Hi, My name is Serina Doolittle. I am an undergraduate research student at Armstrong Atlantic State University in Savannah, Ga. I am currently using Chimera to build two protein models. I have the proteins in the form that I want them in to 3D print. However, one of them is not a single chain protein. It has chain A and B. I hid chain B and focused on chain A because of the simplicity for the 3D protein model that I want. However, when you hide chain B and you put chain A on "show surface" that are like little holes or blotches missing from the protein where chain B is suppose to be. Is there anyway that I can fix this problem and single out chain A to make it look like it is completely lone in the "show surface" view. If you would like I will send you the Chimera file ("session"). That way you can visualize what I am trying to do. Serina Doolittle serinadoolittle@me.com 912-665-3259 Armstrong Atlantic State University Student
Hi Serina, This is a commonly encountered issue: by default the whole macromolecule is enclosed in one surface. However, there are at least a couple ways to tell Chimera to enclose each chain in a separate surface instead: (1) use command "split" to put the separate chains into separate models. The advantage is that it's easy; if you only have that one structure, all you have to do is enter the command: split and then use the hydrophobicity preset again (or show surface and apply your own hydrophobicity coloring scheme with the Render by Attribute tool or the "rangecolor" command). Possible disadvantages of split are if you have already saved positions (from "savepos") they will not work with the new split models, and if you already made the surface around both, it will not go away automatically. You would either need to close that surface (say from Model Panel, under Favorites in the menu) or just close everything, then reopen the structure and split before showing any molecular surfaces. If your original structure is model #0 with chains A and B, split will replace that with new models #0.1 with chain A and #0.2 with chain B. One way to control which models are shown/hidden is with the "S" checkboxes in the Model Panel. (2) use command "surfcat" to tell Chimera exactly which atoms should be grouped together into a surface. The advantages are that any saved positions will continue to work, and the first surface enclosing both will automatically go away. The possible disadvantage is that one should be careful not to include waters and stuff like that in the specification. For example, just today I used the following when making some figures: surfcat achain :.a&protein surfcat bchain :.b&protein surface achain surface bchain ... where the surfcat commands specify atoms with a particular chain ID that are also protein (not solvent, ions, etc.). Then you can use the preset again or show surface and apply your own coloring scheme with Render by Attribute or rangecolor. Of course you could undisplay a chain and its surface, for example: ~surf achain ~ribbon :.a ~display :.a ... where these commands hide the surface, ribbon, and atoms/bonds, respectively. Commands documentation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> Command-line atom specification: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.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 Sep 15, 2013, at 1:57 PM, Serina Doolittle <serinadoolittle@me.com> wrote:
Hi, My name is Serina Doolittle. I am an undergraduate research student at Armstrong Atlantic State University in Savannah, Ga. I am currently using Chimera to build two protein models. I have the proteins in the form that I want them in to 3D print. However, one of them is not a single chain protein. It has chain A and B. I hid chain B and focused on chain A because of the simplicity for the 3D protein model that I want. However, when you hide chain B and you put chain A on "show surface" that are like little holes or blotches missing from the protein where chain B is suppose to be. Is there anyway that I can fix this problem and single out chain A to make it look like it is completely lone in the "show surface" view.
If you would like I will send you the Chimera file ("session"). That way you can visualize what I am trying to do.
Or, if you are sure you don't want chain B, just delete it. Could be done with the menu or with command: delete :.b Elaine On Sep 16, 2013, at 10:09 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Serina, This is a commonly encountered issue: by default the whole macromolecule is enclosed in one surface.
However, there are at least a couple ways to tell Chimera to enclose each chain in a separate surface instead:
(1) use command "split" to put the separate chains into separate models. The advantage is that it's easy; if you only have that one structure, all you have to do is enter the command:
split
and then use the hydrophobicity preset again (or show surface and apply your own hydrophobicity coloring scheme with the Render by Attribute tool or the "rangecolor" command). Possible disadvantages of split are if you have already saved positions (from "savepos") they will not work with the new split models, and if you already made the surface around both, it will not go away automatically. You would either need to close that surface (say from Model Panel, under Favorites in the menu) or just close everything, then reopen the structure and split before showing any molecular surfaces. If your original structure is model #0 with chains A and B, split will replace that with new models #0.1 with chain A and #0.2 with chain B. One way to control which models are shown/hidden is with the "S" checkboxes in the Model Panel.
