[Chimera-users] Multi-PDB fitting question

Tom Goddard goddard at sonic.net
Wed Mar 21 12:44:02 PDT 2012

> 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:


Here is the fitmap command documentation which will be updated later 
this week or next week.


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.


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