Bruce, Demeter is a wonderful program and the GUI is beautiful! I am old enough to remember the time when we were doing things by commands. I am also rusty and have not done EXAFS in years. Is there an easy way to convert a PDB file into a feff.inp file? I am working on a protein with a [4Fe-4S] cluster. I have generated a PDB file with just the iron-sulfur cluster in it. File attached. I am having a hard time with ATOMS, even when I use a single Fe atom placed at the origin. Thanks, - Eva
Is there an easy way to convert a PDB file into a feff.inp file? I am working on a protein with a [4Fe-4S] cluster. I have generated a PDB file with just the iron-sulfur cluster in it. File attached. I am having a hard time with ATOMS, even when I use a single Fe atom placed at the origin.
Eva, See the "Molecule" section of the "noxtal.pdf" file at https://github.com/bruceravel/XAS-Education/downloads B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter
Hi, I'd like to say a few more words about this. My answer to Eva was not wrong and will help her over her immediate hurdle. But it was not a very complete or satisfying answer to her question. The problem of converting a PDB file to a feff.inp file is a common one. In fact, there are a lot of ways of specifying the structure of a molecule -- PDB is just one common way of doing so. There is an interesting tool out there called Open Babel http://openbabel.org/wiki/Main_Page OB is, among other things, a framework for converting between different ways of specifying a molecule. For example, OB solves the problem of converting between PDB and Chemical Markup Language or any of dozens of other formats. It's very cool. The people who wrote OB did a really good job of making it easy to add new file formats. The various file formats are handled by small pieces of C++ code -- one for importing and one for exporting. Writing those converters for Feff has long been on my list of things to do. Once that is done, it would be a simple matter to write an OB interface for Artemis, allowing you to import anything that OB recognizes as your feff input data. Wouldn't that be great?! This is something that somoeone with a bit of C++ knowledge could do to contribute to the Ifeffit project. I don't think it would take very long and it would have a profound impact on how people use Artemis. B On Monday, April 23, 2012 09:20:21 am Bruce Ravel wrote:
Is there an easy way to convert a PDB file into a feff.inp file? I am working on a protein with a [4Fe-4S] cluster. I have generated a PDB file with just the iron-sulfur cluster in it. File attached. I am having a hard time with ATOMS, even when I use a single Fe atom placed at the origin.
Eva,
See the "Molecule" section of the "noxtal.pdf" file at
https://github.com/bruceravel/XAS-Education/downloads
B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter
participants (2)
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Bruce Ravel -
Vanamee, Eva