Hi Mazdak, To fit a PDB model in a map in Chimera you can hand place the model in roughly the right location and then do a computational optimization that maximizes the density at the atom positions. Here are instructions: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmode... Your map grid plane spacing has to be set correctly in Angstroms since the PDB model coordinates are in Angstroms. Adjust the map grid plane spacing using the volume dialog menu entry Features / Origin and Scale and change the Voxel Size entry fields and press the Enter key to use those new values. Voxel size is the same as grid plane spacing. You can measure the length between two markers. Just select the link (ctrl click on it with the left mouse button) and use keyboard shortcut "pl". You first have to turn on keyboard shortcuts using menu entry Tools / General Controls / Accelerators On. Here are more details http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#pathlen... For more info on volume data capabilities look at the Guide to Volume Data Display http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html I will look at map merging today if I have time. So far I have been busy all week. Tom Mazdak Radjainia wrote:
Hi Tom,
There are actually two more tasks where I was hoping that chimera could help me.
1. I would like to fit high resolution data from a coordinate file in a low-electron density map. Can chimera perform such a docking/fitting? I tried to do it manually but I couldn't resize the opened pdb file towards my .mrc electron density map.
2. Is it possible to measure the length of a link between two markers? I tried to use the experimental "distance to surface" feature. But it never measures the distance between two markers which I hoped it could do.
I really appreciate that you are already helping me out with map-merging feature which I hope doesn't cause too much trouble. It's just great to know if I could do the entire molecular visualization and structure analysis in chimera?
Cheers Mazdak