question about specific protein display
Hi, I am using Chimera to display a protein domain in my paper. The domain has two mutations in the hydrophobic core: I would like to display the protein domain open in two parts, to show the buried residues exposed. Could you guide me on how to do this? Thank you so much for your help! Best, Giulia Galotto PhD Student Vidali Lab Worcester Polytechnic Institute
Hi Giulia, First you have to decide how to divide the structure, e.g. figure out lists/ranges of residue numbers that will be in part 1, everything else in part 2. Open the structure and split it, specifying this list of residues. For example, command open mystructure.pdb split atoms :20-46.A,200-350.A ... to put residues 20-46 and 200-350 of chain A in one part, everything else in the other. (If you don't need anything for your figures except the protein, it may be simpler to delete all nonprotein parts first, e.g. command "delete ~protein" before the split command.) See explanation of "split" command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html> Then see this "opened interface" image tutorial for ideas on how to make a figure showing the interior. You can generalize, i.e. you don't have to follow all the steps, just the ones that do the things you want like positioning the two parts, and you could use different display styles (spheres rather than molecular surface, for example), coloring, etc. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html> There are lots of tutorials including "getting started" if you don't know how to change display styles, colors, etc. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 13, 2020, at 9:06 AM, Galotto, Giulia <ggalotto@wpi.edu> wrote:
Hi, I am using Chimera to display a protein domain in my paper. The domain has two mutations in the hydrophobic core: I would like to display the protein domain open in two parts, to show the buried residues exposed. Could you guide me on how to do this? Thank you so much for your help! Best, Giulia Galotto PhD Student Vidali Lab Worcester Polytechnic Institute
Elaine, thank you for your reply! I was able to split the sequence in two, and now I have two chains. I am having trouble separating the two chain in the display. I would like to physically separate them and orient them at an angle to show the residues. Thank you! Best, Giulia ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 13, 2020 4:08 PM To: Galotto, Giulia <ggalotto@wpi.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: [EXT] Re: [Chimera-users] question about specific protein display Hi Giulia, First you have to decide how to divide the structure, e.g. figure out lists/ranges of residue numbers that will be in part 1, everything else in part 2. Open the structure and split it, specifying this list of residues. For example, command open mystructure.pdb split atoms :20-46.A,200-350.A ... to put residues 20-46 and 200-350 of chain A in one part, everything else in the other. (If you don't need anything for your figures except the protein, it may be simpler to delete all nonprotein parts first, e.g. command "delete ~protein" before the split command.) See explanation of "split" command: <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fsplit.html&data=02%7C01%7Cggalotto%40wpi.edu%7C805fd1dec8884d0f905a08d7c78a5ca6%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637197269402256083&sdata=xg1Ji6B%2FX%2B1gPlTexxB9ra3zKCoBA5bfC%2FWWWWqSr9c%3D&reserved=0> Then see this "opened interface" image tutorial for ideas on how to make a figure showing the interior. You can generalize, i.e. you don't have to follow all the steps, just the ones that do the things you want like positioning the two parts, and you could use different display styles (spheres rather than molecular surface, for example), coloring, etc. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fopenbook.html&data=02%7C01%7Cggalotto%40wpi.edu%7C805fd1dec8884d0f905a08d7c78a5ca6%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637197269402256083&sdata=ynh7AJU16s1wjGbs2%2Ft3D2kURfOI9GuYdqT4yAe9L8k%3D&reserved=0> There are lots of tutorials including "getting started" if you don't know how to change display styles, colors, etc. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fframetut.html&data=02%7C01%7Cggalotto%40wpi.edu%7C805fd1dec8884d0f905a08d7c78a5ca6%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637197269402256083&sdata=8nxqt72HSvq0HFkavnLStrhuX9t9v%2BQnw%2FgmMkwytVQ%3D&reserved=0> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 13, 2020, at 9:06 AM, Galotto, Giulia <ggalotto@wpi.edu> wrote:
Hi, I am using Chimera to display a protein domain in my paper. The domain has two mutations in the hydrophobic core: I would like to display the protein domain open in two parts, to show the buried residues exposed. Could you guide me on how to do this? Thank you so much for your help! Best, Giulia Galotto PhD Student Vidali Lab Worcester Polytechnic Institute
Hi Giulia, The tutorial link I sent in the previous message covers that part. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#ope...> Elaine
On Mar 13, 2020, at 2:04 PM, Galotto, Giulia <ggalotto@wpi.edu> wrote:
Elaine, thank you for your reply! I was able to split the sequence in two, and now I have two chains. I am having trouble separating the two chain in the display. I would like to physically separate them and orient them at an angle to show the residues.
Thank you!
Best, Giulia From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 13, 2020 4:08 PM To: Galotto, Giulia <ggalotto@wpi.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: [EXT] Re: [Chimera-users] question about specific protein display
Hi Giulia, First you have to decide how to divide the structure, e.g. figure out lists/ranges of residue numbers that will be in part 1, everything else in part 2.
Open the structure and split it, specifying this list of residues. For example, command
open mystructure.pdb split atoms :20-46.A,200-350.A
... to put residues 20-46 and 200-350 of chain A in one part, everything else in the other. (If you don't need anything for your figures except the protein, it may be simpler to delete all nonprotein parts first, e.g. command "delete ~protein" before the split command.)
