Hello Chimera gurus, I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module. Here is the rough order of what I am doing from the graphical user interface: Open model 2QA0 Tools menu -> Higher-order structure -> Multiscale Models panel (The following actions are all in the Multiscale Models panel) Click "Make models" button in "Models from molecules and matrices" section Click "All" button in "Select chains:" section Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection Click "All" button in "Select chains:" section (again) Select "Ribbon" from "Style" menu in "Act on selected chains" section (then back to the main view) Zoom out (with mouse wheel) Favorites menu -> Command Line Type "select :10,20,30" (amino acids I want to highlight) Here is what I've got so far in terms of equivalent Python code: import os from chimera import runCommand as rc rc("open 2QA0") # make multiscale model here? rc("select :10,20,30") # select some residues Your help would be appreciated - thanks! Ian
Hi Ian, To show the 2qa0 virus capsid as ribbons open 2qa0 sym #0 Then to zoom to show the full virus window The sym command also has options to make surfaces like the multiscale model if you want those. Tom
On Dec 20, 2016, at 3:39 PM, Ian Holmes wrote:
Hello Chimera gurus,
I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module.
Here is the rough order of what I am doing from the graphical user interface:
Open model 2QA0 Tools menu -> Higher-order structure -> Multiscale Models panel (The following actions are all in the Multiscale Models panel) Click "Make models" button in "Models from molecules and matrices" section Click "All" button in "Select chains:" section Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection Click "All" button in "Select chains:" section (again) Select "Ribbon" from "Style" menu in "Act on selected chains" section (then back to the main view) Zoom out (with mouse wheel) Favorites menu -> Command Line Type "select :10,20,30" (amino acids I want to highlight)
Here is what I've got so far in terms of equivalent Python code:
import os from chimera import runCommand as rc rc("open 2QA0") # make multiscale model here? rc("select :10,20,30") # select some residues
Your help would be appreciated - thanks! Ian
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Hi Ian, You would use the “sym” command. There is an option to create the multiscale-type low-resolution surfaces instead of loading all the atomic copies, but since you want ribbons rather than the surfaces, there is no need. So, I’m thinking commands: open 2qa0 sym #0 focus sel :300,600 (this file doesn’t have residues 10,20,30) I think you can just use the runcommand thing to convert to python: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> sym: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2016, at 3:39 PM, Ian Holmes <ihholmes@gmail.com> wrote:
Hello Chimera gurus,
I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module.
Here is the rough order of what I am doing from the graphical user interface:
Open model 2QA0 Tools menu -> Higher-order structure -> Multiscale Models panel (The following actions are all in the Multiscale Models panel) Click "Make models" button in "Models from molecules and matrices" section Click "All" button in "Select chains:" section Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection Click "All" button in "Select chains:" section (again) Select "Ribbon" from "Style" menu in "Act on selected chains" section (then back to the main view) Zoom out (with mouse wheel) Favorites menu -> Command Line Type "select :10,20,30" (amino acids I want to highlight)
Here is what I've got so far in terms of equivalent Python code:
import os from chimera import runCommand as rc rc("open 2QA0") # make multiscale model here? rc("select :10,20,30") # select some residues
Your help would be appreciated - thanks! Ian
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you very much Elaine and Tom! Ian On Tue, Dec 20, 2016 at 3:56 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ian, You would use the “sym” command. There is an option to create the multiscale-type low-resolution surfaces instead of loading all the atomic copies, but since you want ribbons rather than the surfaces, there is no need. So, I’m thinking commands:
open 2qa0 sym #0 focus sel :300,600
(this file doesn’t have residues 10,20,30)
I think you can just use the runcommand thing to convert to python: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
sym: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2016, at 3:39 PM, Ian Holmes <ihholmes@gmail.com> wrote:
Hello Chimera gurus,
I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module.
Here is the rough order of what I am doing from the graphical user interface:
Open model 2QA0 Tools menu -> Higher-order structure -> Multiscale Models panel (The following actions are all in the Multiscale Models panel) Click "Make models" button in "Models from molecules and matrices" section Click "All" button in "Select chains:" section Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection Click "All" button in "Select chains:" section (again) Select "Ribbon" from "Style" menu in "Act on selected chains" section (then back to the main view) Zoom out (with mouse wheel) Favorites menu -> Command Line Type "select :10,20,30" (amino acids I want to highlight)
Here is what I've got so far in terms of equivalent Python code:
import os from chimera import runCommand as rc rc("open 2QA0") # make multiscale model here? rc("select :10,20,30") # select some residues
Your help would be appreciated - thanks! Ian
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/ mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Ian Holmes -
Tom Goddard