-r08-2016jun02, by xiangjun@x3dna.org
This program is being actively maintained and developed. As always,
I greatly appreciate your feedback! Please report all SNAP-related
issues on the 3DNA Forum (forum.x3dna.org). I strive to respond
*promptly* to *any questions* posted there.
Time used: 00:00:00:00
--- End code ---
As you can see, most of the PDB files are left behind. I'm using the linux binary on linux Mint 17.
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.