(2) use command "surfcat" to tell Chimera exactly which atoms should be grouped together into a surface. The advantages are that any saved positions will continue to work, and the first surface enclosing both will automatically go away. The possible disadvantage is that one should be careful not to include waters and stuff like that in the specification. For example, just today I used the following when making some figures:
surfcat achain :.a&protein surfcat bchain :.b&protein surface achain surface bchain
... where the surfcat commands specify atoms with a particular chain ID that are also protein (not solvent, ions, etc.). Then you can use the preset again or show surface and apply your own coloring scheme with Render by Attribute or rangecolor. Of course you could undisplay a chain and its surface, for example:
~surf achain ~ribbon :.a ~display :.a
... where these commands hide the surface, ribbon, and atoms/bonds, respectively.
Commands documentation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
Command-line atom specification: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.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 Sep 15, 2013, at 1:57 PM, Serina Doolittle <serinadoolittle@me.com> wrote:
Hi, My name is Serina Doolittle. I am an undergraduate research student at Armstrong Atlantic State University in Savannah, Ga. I am currently using Chimera to build two protein models. I have the proteins in the form that I want them in to 3D print. However, one of them is not a single chain protein. It has chain A and B. I hid chain B and focused on chain A because of the simplicity for the 3D protein model that I want. However, when you hide chain B and you put chain A on "show surface" that are like little holes or blotches missing from the protein where chain B is suppose to be. Is there anyway that I can fix this problem and single out chain A to make it look like it is completely lone in the "show surface" view.
If you would like I will send you the Chimera file ("session"). That way you can visualize what I am trying to do.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I tried to read the chimera manual/ how to guide to figure out how to delete it. But I couldn't. Is it so simple that I'm making this hard? Do you know the steps? Serina Sent from iPhone On Sep 16, 2013, at 13:22, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Or, if you are sure you don't want chain B, just delete it. Could be done with the menu or with command:
delete :.b
Elaine
On Sep 16, 2013, at 10:09 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Serina, This is a commonly encountered issue: by default the whole macromolecule is enclosed in one surface.
However, there are at least a couple ways to tell Chimera to enclose each chain in a separate surface instead:
(1) use command "split" to put the separate chains into separate models. The advantage is that it's easy; if you only have that one structure, all you have to do is enter the command:
split
and then use the hydrophobicity preset again (or show surface and apply your own hydrophobicity coloring scheme with the Render by Attribute tool or the "rangecolor" command). Possible disadvantages of split are if you have already saved positions (from "savepos") they will not work with the new split models, and if you already made the surface around both, it will not go away automatically. You would either need to close that surface (say from Model Panel, under Favorites in the menu) or just close everything, then reopen the structure and split before showing any molecular surfaces. If your original structure is model #0 with chains A and B, split will replace that with new models #0.1 with chain A and #0.2 with chain B. One way to control which models are shown/hidden is with the "S" checkboxes in the Model Panel.
(2) use command "surfcat" to tell Chimera exactly which atoms should be grouped together into a surface. The advantages are that any saved positions will continue to work, and the first surface enclosing both will automatically go away. The possible disadvantage is that one should be careful not to include waters and stuff like that in the specification. For example, just today I used the following when making some figures:
surfcat achain :.a&protein surfcat bchain :.b&protein surface achain surface bchain
... where the surfcat commands specify atoms with a particular chain ID that are also protein (not solvent, ions, etc.). Then you can use the preset again or show surface and apply your own coloring scheme with Render by Attribute or rangecolor. Of course you could undisplay a chain and its surface, for example:
~surf achain ~ribbon :.a ~display :.a
... where these commands hide the surface, ribbon, and atoms/bonds, respectively.
