Global Fit List and Model Seperation
Dear ChimeraX-Team & MailingListUsers, My question is actually two different questions: I would like to perform a global fitting in ChimeraX and seperate all fitting solutions into independent models. I loaded the map (#1) and a dimeric model (#2) into ChimeraX and perform the global fitting by: fit #2 inMap #1 search 50 My map represents a homo-oligomeric model with 40+ monomers (20+ dimers), so multiple fitting solutions are probably correct solutions. This is the log of the fitting: "Found 41 fits. List window not yet implemented." which matches with my assumption. I would like to now (a) inspect all fittings, but the list window is not implemented yet. Can I access the fitting solutions via console commands? And (b) I would like to save each fitted solution as an indepent object, reconstruction the entire model in the map for furhter refinement. Again, could this be done via commands like: "fit #2 inMap #2 search 50 saveFit fittings.pdb", which results in a multi-state pdb? The "Save PDB" button is probably only available in the List windows, which is not implemented yet. Thanks in advance Best Christian
Hi Christian, I added the fit list panel to ChimeraX. It will be in tonight's ChimeraX builds dated June 29, 2021. Tom
On Jun 28, 2021, at 2:32 AM, Christian Tüting via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX-Team & MailingListUsers,
My question is actually two different questions: I would like to perform a global fitting in ChimeraX and seperate all fitting solutions into independent models.
I loaded the map (#1) and a dimeric model (#2) into ChimeraX and perform the global fitting by: fit #2 inMap #1 search 50
My map represents a homo-oligomeric model with 40+ monomers (20+ dimers), so multiple fitting solutions are probably correct solutions. This is the log of the fitting: "Found 41 fits. List window not yet implemented." which matches with my assumption.
I would like to now (a) inspect all fittings, but the list window is not implemented yet. Can I access the fitting solutions via console commands? And (b) I would like to save each fitted solution as an indepent object, reconstruction the entire model in the map for furhter refinement. Again, could this be done via commands like: "fit #2 inMap #2 search 50 saveFit fittings.pdb", which results in a multi-state pdb? The "Save PDB" button is probably only available in the List windows, which is not implemented yet.
Thanks in advance
Best Christian
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Hi Tom, thank you very much :) I overcome the issue by performing the search multiple times (with each N = 50 searches). As multiple "correct" fittings are present, I ended up with nearly all solutions. But having the list will help for sure in the future. best Christian
Tom Goddard <goddard@sonic.net> 29.06.21 0.05 Uhr >>> Hi Christian,
I added the fit list panel to ChimeraX. It will be in tonight's ChimeraX builds dated June 29, 2021. Tom
On Jun 28, 2021, at 2:32 AM, Christian Tüting via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX-Team & MailingListUsers,
My question is actually two different questions: I would like to perform a global fitting in ChimeraX and seperate all fitting solutions into independent models.
I loaded the map (#1) and a dimeric model (#2) into ChimeraX and perform the global fitting by: fit #2 inMap #1 search 50
My map represents a homo-oligomeric model with 40+ monomers (20+ dimers), so multiple fitting solutions are probably correct solutions. This is the log of the fitting: "Found 41 fits. List window not yet implemented." which matches with my assumption.
I would like to now (a) inspect all fittings, but the list window is not implemented yet. Can I access the fitting solutions via console commands? And (b) I would like to save each fitted solution as an indepent object, reconstruction the entire model in the map for furhter refinement. Again, could this be done via commands like: "fit #2 inMap #2 search 50 saveFit fittings.pdb", which results in a multi-state pdb? The "Save PDB" button is probably only available in the List windows, which is not implemented yet.
Thanks in advance
Best Christian
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participants (2)
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Christian Tüting -
Tom Goddard