Precision of fragment files
- Jirsak
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8 years 1 month ago #102
by Jirsak
Dear community,
is there any possibility to increase precision for generating coordinates in fragment files? Rounding to third decimal distorts geometry of rigid fragments. It is not a big deal, relative deviation of angles and lengths is about 0.0001, but still it is an unnecessary source of error.
Thanks, Jan
is there any possibility to increase precision for generating coordinates in fragment files? Rounding to third decimal distorts geometry of rigid fragments. It is not a big deal, relative deviation of angles and lengths is about 0.0001, but still it is an unnecessary source of error.
Thanks, Jan
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- ryangmullen
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8 years 1 month ago #103
by ryangmullen
Hi Jan,
I can look into that. At what stage in the process are your fragment files being rounded? Is it when you use the python script mcfgen.py, when you are generating the library of fragment conformations, or at some other stage?
Ryan
I can look into that. At what stage in the process are your fragment files being rounded? Is it when you use the python script mcfgen.py, when you are generating the library of fragment conformations, or at some other stage?
Ryan
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8 years 4 weeks ago - 8 years 4 weeks ago #105
by ryangmullen
Hi Jan,
It doesn't look like that will be a simple edit. In the current workflow of library_setup.py, the supplied .cml file is converted to a .pdb file. The .pdb format is independent of Cassandra and fixed at 80-characters per line, with only 3 decimal points allotted for coordinate precision.
The .cml to .pdb conversion is certainly not necessary, so if you (or any helpful Cassandra user) wants to edit library_setup.py and send us the new code, we can incorporate that into future releases.
Ryan
It doesn't look like that will be a simple edit. In the current workflow of library_setup.py, the supplied .cml file is converted to a .pdb file. The .pdb format is independent of Cassandra and fixed at 80-characters per line, with only 3 decimal points allotted for coordinate precision.
The .cml to .pdb conversion is certainly not necessary, so if you (or any helpful Cassandra user) wants to edit library_setup.py and send us the new code, we can incorporate that into future releases.
Ryan
Last Edit: 8 years 4 weeks ago by ryangmullen.
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