[Chimera-users] Multi-PDB fitting question

[Tom Goddard]

> 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