Commands documentation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
Command-line atom specification: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.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 Sep 15, 2013, at 1:57 PM, Serina Doolittle <serinadoolittle@me.com> wrote:
Hi, My name is Serina Doolittle. I am an undergraduate research student at Armstrong Atlantic State University in Savannah, Ga. I am currently using Chimera to build two protein models. I have the proteins in the form that I want them in to 3D print. However, one of them is not a single chain protein. It has chain A and B. I hid chain B and focused on chain A because of the simplicity for the 3D protein model that I want. However, when you hide chain B and you put chain A on "show surface" that are like little holes or blotches missing from the protein where chain B is suppose to be. Is there anyway that I can fix this problem and single out chain A to make it look like it is completely lone in the "show surface" view.
If you would like I will send you the Chimera file ("session"). That way you can visualize what I am trying to do.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Serina, You could either use the command from my previous message: delete :.b … or the menu-only approach: Select… Chain… B Actions… Atoms/Bonds… Delete Best, Elaine On Sep 16, 2013, at 11:20 AM, Serina Doolittle <serinadoolittle@me.com> wrote:
I tried to read the chimera manual/ how to guide to figure out how to delete it. But I couldn't. Is it so simple that I'm making this hard? Do you know the steps?
Serina Sent from iPhone
On Sep 16, 2013, at 13:22, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Or, if you are sure you don't want chain B, just delete it. Could be done with the menu or with command:
delete :.b
Elaine
On Sep 16, 2013, at 10:09 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Serina, This is a commonly encountered issue: by default the whole macromolecule is enclosed in one surface.
However, there are at least a couple ways to tell Chimera to enclose each chain in a separate surface instead:
(1) use command "split" to put the separate chains into separate models. The advantage is that it's easy; if you only have that one structure, all you have to do is enter the command:
split
and then use the hydrophobicity preset again (or show surface and apply your own hydrophobicity coloring scheme with the Render by Attribute tool or the "rangecolor" command). Possible disadvantages of split are if you have already saved positions (from "savepos") they will not work with the new split models, and if you already made the surface around both, it will not go away automatically. You would either need to close that surface (say from Model Panel, under Favorites in the menu) or just close everything, then reopen the structure and split before showing any molecular surfaces. If your original structure is model #0 with chains A and B, split will replace that with new models #0.1 with chain A and #0.2 with chain B. One way to control which models are shown/hidden is with the "S" checkboxes in the Model Panel.
(2) use command "surfcat" to tell Chimera exactly which atoms should be grouped together into a surface. The advantages are that any saved positions will continue to work, and the first surface enclosing both will automatically go away. The possible disadvantage is that one should be careful not to include waters and stuff like that in the specification. For example, just today I used the following when making some figures:
surfcat achain :.a&protein surfcat bchain :.b&protein surface achain surface bchain
... where the surfcat commands specify atoms with a particular chain ID that are also protein (not solvent, ions, etc.). Then you can use the preset again or show surface and apply your own coloring scheme with Render by Attribute or rangecolor. Of course you could undisplay a chain and its surface, for example:
~surf achain ~ribbon :.a ~display :.a
... where these commands hide the surface, ribbon, and atoms/bonds, respectively.
Commands documentation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
Command-line atom specification: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.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 Sep 15, 2013, at 1:57 PM, Serina Doolittle <serinadoolittle@me.com> wrote:
Hi, My name is Serina Doolittle. I am an undergraduate research student at Armstrong Atlantic State University in Savannah, Ga. I am currently using Chimera to build two protein models. I have the proteins in the form that I want them in to 3D print. However, one of them is not a single chain protein. It has chain A and B. I hid chain B and focused on chain A because of the simplicity for the 3D protein model that I want. However, when you hide chain B and you put chain A on "show surface" that are like little holes or blotches missing from the protein where chain B is suppose to be. Is there anyway that I can fix this problem and single out chain A to make it look like it is completely lone in the "show surface" view.
If you would like I will send you the Chimera file ("session"). That way you can visualize what I am trying to do.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
You were right - something so simple! Thank you so much for all your help! Serina Doolittle On Sep 16, 2013, at 5:00 PM, Elaine Meng wrote:
Hi Serina, You could either use the command from my previous message:
delete :.b
… or the menu-only approach:
Select… Chain… B Actions… Atoms/Bonds… Delete
Best, Elaine
On Sep 16, 2013, at 11:20 AM, Serina Doolittle <serinadoolittle@me.com> wrote:
I tried to read the chimera manual/ how to guide to figure out how to delete it. But I couldn't. Is it so simple that I'm making this hard? Do you know the steps?
