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
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@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
Hi Elaine, Thanks a lot for the reply. I done sequential fitting of 3 models which is looking good. I will play with the way you mentioned to see whether I can get it better. Have good night, Yanhe Elaine Meng <meng@cgl.ucsf.edu> 于2021年9月8日周三 下午8:05写道：
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@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
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@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@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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participants (3)
-
Elaine Meng -
Tom Goddard -
Yanhe Zhao