Dear Tom,

... Currently we are trying to use a lot of PDBs (hundreds!) to fit one density map and trying to find out the best fitted PDB, and we found that fitting the PDBs one by one manually was very time-consuming and low-efficiency. So we are wondering that if there is any advanced way or batch file that can speedup this process?

Thank you so much and we are looking forward your reply.

Best Regards, Lei

Hi Lei, Ok, I added a new "eachModel" option to the Chimera fitmap command so that one command can independently fit many molecules in the same map. For example, fit #1-50 #0 resolution 13.5 eachModel true listFits true will fit PDB models with id numbers 1 to 50 into map with id #0 and list the fits in a dialog. Each of the fits is done independently (no account for clashes between molecules). Details on each fit are given in the Reply Log dialog (menu Favorites / Reply Log). This will be in tonight's Chimera daily builds (run at midnight) if they succeed: http://www.cgl.ucsf.edu/chimera/download.html#daily Here is the fitmap command documentation which will be updated later this week or next week. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html You will probably find that you can't open hundreds of PDB molecules in Chimera because it takes too much memory. But you can fit them in a few batches if this happens. Tom