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Thanks a lot for a great software !Thanks for using 3DNA and for your nice words about the software.
I've found that rebuild utility accepts 'stdin' option for input e.g.I can reproduce the problem you reported here. You may take it as a bug or inconsistency in 3DNA's handling of 'stdin' input. Internally, the parameter input file is read twice: the first time for the number of base pairs to allocate the data structure, and the second time to fill in the contents. That's why 'stdin' does not work. I will try to fix this issue in the coming release of 3DNA v2.2. In the meantime, just remember to always use an explicit parameter file.
cat custom_step.par | rebuild -atomic stdin gorgeous_structure.pdb
But it always fails with :
"error reading parameter file: step or helical option"
but rebuild -atomic custom_step.par gorgeous_structure.pdb works just fine
Am I doing something wrong or is that a bug?
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.