On Thursday 13 May 2004 06:30 am, Stefano Ciurli wrote:
Hello,
just a thought: wouldn't it be nice to be able to read the feff.inp file directly into a simple molecular graphics program in order to see if the used coordinates contain any error? Maybe it is possible already and I am not aware of it. I understand that the program is mainly used by material scientists, but for us working with biological samples of metalloproteins it would be nice. Another suggestion: I know that Excurve is able to treat the histidine rings as a unity, and when performing the fit that program is able to maintain the ring rigid while fitting the distance between the metal and the imidazole ring of the histidine. How can I do that simply using your suite?
Stefano
The notion of having a viewer of ball-and-stick images built into the software is not a new one. Indeed that's part of Cerius and, as I recall, EXAFSPAK does that as well. Maybe others, too. I agree that it's an excellent idea and I certainly understand the value of it. But I don't plan on working on such a tool any time soon. Then Mauro wrote:
With tkatoms you can save your feff.inp in .pdb format and open it with RasMol.
This is correct. Atoms already converts crystallographic data into pdb (and other formats). This can be done with command line atoms, TkAtoms, or Artemis. (And WebAtoms, in principle. It would be easy to do if it doesn't already, which I can't remember one way or the other.) Indeed, any version of atoms can be coerced into writing just about any file for use with a molecule viewer just by creating an appropriate template file. Then Stafano wrote:
it would be nice to be able, with Tkatoms, to read coordinates from pdb files and output feff.inp files... but maybe this will come.
That question is the exact opposite of your original question. Indeed reading pdb files is one of my eventual goals for Artemis. One could jump-start that effort by showing me how it's done, preferably (but not necessarily) in perl. In any case, it's not rocket science to make a feff.inp from a PDB. Look at page 19 of this for an example using a very small PDB: http://cars9.uchicago.edu/xafs/NSLS_EDCA/Sept2002/Ravel.pdf And remember, Feff does NOT require the absorber to be at (0,0,0). B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/