After executing the modeller compare.py command I noticed that the resolution is incorrectly listed in the log file.
as an example the resolution for the 1GV0.pdb this is not 2.0 but 2.5 REMARK 2 RESOLUTION. 2.5 ANGSTROMS.
Do I interprete this value incorrectly?
.------------------------------------------ 1a5zA @2.0 62.0000 | .------------------------------------------------ 1ez4B @2.0 69.3750 | | .----------------------------------------- 2a92A @2.0 61.0000 | | | .------------------------------------------- 2ewdA @2.0 62.7500 | | | | .--- 1guzA @2.0 13.0000 | | | .-------------------------------------------------------- 1gv0A @2.0 78.4375 | | .---------------------------- 2cmdA @1.0 44.0000 | | .---------------------------------------------------------- 2dfdA @1.0 81.8516 | | .----------- 1b8pA @1.9 23.0000 | | | .------------------------------------- 3d5tA @2.0 55.5000 | | | .-------------------------------------------------------- 1civA @2.0 79.0000 | | .------------------------------------------------------------ 3fi9A @1.0
many thanks, Marc De Maeyer Leuven Belgium
Marc De Maeyer wrote: > After executing the modeller compare.py command I noticed that the > resolution is incorrectly listed in the log file. > > as an example the resolution for the 1GV0.pdb this is not 2.0 but 2.5 > REMARK 2 RESOLUTION. 2.5 ANGSTROMS. > > Do I interprete this value incorrectly?
You're absolutely right. Modeller expects PDB v2 format when parsing the RESOLUTION line from PDB files, and does not understand the new-style (remediated, v3) format. In v2 format, the resolution is expected to be in columns 23-27, while in v3, it is in columns 24-30. So in this case, Modeller reads ' 2' from your PDB file rather than ' 2.5' which explains the behavior you're seeing.
This is, of course, a bug. I've fixed it for the next Modeller release. As a workaround for now, you could manually edit your PDB files and delete three spaces from between RESOLUTION. and the actual value.
Ben Webb, Modeller Caretaker
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Marc De Maeyer -
Modeller Caretaker