Hi Tatiana, Sure, just open multiple .mrc files (for example with "File... Open" in the main menu or "File... Open map" in the Volume Viewer menu). Each will be treated as a "model" in Chimera. You can freeze/ unfreeze any of the models using the "Active" checkboxes in the Model Panel (under Favorites in the main Chimera menu). By freeze I mean make the model unresponsive to movement with the mouse or various movement commands, while the others remain movable. When you have a lot of data open, however, interactive responsiveness may become an issue depending on the capabilities of your computer. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 3, 2007, at 7:43 AM, Gorelik, Tatiana wrote:

Dear Chimera-team,

Can I load several .mrc maps at a time and rotate them one against another?

Thanks,

Tatiana

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Tatiana Gorelik, PhD,

Institut für Physikalische Chemie

Johannes Gutenberg-Universität Mainz

Welderweg 11

55099 Mainz

Germany

Tel.: 0049 6131 39 22347

Fax: 0049 6131 39 23768

e-mail:gorelik@uni-mainz.de

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Dear Ben, Chimera doesn't have the ability to figure out for you the proper position of one copy relative to another. You could open multiple copies, perform manual positioning, and then write out all the coordinates, but I imagine it might be difficult to get the right position of one copy relative to another, even manually/interactively. To manually position a structure relative to another, you could interactively rotate/translate and/or use the "move" (translation) and "turn" (rotation) commands. You can freeze/unfreeze a copy using the Active checkbox in the Model Panel (in the Favorites menu by default), the command "select," or the little checkboxes under the Command Line (also under Favorites). If you did manage to position copy 2 relative to copy 1 to your liking, you could write the transformation matrices out (see "matrixget" command). From those you could calculate the transformation of 2 relative to 1 and also generate appropriate matrices that would then position 3, 4, ... correctly (see "matrixset" command). I admit I don't know how to do those calculations. Anyone? Yet another snag depends on how you will be using these coordinates. Does it require all the PDB files to be merged into one? If so, can they be in a multi-MODEL form, or in a single model? Chimera can output separate PDB files or a single multi-MODEL PDB file. If you need all the coordinates to be in one model, however, you would have to edit the PDB output from Chimera so there are not atoms with duplicate atom numbers and chain IDs. However, it all depends on what the *next* program you will be using requires and expects. If you will just be using Chimera, however, no further editing would be required (in fact, you could just save a session rather than writing out coordinates). Maybe someone else will have a smarter and less discouraging set of suggestions! Best, Elaine On Aug 10, 2007, at 12:53 PM, Ben Keshet wrote:

Dear Chimera fans and team,

I have a pdb file of a fragment of an amyloid fibril constructed of 8 layers (8 parallel strands of beta sheet). I would like to overcome the end effects when modeling it, so I would like extend the existing structure by duplicating it at its end.

Does Chimera has a tool do the following: duplicate existing pdb molecule coordinates, position the duplicated molecule at a desired location, and then align it reasonably with respect to the original molecule?

Thank you very much for your time and help.

Ben

Hi Ben, Here's a Python script to help you make a filament in Chimera. You first have to orient two monomers relative to each other in Chimera, for example by moving one with the mouse by hand. Then opening this script (use File / Open) will add a third monomer using the position of the 2nd monomer relative to the 1st. You can edit the last line of the script to add more than one monomer. Tom # ----------------------------------------------------------------------------- # Script to make a filament from monomers. # # Open two copies of the monomer and position them relative to one another # by hand or other means. Then open this script to create a 3rd copy # having the same relative position to the 2nd copy as the 2nd has relative # to the first. The two copies used are the molecules with the highest two # model id numbers. # # To add multiple monomers edit the last line of the script. # def extend_filament(copies): from chimera import openModels, Molecule mlist = openModels.list(modelTypes = [Molecule]) mlist.sort(lambda m1,m2: cmp(m1.id, m2.id)) m1 = mlist[-2] m2 = mlist[-1] for c in range(copies): m3 = add_monomer(m1, m2) m1 = m2 m2 = m3 # ----------------------------------------------------------------------------- # def add_monomer(m1, m2): path, filetype = m2.openedAs[:2] from chimera import openModels m3 = openModels.open(path, filetype)[0] xf = m2.openState.xform xf.premultiply(m1.openState.xform.inverse()) xf.premultiply(m2.openState.xform) m3.openState.xform = xf return m3 # ----------------------------------------------------------------------------- # Change copies values to add more than one monomer if desired. # extend_filament(copies = 1)