You have been very helpful in explaining different items that use the command line. I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc. So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number. I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model. Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec <frameatom_spec.html> I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1. So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly. Thank you Arthur G. Szabo
Hi Arthur, Unfortunately “ribbackbone” only applies to the whole model. However, it is merely an “enabler” allowing backbone atoms and ribbon to be shown at the same time, if the atoms and ribbon both happen to be displayed for the same residue. You can still hide (~display) any atoms you don’t want to see and hide ribbon (~ribbon) of any residue whose ribbon segment you don’t want to see. So you would have to use “ribbackbone #0.1” or something like that on the whole model, but then hide all the atoms you don’t want, say “~disp #0.1” to hide all atoms, and then to show all atoms of glycines 33,37,38 it could be something like “disp #0.1:33.A,37.A,38.A” (for example, if they are in chain A of model #0.1). Again, you can use Selection Inspector instead of commands for many things, although commands are better for doing things with specific residue numbers. 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 2, 2016, at 9:33 AM, A G Szabo <agszabo@bell.net> wrote:
You have been very helpful in explaining different items that use the command line.
I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc.
So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number.
I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model.
Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K.
The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec
I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don’t think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1.
So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly.
Thank you
Arthur G. Szabo
Elaine I am including the structure I am working with in Chimera. Don't know if you can see it in the message. So I attached a copy You can see that I have shown a selection of residues. If I were to use the command "~disp #0.1" then the other residues would disappear. I tried to use the command you suggested "disp #0.1:33.K,37.K,38.K" since the Gly residues are on Chain K #0.1. and I wanted to retain the atoms of the displayed side chains on Chain C #0.1 and Chain E #0.1. I had turned ribbackbone off since I thought according to your suggestion I could display all the atoms of the three Gly residues on Chain K #0.1. Unfortunately it didn't work. But thanks for your suggestions. arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-02-16 12:47 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question Hi Arthur, Unfortunately "ribbackbone" only applies to the whole model. However, it is merely an "enabler" allowing backbone atoms and ribbon to be shown at the same time, if the atoms and ribbon both happen to be displayed for the same residue. You can still hide (~display) any atoms you don't want to see and hide ribbon (~ribbon) of any residue whose ribbon segment you don't want to see. So you would have to use "ribbackbone #0.1" or something like that on the whole model, but then hide all the atoms you don't want, say "~disp #0.1" to hide all atoms, and then to show all atoms of glycines 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for example, if they are in chain A of model #0.1). Again, you can use Selection Inspector instead of commands for many things, although commands are better for doing things with specific residue numbers. 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 2, 2016, at 9:33 AM, A G Szabo <agszabo@bell.net> wrote:
You have been very helpful in explaining different items that use the command line.
I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc.
So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number.
I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model.
Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K.
The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec
I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1.
So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly.
Thank you
Arthur G. Szabo
Elaine The essential issue is that all of the Atoms of Gly are part of the backbone. So in order to visualize those atoms one has to turn them on with ribbackbone. But visualizing the backbone atoms of other residues with longer side chains clutters up the image, and I would rather have the backbone atoms of such amino acids turned off. I sent you a power point attachment with the structure I am working with. This is the partial structure of a beta sheet amyloid made up of the same peptide all in a stack. So in order to show the key intramolecular interactions in one of the peptides in the stack one can show the selected residues. Only issue is that one cannot visualize Gly in any meaningful way unless ribbackbone is turned on. Thanks for your assistance Much appreciated arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-02-16 12:47 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question Hi Arthur, Unfortunately "ribbackbone" only applies to the whole model. However, it is merely an "enabler" allowing backbone atoms and ribbon to be shown at the same time, if the atoms and ribbon both happen to be displayed for the same residue. You can still hide (~display) any atoms you don't want to see and hide ribbon (~ribbon) of any residue whose ribbon segment you don't want to see. So you would have to use "ribbackbone #0.1" or something like that on the whole model, but then hide all the atoms you don't want, say "~disp #0.1" to hide all atoms, and then to show all atoms of glycines 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for example, if they are in chain A of model #0.1). Again, you can use Selection Inspector instead of commands for many things, although commands are better for doing things with specific residue numbers. 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 2, 2016, at 9:33 AM, A G Szabo <agszabo@bell.net> wrote:
You have been very helpful in explaining different items that use the command line.
I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc.
So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number.
I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model.
Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K.
The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec
I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1.
So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly.
