Comments (5)
sludtke42
commented on August 27, 2024
There is some redundancy here. The main program we use for converting a PDB to a density is e2pdb2mrc.py, which has been maintained and updated over the years. I'm not sure any more (you can check git if you like) who even wrote e2pdb2em... You probably won't get an answer by posting here, since the author likely is not in this Github group.
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commented on August 27, 2024
Maybe I wrote it? There is sxpdb2em.py, so maybe there is some relation.
Regards,
Pawel
… On Feb 10, 2017, at 12:04 AM, Steve Ludtke ***@***.***> wrote:
There is some redundancy here. The main program we use for converting a PDB to a density is e2pdb2mrc.py, which has been maintained and updated over the years. I'm not sure any more (you can check git if you like) who even wrote e2pdb2em... You probably won't get an answer by posting here, since the author likely is not in this Github group.
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crimsonlander
commented on August 27, 2024
I have another question: there are only few atoms defined in atomdefs in both e2pdb2mrc.py and e2pdb2em.py. Are there any specific reason to ignore other atoms?
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sludtke42
commented on August 27, 2024
Not really. They get added as needed. Note that the list includes things like "W" for water, which exists in some PDB files, or "HO" which is a hydrogen+oxygen as one "atom". Aside from the odd coordinated metal atom, the defined atoms here cover biomolecules pretty completely. We don't like to add new ones without having a representative file to test on, and nobody using it has been doing anything where the missing atoms were worth considering.
Pawel, I think this may be one you inherited from someone here rather than writing it from scratch, but you're welcome to answer his question if you like :^)
… On Feb 10, 2017, at 12:17 AM, crimsonlander ***@***.***> wrote:
I have another question: there are only few atoms defined in atomdefs in both e2pdb2mrc.py and e2pdb2em.py. Are there any specific reason to ignore other atoms?
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Steven Ludtke, Ph.D.
Professor, Dept of Biochemistry and Mol. Biol. (www.bcm.edu/biochem)
Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu)
Co-Director CIBR Center (www.bcm.edu/research/cibr)
Baylor College of Medicine
[email protected]
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commented on August 27, 2024
Hi
I finally had a chance to look at it. It is indeed something I was messing it and I would stronglysuggest to remove it from the system.
Pawel.
Pawel, I think this may be one you inherited from someone here rather than writing it from scratch, but you're welcome to answer his question if you like :^)
… On Feb 10, 2017, at 12:17 AM, crimsonlander ***@***.***> wrote:
I have another question: there are only few atoms defined in atomdefs in both e2pdb2mrc.py and e2pdb2em.py. Are there any specific reason to ignore other atoms?
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Professor, Dept of Biochemistry and Mol. Biol. (www.bcm.edu/biochem)
Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu)
Co-Director CIBR Center (www.bcm.edu/research/cibr)
Baylor College of Medicine
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Related Issues (20)
- lacks a type converter from python utf string or bytes to std::string
- GPU too old HOT 4
- Questionable detection of 8-bit-packed mode from MRC headers HOT 4
- Useless code in libEM/emdata_transform.cpp
- Incorrect convolution processing under some circumstances HOT 1
- Bogus method wrappers HOT 5
- No rule to make target `/usr/lib64/libGLX.so' HOT 11
- New release supporting recent boost.python HOT 1
- Status of tomo in devel? HOT 4
- How to determine pixel width (Angstrom) when calculating FSC using e2proc3d? HOT 2
- corner cases of Transform class HOT 7
- Not defined variable in e2spt_tempmatch.py HOT 4
- e2ctf_auto in lores mode does not produce particle sets
- RuntimeError: std::exception caused by xform_align_nbest HOT 1
- libboost_python37.so.1.76.0: cannot open shared when test e2speedtest.py HOT 1
- cannot find fftw3d and fftw3f header files. HOT 13
- Dependency installation issue HOT 1
- substitution for runpar in eman2 HOT 3
- instructions to install to existing anaconda HOT 5
- Installation through conda HOT 1
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