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
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sherden@caltech.edu