ISOLDE: unable to work with map after selecting another model
Hi Tristan, ISOLDE users,
Sometimes it's useful to create a new model (e.g. by merging the model of the protein you've been working on with an initial model of the ligand) and then continue working with this new model in ISOLDE. For me, this leads to trouble.
Specifically, here's what I do: - start ChimeraX - open a PDB and a map - start ISOLDE - select the PDB model in the "Working on" dropdown - select the map in the "From loaded volume" dropdown - do some simulations until I'm happy with the protein - open a PDB of the ligand - combine the ligand model with the protein model - select the combination model in the "Working on" dropdown - press "start simulation"... get warning "about to start simulation with no map" - press Cancel - check the "From loaded volume" dropdown - it's not possible to select the already-loaded map, which is in the initial "Data manager"
Is this intended behavior? I was hoping to be able to continue working against the same map.
Cheers, Alexis
Hi Alexis,
I’m afraid that’s the way it’s set up at the moment, yes - once a map is associated with a model I haven’t provided a mechanism to transplant it to a new one. But there is good news: in the top menu there’s an entry “ISOLDE/Model Building/Merge Selected Model(s) Into Working Model”. Select the ligand model and use that, and it should do what you’re after. Also works for merging in new protein chains (but not at present for adding new fragments of an existing chain).
Best, Tristan
On Wed, 6 Mar 2024 at 21:38, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Tristan, ISOLDE users,
Sometimes it's useful to create a new model (e.g. by merging the model of the protein you've been working on with an initial model of the ligand) and then continue working with this new model in ISOLDE. For me, this leads to trouble.
Specifically, here's what I do:
- start ChimeraX
- open a PDB and a map
- start ISOLDE
- select the PDB model in the "Working on" dropdown
- select the map in the "From loaded volume" dropdown
- do some simulations until I'm happy with the protein
- open a PDB of the ligand
- combine the ligand model with the protein model
- select the combination model in the "Working on" dropdown
- press "start simulation"... get warning "about to start simulation with
no map"
- press Cancel
- check the "From loaded volume" dropdown - it's not possible to select
the already-loaded map, which is in the initial "Data manager"
Is this intended behavior? I was hoping to be able to continue working against the same map.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Excellent, thanks Tristan!
On Wed, Mar 6, 2024 at 1:50 PM Tristan Croll tcroll@altoslabs.com wrote:
Hi Alexis,
I’m afraid that’s the way it’s set up at the moment, yes - once a map is associated with a model I haven’t provided a mechanism to transplant it to a new one. But there is good news: in the top menu there’s an entry “ISOLDE/Model Building/Merge Selected Model(s) Into Working Model”. Select the ligand model and use that, and it should do what you’re after. Also works for merging in new protein chains (but not at present for adding new fragments of an existing chain).
Best, Tristan
On Wed, 6 Mar 2024 at 21:38, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Tristan, ISOLDE users,
Sometimes it's useful to create a new model (e.g. by merging the model of the protein you've been working on with an initial model of the ligand) and then continue working with this new model in ISOLDE. For me, this leads to trouble.
Specifically, here's what I do:
- start ChimeraX
- open a PDB and a map
- start ISOLDE
- select the PDB model in the "Working on" dropdown
- select the map in the "From loaded volume" dropdown
- do some simulations until I'm happy with the protein
- open a PDB of the ligand
- combine the ligand model with the protein model
- select the combination model in the "Working on" dropdown
- press "start simulation"... get warning "about to start simulation
with no map"
- press Cancel
- check the "From loaded volume" dropdown - it's not possible to select
the already-loaded map, which is in the initial "Data manager"
Is this intended behavior? I was hoping to be able to continue working against the same map.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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participants (2)
-
Alexis Rohou -
Tristan Croll