I can't seem to get the thermal ellipsoids to work. I have a number of .cif files that are all perfectly good files (have been cif-checked) and all of which I know for a fact have anisotropic data as I can get thermal ellipsoids to display from these files in other programs like Diamond (which we are trying to move away from). But any time I select an atom or group of atoms and use either the "aniso" command or the "Show Thermal Ellipsoids" dialogue box I just get: "No atoms chosen had anisotropic information." This is just not true though, I can open up the .cif files in question and see the anisotropic data listed for the given atoms with my own two eyes. Any thoughts? I am probably doing something immensely stupid, that is usually the case with such situations. --Nat (Nathaniel Sherden) California Institute of Technology Department of Chemistry
Hi Nat, You are not doing anything wrong -- it may be that you need a newer version of Chimera. For a while Chimera only read the anisotropic B-factor information from PDB files. I believe that is true for version 1.4, but if you get version 1.5 (in the daily builds part of the download page) it should work with CIF anisotropy information too. I just tried a CIF file of my own with both these versions. Guess this should be mentioned in the "what's new" release notes, but I didn't know until now that the problem had been fixed! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 30, 2010, at 1:19 AM, sherden@caltech.edu wrote:
I can't seem to get the thermal ellipsoids to work. I have a number of .cif files that are all perfectly good files (have been cif-checked) and all of which I know for a fact have anisotropic data as I can get thermal ellipsoids to display from these files in other programs like Diamond (which we are trying to move away from). But any time I select an atom or group of atoms and use either the "aniso" command or the "Show Thermal Ellipsoids" dialogue box I just get: "No atoms chosen had anisotropic information." This is just not true though, I can open up the .cif files in question and see the anisotropic data listed for the given atoms with my own two eyes.
Any thoughts? I am probably doing something immensely stupid, that is usually the case with such situations.
--Nat (Nathaniel Sherden)
California Institute of Technology Department of Chemistry
Okay, thanks, I'll have to go check out the daily builds and then get back to you on this. --Nat (Nathaniel Sherden)
Hi Nat, You are not doing anything wrong -- it may be that you need a newer version of Chimera.
For a while Chimera only read the anisotropic B-factor information from PDB files. I believe that is true for version 1.4, but if you get version 1.5 (in the daily builds part of the download page) it should work with CIF anisotropy information too. I just tried a CIF file of my own with both these versions. Guess this should be mentioned in the "what's new" release notes, but I didn't know until now that the problem had been fixed!
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 30, 2010, at 1:19 AM, sherden@caltech.edu wrote:
I can't seem to get the thermal ellipsoids to work. I have a number of .cif files that are all perfectly good files (have been cif-checked) and all of which I know for a fact have anisotropic data as I can get thermal ellipsoids to display from these files in other programs like Diamond (which we are trying to move away from). But any time I select an atom or group of atoms and use either the "aniso" command or the "Show Thermal Ellipsoids" dialogue box I just get: "No atoms chosen had anisotropic information." This is just not true though, I can open up the .cif files in question and see the anisotropic data listed for the given atoms with my own two eyes.
Any thoughts? I am probably doing something immensely stupid, that is usually the case with such situations.
--Nat (Nathaniel Sherden)
California Institute of Technology Department of Chemistry
participants (2)
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Elaine Meng -
sherden＠caltech.edu