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Questions and answers => DNA/RNA-protein interactions (SNAP) => Topic started by: jms89 on September 24, 2016, 06:18:48 pm

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Title: --cleanup option doesn't work
Post by: jms89 on September 24, 2016, 06:18:48 pm

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.

Title: Re: --cleanup option doesn't work
Post by: xiangjun on September 24, 2016, 06:29:21 pm

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

Title: Re: --cleanup option doesn't work
Post by: jms89 on September 25, 2016, 06:13:43 pm

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.

Title: Re: --cleanup option doesn't work
Post by: xiangjun on September 25, 2016, 06:32:27 pm

The --cleanup option in SNAP should have already done what you suggested, as shown below:

Code: [Select]

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
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

Title: Re: --cleanup option doesn't work
Post by: jms89 on September 26, 2016, 04:26:10 pm

Here's the exact output and behaviour I get.

Code: [Select]

$ 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

As you can see, most of the PDB files are left behind. I'm using the linux binary on linux Mint 17.

Title: Re: --cleanup option doesn't work
Post by: xiangjun on September 26, 2016, 04:34:35 pm

What you saw with x3dna-snap --cleanup should not happen, as demonstrated with my previous response. I am puzzled.

Could you try SNAP on another Linux distribution, e.g., Ubuntu, to see if you still get the same issue? Better yet, run SNAP on Mac OS X and Windows to see if you get the same result as you did on linux Mint 17.

I do not have access to linux Mint 17 yet, but I will try to install one to reproduce the issue.

Xiang-Jun

Title: Re: --cleanup option doesn't work
Post by: xiangjun on September 28, 2016, 12:31:12 am

It is bug, which has been fixed in SNAP beta-r09-2016sept28. Please try the new release and let me know if you have any further problems.

Thanks for reporting!

Xiang-Jun

Title: Re: --cleanup option doesn't work
Post by: jms89 on October 11, 2016, 07:25:15 pm

Yup, everything seems to be fixed. Thanks for the prompt response!

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University