Thank you
Arthur G. Szabo
Hi Arthur, I believe I understand completely, but I can only repeat my suggestions from before. You would use “ribbackbone” to allow both ribbon and backbone atoms, and then use “disp” to show the atoms you want to see and “~disp” to hide the atoms you don’t want to see. Don’t know what you mean by “didn’t work”. The exact disp and ~disp commands depend on the models, chains, residues,…. in your structure. Here is an example with PDB entry 2gbp, pretending I want to see all atoms of residues 40-50 but sidechain only of residues 20-30; everything in that structure is chain A: open 2gbp ribbackbone ~disp disp #0:40-50.A disp #0:20-30.A & with CA/C1’ The last part of the last line means sidechains only. However, another way to the same result is to display all atoms of those residues but then hide their backbone atoms like we talked about before: disp #0:20-30.A ~disp #0:20-30.A@n,c,o,h Still one more step if you don’t want fake CA-CA bonds between adjacent residues for which you are showing sidechain only: setattr m autochain false 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 2, 2016, at 11:21 AM, A G Szabo <agszabo@bell.net> wrote:
Elaine
The essential issue is that all of the Atoms of Gly are part of the backbone. So in order to visualize those atoms one has to turn them on with ribbackbone. But visualizing the backbone atoms of other residues with longer side chains clutters up the image, and I would rather have the backbone atoms of such amino acids turned off.
I sent you a power point attachment with the structure I am working with. This is the partial structure of a beta sheet amyloid made up of the same peptide all in a stack. So in order to show the key intramolecular interactions in one of the peptides in the stack one can show the selected residues. Only issue is that one cannot visualize Gly in any meaningful way unless ribbackbone is turned on.
Thanks for your assistance
Much appreciated
arthur
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-02-16 12:47 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question
Hi Arthur, Unfortunately "ribbackbone" only applies to the whole model. However, it is merely an "enabler" allowing backbone atoms and ribbon to be shown at the same time, if the atoms and ribbon both happen to be displayed for the same residue. You can still hide (~display) any atoms you don't want to see and hide ribbon (~ribbon) of any residue whose ribbon segment you don't want to see.
So you would have to use "ribbackbone #0.1" or something like that on the whole model, but then hide all the atoms you don't want, say "~disp #0.1" to hide all atoms, and then to show all atoms of glycines 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for example, if they are in chain A of model #0.1).
Again, you can use Selection Inspector instead of commands for many things, although commands are better for doing things with specific residue numbers. 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 2, 2016, at 9:33 AM, A G Szabo <agszabo@bell.net> wrote:
You have been very helpful in explaining different items that use the command line.
I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc.
So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number.
I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model.
Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K.
The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec
I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1.
So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly.
Thank you
Arthur G. Szabo
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine Your message was helpful as it taught me how to specify residues within one chain out of a large number of chains, i.e. Chain #0.1: Res#.K That is Chain #0.1.K and res#. However, after trying a number of command ideas, I do not think it is possible to do what I would like to do. I know how to hide all the chains in the data base, and visualize the individual the ribbons of the chains that I want. I visualize the ribbons for Chain #0.1 E, and #0.1 K. PDB 2LMN I then go to "Tools" ; "Sequence" and select two chain sequences. I select a residue, Met 35 on #0.1 E, and then, "Actions" ; "Atoms/bonds" ; "Show". The side chain Met 35 pops up on Chain #0.1 E. then "ball and stick" (no problem so far have done this many times) the side chain of Met 35 shows as balls and sticks. If I color the atoms of Met35 a color different from the ribbon, the CA atom is nicely embedded in the ribbon. I also know that when I use the command line and enter "disp #0.1:35.E" I can achieve the same result without having to highlight the residue in the sequence of that chain. I can visualize several residues using the same command style. If I use the command line and enter "ribbackbone", the backbone atoms of Met 35 are displayed. When one visualizes four or five side chains on a chain, the presence of the backbone atoms starts to clutter up the image. The backbone atoms do not add to the information regarding the inter or intramolecular interactions that one would like to display between the different side chains. I then use your suggestion and enter the command "~disp #0.1:35.E @N,C,O,H" The backbone atoms of Met 35 disappear, BUT the rest of the side chain remains sitting above the ribbon. There is a gap between the side chain and the ribbon. Further to this imaging, I would like select and visualize some Gly residues on part of Chain #0.1K. Met35 of Chain #0.1E interacts with these Gly residues. With "ribbackbone" in effect the Gly residues show up as the five backbone atoms, C, N, O, and 2 H atoms. That would be fine but the esthetically it doesn't look good with the Met35 side chain and others just hanging there not attached to ribbon, and if I turn "ribbackbone" off in order to get CA of Met35 in the ribbon, then the Gly residues no longer have any atoms visualized and disappear into the ribbon.. I have tried various permutations, such as "disp #0.1:33.K,37.K,38.K @N,C,O,H" hoping that I might be able to visualize the Gly residues, it doesn't work. So that leads me back to my original statement that I don't think I can achieve