See explanation of "split" command: <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fsplit.html&data=02%7C01%7Cggalotto%40wpi.edu%7C805fd1dec8884d0f905a08d7c78a5ca6%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637197269402256083&sdata=xg1Ji6B%2FX%2B1gPlTexxB9ra3zKCoBA5bfC%2FWWWWqSr9c%3D&reserved=0>
Then see this "opened interface" image tutorial for ideas on how to make a figure showing the interior. You can generalize, i.e. you don't have to follow all the steps, just the ones that do the things you want like positioning the two parts, and you could use different display styles (spheres rather than molecular surface, for example), coloring, etc. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fopenbook.html&data=02%7C01%7Cggalotto%40wpi.edu%7C805fd1dec8884d0f905a08d7c78a5ca6%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637197269402256083&sdata=ynh7AJU16s1wjGbs2%2Ft3D2kURfOI9GuYdqT4yAe9L8k%3D&reserved=0>
There are lots of tutorials including "getting started" if you don't know how to change display styles, colors, etc. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fframetut.html&data=02%7C01%7Cggalotto%40wpi.edu%7C805fd1dec8884d0f905a08d7c78a5ca6%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637197269402256083&sdata=8nxqt72HSvq0HFkavnLStrhuX9t9v%2BQnw%2FgmMkwytVQ%3D&reserved=0>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 13, 2020, at 9:06 AM, Galotto, Giulia <ggalotto@wpi.edu> wrote:
Hi, I am using Chimera to display a protein domain in my paper. The domain has two mutations in the hydrophobic core: I would like to display the protein domain open in two parts, to show the buried residues exposed. Could you guide me on how to do this? Thank you so much for your help! Best, Giulia Galotto PhD Student Vidali Lab Worcester Polytechnic Institute
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
To clarify: that tutorial uses commands to exactly rotate the two parts 90 degrees each. If you just wanted to do it roughly by hand instead, you can freeze/unfreeze one model or the other using the "A" (activation for motion) checkboxes in the Model Panel as mentioned here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> You can open the Model Panel from the Favorites menu. If you mess up and want to put the two parts back together in their original positions and start over, try command "reset". <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> Elaine
On Mar 13, 2020, at 3:18 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Giulia, The tutorial link I sent in the previous message covers that part.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#ope...>
Elaine
On Mar 13, 2020, at 2:04 PM, Galotto, Giulia <ggalotto@wpi.edu> wrote:
Elaine, thank you for your reply! I was able to split the sequence in two, and now I have two chains. I am having trouble separating the two chain in the display. I would like to physically separate them and orient them at an angle to show the residues.
Thank you!
Best, Giulia From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 13, 2020 4:08 PM To: Galotto, Giulia <ggalotto@wpi.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: [EXT] Re: [Chimera-users] question about specific protein display
Hi Giulia, First you have to decide how to divide the structure, e.g. figure out lists/ranges of residue numbers that will be in part 1, everything else in part 2.
Open the structure and split it, specifying this list of residues. For example, command
open mystructure.pdb split atoms :20-46.A,200-350.A
... to put residues 20-46 and 200-350 of chain A in one part, everything else in the other. (If you don't need anything for your figures except the protein, it may be simpler to delete all nonprotein parts first, e.g. command "delete ~protein" before the split command.)
See explanation of "split" command: <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fsplit.html&data=02%7C01%7Cggalotto%40wpi.edu%7C805fd1dec8884d0f905a08d7c78a5ca6%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637197269402256083&sdata=xg1Ji6B%2FX%2B1gPlTexxB9ra3zKCoBA5bfC%2FWWWWqSr9c%3D&reserved=0>
Then see this "opened interface" image tutorial for ideas on how to make a figure showing the interior. You can generalize, i.e. you don't have to follow all the steps, just the ones that do the things you want like positioning the two parts, and you could use different display styles (spheres rather than molecular surface, for example), coloring, etc. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fopenbook.html&data=02%7C01%7Cggalotto%40wpi.edu%7C805fd1dec8884d0f905a08d7c78a5ca6%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637197269402256083&sdata=ynh7AJU16s1wjGbs2%2Ft3D2kURfOI9GuYdqT4yAe9L8k%3D&reserved=0>
There are lots of tutorials including "getting started" if you don't know how to change display styles, colors, etc. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fframetut.html&data=02%7C01%7Cggalotto%40wpi.edu%7C805fd1dec8884d0f905a08d7c78a5ca6%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637197269402256083&sdata=8nxqt72HSvq0HFkavnLStrhuX9t9v%2BQnw%2FgmMkwytVQ%3D&reserved=0>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 13, 2020, at 9:06 AM, Galotto, Giulia <ggalotto@wpi.edu> wrote:
Hi, I am using Chimera to display a protein domain in my paper. The domain has two mutations in the hydrophobic core: I would like to display the protein domain open in two parts, to show the buried residues exposed. Could you guide me on how to do this? Thank you so much for your help! Best, Giulia Galotto PhD Student Vidali Lab Worcester Polytechnic Institute
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Galotto, Giulia