9/18 To whom it may concern: I would like an abbreviated guide to loading a pdb and an electron density map into chimera for comparison and hand docking. I have only worked with visualization software for a few months and still, frequently, can't do what I want with it. Chimera was suggested as the easiest or perhaps only software to do what I need to do. Currently, I only have only got VMD downloaded, but can install chimera if its worthwhile. Sincerely, Rich Kaufman, U.KS. biochem. dept, Kansas City, Ks.
Hi Rich, Here are brief instructions to display a PDB and electron density map in Chimera and align them. Download Chimera 1.2255 from the Snapshot section of the download page http://www.cgl.ucsf.edu/chimera/download.html and run the installer. Open the PDB and map using Chimera menu entry File / Open.... If you do this with a PDB file from the Protein Data Bank (www.pdb.org) and an electron density map from the Electron Density Server (eds.bmc.uu.se/eds) then they will be displayed aligned. Click on the "Mesh" button on the volume dialog that was displayed when the map was opened. This allows you to see through the mesh. Adjust the contouring level by dragging the vertical bar on the histogram shown in the volume dialog. Use menu entry "Actions / Atoms&Bonds / Stick" to fatten the displayed molecule so it is more visible. Use menu entry "Actions / Color / Red" to make the molecule more visible. To show only the density near the molecular model use the "Features / Zone" menu entry on the volume dialog (Chimera 1.2255 or newer). Then select all the atoms with menu entry "Select / Select all" on the main Chimera window. Then press the "Zone" button at the bottom of the volume dialog. This restricts the mesh display to only points within 2 Angstroms of the selected atoms. If the model does not fit in the map you can move it (rigidly) with the mouse. Use menu entry "Favorites / Model Panel". Switch off the checkbutton next to the map in the column with heading "active". This freezes the map so it is not moved when you use the mouse. Now rotate and translate the PDB model by dragging with the left and middle mouse buttons. To shift the model into or out of the screen hold the ctrl key while dragging with the middle mouse button. If you get the model close to the right position in the map you can locally optimize its position using the "Fit models in maps" tool, menu entry "Tools / Volume data / Fit models in maps". Select the atoms (menu "Actions / Select all") and press the Fit button on the fitting dialog and the PDB model will be moved to the optimal local position. If you need to change the molecule conformation or reorient residues there are other tools that I will describe if you need them. Here is more info about map display in Chimera. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html More detailed Chimera documentation is in the User's Guide. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html Tom
participants (2)
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Rich Kaufman -
Thomas Goddard