Serina Sent from iPhone
On Sep 16, 2013, at 13:22, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Or, if you are sure you don't want chain B, just delete it. Could be done with the menu or with command:
delete :.b
Elaine
On Sep 16, 2013, at 10:09 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Serina, This is a commonly encountered issue: by default the whole macromolecule is enclosed in one surface.
However, there are at least a couple ways to tell Chimera to enclose each chain in a separate surface instead:
(1) use command "split" to put the separate chains into separate models. The advantage is that it's easy; if you only have that one structure, all you have to do is enter the command:
split
and then use the hydrophobicity preset again (or show surface and apply your own hydrophobicity coloring scheme with the Render by Attribute tool or the "rangecolor" command). Possible disadvantages of split are if you have already saved positions (from "savepos") they will not work with the new split models, and if you already made the surface around both, it will not go away automatically. You would either need to close that surface (say from Model Panel, under Favorites in the menu) or just close everything, then reopen the structure and split before showing any molecular surfaces. If your original structure is model #0 with chains A and B, split will replace that with new models #0.1 with chain A and #0.2 with chain B. One way to control which models are shown/hidden is with the "S" checkboxes in the Model Panel.
(2) use command "surfcat" to tell Chimera exactly which atoms should be grouped together into a surface. The advantages are that any saved positions will continue to work, and the first surface enclosing both will automatically go away. The possible disadvantage is that one should be careful not to include waters and stuff like that in the specification. For example, just today I used the following when making some figures:
surfcat achain :.a&protein surfcat bchain :.b&protein surface achain surface bchain
... where the surfcat commands specify atoms with a particular chain ID that are also protein (not solvent, ions, etc.). Then you can use the preset again or show surface and apply your own coloring scheme with Render by Attribute or rangecolor. Of course you could undisplay a chain and its surface, for example:
~surf achain ~ribbon :.a ~display :.a
... where these commands hide the surface, ribbon, and atoms/bonds, respectively.
Commands documentation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
Command-line atom specification: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.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 Sep 15, 2013, at 1:57 PM, Serina Doolittle <serinadoolittle@me.com> wrote:
Hi, My name is Serina Doolittle. I am an undergraduate research student at Armstrong Atlantic State University in Savannah, Ga. I am currently using Chimera to build two protein models. I have the proteins in the form that I want them in to 3D print. However, one of them is not a single chain protein. It has chain A and B. I hid chain B and focused on chain A because of the simplicity for the 3D protein model that I want. However, when you hide chain B and you put chain A on "show surface" that are like little holes or blotches missing from the protein where chain B is suppose to be. Is there anyway that I can fix this problem and single out chain A to make it look like it is completely lone in the "show surface" view.
If you would like I will send you the Chimera file ("session"). That way you can visualize what I am trying to do.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, I'm getting this on the 17th of Sep. New to the group so not sure if the delay is normal. Either delete chain B first in chimera or, failing that, use a text editor to remove chain B from your input file. On Sun, Sep 15, 2013 at 9:57 PM, Serina Doolittle <serinadoolittle@me.com>wrote:
Hi,
My name is Serina Doolittle. I am an undergraduate research student at Armstrong Atlantic State University in Savannah, Ga. I am currently using Chimera to build two protein models. I have the proteins in the form that I want them in to 3D print. However, one of them is not a single chain protein. It has chain A and B. I hid chain B and focused on chain A because of the simplicity for the 3D protein model that I want. However, when you hide chain B and you put chain A on "show surface" that are like little holes or blotches missing from the protein where chain B is suppose to be. Is there anyway that I can fix this problem and single out chain A to make it look like it is completely lone in the "show surface" view.
If you would like I will send you the Chimera file ("session"). That way you can visualize what I am trying to do.
Serina Doolittle
serinadoolittle@me.com 912-665-3259 Armstrong Atlantic State University Student _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Oliver Grant -
Serina Doolittle