make_rot_lib issue

[Anonymous]

I am going through the tutorial on how to add the NCAA’s to Rosetta
on the example of ornithine. I managed to create the param file, and now
I am trying to create the rotamer library by using make_rot_lib application.

I noticed a strange behavior of the program for some values of phi and psi
angles. It works fine for the negative angles, but for some combinations of
positive angles I get errors. For instance for phi=40, psi=60, everything works fine,
but for phi=60, psi=40 I get a pdb file with two zeros in name instead of 60 and 40:
C40_0_0_INP_CHI_0_0_0_MIN_CHI_0_0_0_final.pdb
and the rotlib file C40_0_0_bbdep.rotlib

The content of the rotlib file has zeros instead of phi psi angles:
C40 0 0 9999 3 3 2 0 0.372388 -57.1 179.4 -179.7 0.0 7.4 12.1 13.4 0.0
C40 0 0 9999 3 2 1 0 0.266511 -63.8 -179.2 -67.7 0.0 5.8 14.4 9.7 0.0
C40 0 0 9999 3 2 3 0 0.210074 -58.0 179.6 62.9 0.0 8.2 12.6 8.7 0.0
C40 0 0 9999 3 2 2 0 0.148685 -61.8 -68.7 179.4 0.0 6.2 11.0 10.5 0.0
C40 0 0 9999 3 3 3 0 0.002341 -158.0 74.3 -176.8 0.0 6.0 10.3 9.9 0.0
C40 0 0 9999 3 3 1 0 0.000000 61.2 156.5 -179.8 0.0 3.0 4.0 13.3 0.0
C40 0 0 9999 1 3 1 0 0.000000 0.0 0.0 0.0 0.0 30.1 30.1 30.1 0.0
C40 0 0 9999 1 3 2 0 0.000000 0.0 0.0 0.0 0.0 30.1 30.1 30.1 0.0
C40 0 0 9999 1 3 3 0 0.000000 0.0 0.0 0.0 0.0 30.1 30.1 30.1 0.0
…

While for phi=40, psi=60:
C40 40 60 9999 1 2 2 0 0.333776 -60.1 179.8 -179.9 0.0 7.9 12.8 13.2 0.0
C40 40 60 9999 1 2 1 0 0.292596 -62.6 -178.6 -63.2 0.0 9.2 12.8 9.5 0.0
C40 40 60 9999 1 2 3 0 0.177207 -60.3 179.9 61.3 0.0 7.9 11.6 7.5 0.0
C40 40 60 9999 1 1 2 0 0.119100 -64.3 -65.5 -179.4 0.0 6.2 8.7 10.4 0.0
C40 40 60 9999 1 1 1 0 0.045107 -64.4 -68.6 -64.0 0.0 6.8 10.0 9.7 0.0
…

It seems strange that this behavior depends on the values of the angles.
Any ideas how to solve this issue? I have attached the following files

C40_0_0_bbdep.rotlib.txt (output rotlib file)
C40_0_0_INP_CHI_0_0_0_MIN_CHI_0_0_0_final_pdb.txt (output pdb file)
C40_rot_lib_options_60_40_in.txt (input option file)
C40_rot_lib_options_60_40_log.txt (the log file)

Here’s the command I used:
./make_rot_lib.static.linuxgccrelease -database rosetta_database/ -rot_lib_options_file C40_rot_lib_options_60_40.in > C40_rot_lib_options_60_40.log

Thanks for help

Jarek

[Anonymous]

I’ve forwarded this to Doug for comment.

[Anonymous]

I can reproduce these errors in the 3.4 release but not in the current Rosetta trunk. The make_rot_lib code and ornithine params have undergon very feww changes since the last release. It is not immediately obvious to me what is going on.

[Anonymous]

Hmmm, since I dont have access to the current developer’s version of Rosetta, I’m stuck.
Could you maybe point out at what places in the code make_rot_lib is undergoing changes?

[Anonymous]

make_rot_lib itself has had only cosmetic/insignificant changes (and a change that I think introduces a bug…). I attached a diff and patchfile but I don’t think it will work. I don’t know where lower in the code to look for changes.

The 3.5 release is ready (and has been for a month) – it is caught up in getting the online manual auto-generation working. I expect it to release soon.

[Author]

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