When starting out in the field of cryo-EM it is often the small annoying problems that you waste a lot of time on. These problems are often very difficult to Google as the experienced Cryo-em scientist often take the solutions to them for granted.
One such problem I found difficult in the beginning was how to generate an initial reference map from a PDB model. As always there are more than one way of solving this problem, but what I have found to be the best approach for people new in the field, is using Chimera for it. Chimera have implemented a EMAN program called pdb2mrc and called it molmap. By going through Chimera instead of generating the map via pdb2mrc in a linux terminal, you get to visualize the map and the pdb file, which I think is general easier for people new to cryo-EM. That being said I think pdb2.mrc is better as it has more options and it is the one I use now.
To use mol at you simply open (or fetch) the PDB model of interest in Chimera. In the “model panel” (Tools –> general controls –>model panel) of chimera you should see that your newly loaded PDB molecule should be molecule “#0”, that is having ID 0, unless you have loaded other models beforehand.
You should then activate the command line (as it is not visible by default) by going: Tools –> General controls –> Command line.
Click on the command line (below the window displaying your PDB model).
In the command line you then type “molmap #0 15” and hit enter. This will very quickly generate a simple density map around molecule #0 at a resolution of 15Å.
The general usage of the molmap command is: “molmap atom-selection resolution options. I did not use any options in my example. So if you wanted to change the resolution to e.g. 3Å you just change the number from 15 to 3 in the command line.
When the map is generated a new window should open called “volume viewer”
To save your new map as a MRC file, as used in e.g. Relion and other Cryo-EM programs you need to go to the “volume viewer” window and click file –> save map as. Then choose MRC format (should be pre-selected) and give it a name and save it. Just remember that your new map is not on a absolute intensity/grey scale!
This takes care of generating an initial map (or mask), but chances are good that the map is not centered correctly and is not the right size either. I will cover this another time.
Click on the following link for details on how to change various parameters (pixelsize, box size) for the map you just created (or any other map): Cryo-EM: How to change box size and pixel size