[Chimera-users] local docking

[Tom Goddard]

I think you can fit just one model while subtracting the density of the other models, for example,

	fitmap #1,2,3,4 #5 sequence 1

fits model #1 into map #5 after subtracting off density from models #2,3,4.

	Tom

> On Sep 8, 2021, at 6:05 PM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Yanhe,
> The "fitmap" command with sequential fitting ("sequence" option) will fit/move all of the specified models.  There is no option to keep one model fixed and move only the other ones. 
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> 
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence>
> 
> Also, there is no fitmap option to limit the amount of translation or rotation.  Instead there is only an option to turn off translation completely (shift false) or turn off rotation completely (rotate false).
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#shift>
> 
> A longer method might be to first fit one model, then simulate a map from it with "molmap" and then subtract the molmap result from the original map with "vop subtract," and then use a separate "fitmap" command (with "sequence" if you want to sequentially fit the other two).
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
> 
> I hope this helps,
> Elaine
> 
> 
>> On Sep 8, 2021, at 5:40 PM, Yanhe Zhao via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Greeting,
>> 
>> I tried sequential fitting to fit 3 models to my maps. I was wondering that if I want to fix one model and do local fitting of another models with limited shift and rotation, what command with options should I use? 
>> 
>> Thanks and regards,
>> Yanhe
> 
> 
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