dssr stdin

[zcx]

Can x3dna-dssr uses stdin for input? The following flags apparent do not work (yet):
cat file.pdb | x3dna-dssr -i=stdin
cat file.pdb | x3dna-dssr -i=-
If there is source code for dssr, I am happy to help with implementing such a feature.

[xiangjun]

Can x3dna-dssr uses stdin for input?

Yes.

The following flags apparent do not work (yet):
cat file.pdb | x3dna-dssr -i=stdin
cat file.pdb | x3dna-dssr -i=-

When piping input to DSSR, users must specify the file format via --format. Assuming file.pdb is in PDB format, the following should work:

Code: [Select]

cat file.pdb | x3dna-dssr -i=stdin --format=pdb
cat file.pdb | x3dna-dssr -i=- --format=pdb
Please have a try and report back how it goes.

Best regards,

Xiang-Jun

[xiangjun]

If there is source code for dssr, I am happy to help with implementing such a feature.

Regarding the availability of DSSR source code, please see the thread "Source distribution/Linux packaging" (http://forum.x3dna.org/rna-structures/source-distributionlinux-packaging/). DSSR 2.0 (to be released) will be formally licensed by Columbia University.

There are open source alternatives to DSSR, including MC-Annotate, RNAView, and FR3D, that may better suit your needs.

BTW, does the suggested method work? As a general principle, the user who starts a thread is expected to provide a summary, or at least a simple yes/no response. Other viewers of the thread will benefit from your effort. It will also give me more incentive to answer your future DSSR-related questions (if any).

Best regards,

Xiang-Jun

[zcx]

Yes, stdin works, thank you. It will be good if this feature is documented in the program.