the image that I would like to present. A suggestion would be if one could apply "ribbackbone" only to a specific chain in the model instead of to the entire model. Thanks your assistance, I am learning more and more about nuances of Chimera, which I recommend as a very user friendly package especially if you use the menu section. One thing I have had trouble understanding is the "Inspect Selection" menu that is available under "Actions". You have suggested that I use that on a couple of occasions, but it is a bit unfathomable. Tried to check it out in the Help sections but was unable to make any progress in understanding it. Best regards arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-02-16 3:38 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: showing backbone for some residues and not others Hi Arthur, I believe I understand completely, but I can only repeat my suggestions from before. You would use "ribbackbone" to allow both ribbon and backbone atoms, and then use "disp" to show the atoms you want to see and "~disp" to hide the atoms you don't want to see. Don't know what you mean by "didn't work". The exact disp and ~disp commands depend on the models, chains, residues,.. in your structure. Here is an example with PDB entry 2gbp, pretending I want to see all atoms of residues 40-50 but sidechain only of residues 20-30; everything in that structure is chain A: open 2gbp ribbackbone ~disp disp #0:40-50.A disp #0:20-30.A & with CA/C1' The last part of the last line means sidechains only. However, another way to the same result is to display all atoms of those residues but then hide their backbone atoms like we talked about before: disp #0:20-30.A ~disp #0:20-30.A@n,c,o,h Still one more step if you don't want fake CA-CA bonds between adjacent residues for which you are showing sidechain only: setattr m autochain false 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 2, 2016, at 11:21 AM, A G Szabo <agszabo@bell.net> wrote:
Elaine
The essential issue is that all of the Atoms of Gly are part of the backbone. So in order to visualize those atoms one has to turn them on with ribbackbone. But visualizing the backbone atoms of other residues with longer side chains clutters up the image, and I would rather have the backbone atoms of such amino acids turned off.
I sent you a power point attachment with the structure I am working with. This is the partial structure of a beta sheet amyloid made up of the same peptide all in a stack. So in order to show the key intramolecular interactions in one of the peptides in the stack one can show the selected residues. Only issue is that one cannot visualize Gly in any meaningful way unless ribbackbone is turned on.
Thanks for your assistance
Much appreciated
arthur
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-02-16 12:47 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question
Hi Arthur, Unfortunately "ribbackbone" only applies to the whole model. However, it is merely an "enabler" allowing backbone atoms and ribbon to be shown at the same time, if the atoms and ribbon both happen to be displayed for the same residue. You can still hide (~display) any atoms you don't want to see and hide ribbon (~ribbon) of any residue whose ribbon segment you don't want to see.
So you would have to use "ribbackbone #0.1" or something like that on the whole model, but then hide all the atoms you don't want, say "~disp #0.1" to hide all atoms, and then to show all atoms of glycines 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for example, if they are in chain A of model #0.1).
Again, you can use Selection Inspector instead of commands for many things, although commands are better for doing things with specific residue numbers. 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 2, 2016, at 9:33 AM, A G Szabo <agszabo@bell.net> wrote:
You have been very helpful in explaining different items that use the command line.
I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc.
So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number.
I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model.
Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K.
The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec
I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1.
So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly.
Thank you
Arthur G. Szabo
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Arthur, You are right, you have hit one of the limitations of Chimera: it is not possible to have ribbackbone on only part of a model, and when it is turned on you can only show the “real” positions of the backbone atoms which may appear as detached from the ribbon. Two possibilities are to show the CA as a bigger ball so that the detachment is not so obvious, or to use the cardinal spline for the ribbon which goes through the real CA atom positions, as mentioned earlier. This issue of CA floating away from the ribbon and the ways to (try to) solve it are discussed in the manual here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset> Selection Inspector is simply a dialog that shows the settings of the things you have selected currently, and allows you to change their settings by choosing or entering different values. If using this dialog, you don’t have to remember the commands. For example, instead of using “ribbackbone” command you can just select any atom in the model and use the Selection Inspector: in that dialog “Inspect: Molecule model” and then change its setting “ribbon hides backbone atoms” between true and false. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> Similarly, then I don’t have to explain the commands to change the ribbon from B-spline to cardinal spline… Instead, using the Selection Inspector and inspecting “Molecule model” you can change the settings for “ribbon spline” and “ribbon (cardinal) smoothing”. Best, 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 5, 2016, at 1:54 PM, A G Szabo <agszabo@bell.net> wrote:
Elaine
Your message was helpful as it taught me how to specify residues within one chain out of a large number of chains, i.e. Chain #0.1: Res#.K That is Chain #0.1.K and res#.
