Hello Chimera Feedback Team, For clarity and conciseness, I will jump immediately to my issue. I wish to import a CIF file of an inorganic crystal structure into the Chimera Program so that I can selectively eliminate certain atoms, and potentially create a video similar to one of the examples given on the website with a rotation and zoom into the meat of the structure. The file I import (.CIF) should have the proper symmetry group listed in addition to the lattice parameters of a unit cell, but when I try to generate a unit cell, the space group, cell size, and cell angles sections are blank, and therefore no copies can be made. Also, the viewing options give a choice between part ball and stick, part full atom, and essentially nothing else even with selecting the different presets. I know I am not working with PDB files but if there is anything in there that you could help me with, I would greatly appreciate it. Sincere Thanks, Graeme Gardner Graduate Assistant Rutgers University Department of Chemistry and Chemical Biology
Hi Graeme, Unfortunately the Chimera unit cell dialog only makes use of unit cell angles, edge lengths and the crystal space group from PDB format files. It may be that our CIF reader also reads those parameters, and if it does it should be easy for me to improve the unit cell dialog to work with them. Could you send me a CIF file so I can try with your example? Tom
Hello Chimera Feedback Team,
For clarity and conciseness, I will jump immediately to my issue. I wish to import a CIF file of an inorganic crystal structure into the Chimera Program so that I can selectively eliminate certain atoms, and potentially create a video similar to one of the examples given on the website with a rotation and zoom into the meat of the structure. The file I import (.CIF) should have the proper symmetry group listed in addition to the lattice parameters of a unit cell, but when I try to generate a unit cell, the space group, cell size, and cell angles sections are blank, and therefore no copies can be made. Also, the viewing options give a choice between part ball and stick, part full atom, and essentially nothing else even with selecting the different presets. I know I am not working with PDB files but if there is anything in there that you could help me with, I would greatly appreciate it.
Sincere Thanks,
Graeme Gardner Graduate Assistant Rutgers University Department of Chemistry and Chemical Biology
Hi Graeme, Of course you can display any subset of the atoms, ribbons, etc. in the multiple colors and styles you wish, by selecting parts of the structure and then using the Actions menu to control those parts. The presets are only meant to get you quickly to certain standard displays, but you would not use them for finer control over specific atoms and residues of interest. There are several ways to select, including using Ctrl-click/drag in the main window, or the Select menu, or dragging a box in the Sequence view (under Favorites in the menu). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html> You may want to take a look at the "Getting Started" tutorial or some other tutorials to become more familiar with Chimera. Here is the expanded Getting Started tutorial online: <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html> ... and the User's Guide with more tutorials, which can be accessed here, but also from the Help menu in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html> 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 Jan 24, 2011, at 1:25 PM, graemeg@rci.rutgers.edu wrote:
Hello Chimera Feedback Team,
For clarity and conciseness, I will jump immediately to my issue. I wish to import a CIF file of an inorganic crystal structure into the Chimera Program so that I can selectively eliminate certain atoms, and potentially create a video similar to one of the examples given on the website with a rotation and zoom into the meat of the structure. The file I import (.CIF) should have the proper symmetry group listed in addition to the lattice parameters of a unit cell, but when I try to generate a unit cell, the space group, cell size, and cell angles sections are blank, and therefore no copies can be made. Also, the viewing options give a choice between part ball and stick, part full atom, and essentially nothing else even with selecting the different presets. I know I am not working with PDB files but if there is anything in there that you could help me with, I would greatly appreciate it.
Sincere Thanks,
Graeme Gardner Graduate Assistant Rutgers University Department of Chemistry and Chemical Biology
participants (3)
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Elaine Meng -
graemegļ¼ rci.rutgers.edu -
Tom Goddard