However, after trying a number of command ideas, I do not think it is possible to do what I would like to do.
I know how to hide all the chains in the data base, and visualize the individual the ribbons of the chains that I want. I visualize the ribbons for Chain #0.1 E, and #0.1 K. PDB 2LMN
I then go to "Tools" ; "Sequence" and select two chain sequences. I select a residue, Met 35 on #0.1 E, and then, "Actions" ; "Atoms/bonds" ; "Show". The side chain Met 35 pops up on Chain #0.1 E. then "ball and stick" (no problem so far have done this many times) the side chain of Met 35 shows as balls and sticks. If I color the atoms of Met35 a color different from the ribbon, the CA atom is nicely embedded in the ribbon.
I also know that when I use the command line and enter "disp #0.1:35.E" I can achieve the same result without having to highlight the residue in the sequence of that chain. I can visualize several residues using the same command style.
If I use the command line and enter "ribbackbone", the backbone atoms of Met 35 are displayed.
When one visualizes four or five side chains on a chain, the presence of the backbone atoms starts to clutter up the image. The backbone atoms do not add to the information regarding the inter or intramolecular interactions that one would like to display between the different side chains.
I then use your suggestion and enter the command "~disp #0.1:35.E @N,C,O,H"
The backbone atoms of Met 35 disappear, BUT the rest of the side chain remains sitting above the ribbon. There is a gap between the side chain and the ribbon.
Further to this imaging, I would like select and visualize some Gly residues on part of Chain #0.1K. Met35 of Chain #0.1E interacts with these Gly residues. With "ribbackbone" in effect the Gly residues show up as the five backbone atoms, C, N, O, and 2 H atoms.
That would be fine but the esthetically it doesn't look good with the Met35 side chain and others just hanging there not attached to ribbon, and if I turn "ribbackbone" off in order to get CA of Met35 in the ribbon, then the Gly residues no longer have any atoms visualized and disappear into the ribbon..
I have tried various permutations, such as "disp #0.1:33.K,37.K,38.K @N,C,O,H" hoping that I might be able to visualize the Gly residues, it doesn't work.
So that leads me back to my original statement that I don't think I can achieve the image that I would like to present.
A suggestion would be if one could apply "ribbackbone" only to a specific chain in the model instead of to the entire model.
Thanks your assistance, I am learning more and more about nuances of Chimera, which I recommend as a very user friendly package especially if you use the menu section. One thing I have had trouble understanding is the "Inspect Selection" menu that is available under "Actions". You have suggested that I use that on a couple of occasions, but it is a bit unfathomable. Tried to check it out in the Help sections but was unable to make any progress in understanding it.
Best regards
arthur
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-02-16 3:38 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: showing backbone for some residues and not others
Hi Arthur, I believe I understand completely, but I can only repeat my suggestions from before. You would use "ribbackbone" to allow both ribbon and backbone atoms, and then use "disp" to show the atoms you want to see and "~disp" to hide the atoms you don't want to see. Don't know what you mean by "didn't work".
The exact disp and ~disp commands depend on the models, chains, residues,.. in your structure.
Here is an example with PDB entry 2gbp, pretending I want to see all atoms of residues 40-50 but sidechain only of residues 20-30; everything in that structure is chain A:
open 2gbp ribbackbone ~disp disp #0:40-50.A disp #0:20-30.A & with CA/C1'
The last part of the last line means sidechains only. However, another way to the same result is to display all atoms of those residues but then hide their backbone atoms like we talked about before:
disp #0:20-30.A ~disp #0:20-30.A@n,c,o,h
Still one more step if you don't want fake CA-CA bonds between adjacent residues for which you are showing sidechain only:
setattr m autochain false
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 2, 2016, at 11:21 AM, A G Szabo <agszabo@bell.net> wrote:
Elaine
The essential issue is that all of the Atoms of Gly are part of the backbone. So in order to visualize those atoms one has to turn them on with ribbackbone. But visualizing the backbone atoms of other residues with longer side chains clutters up the image, and I would rather have the backbone atoms of such amino acids turned off.
I sent you a power point attachment with the structure I am working with. This is the partial structure of a beta sheet amyloid made up of the same peptide all in a stack. So in order to show the key intramolecular interactions in one of the peptides in the stack one can show the selected residues. Only issue is that one cannot visualize Gly in any meaningful way unless ribbackbone is turned on.
Thanks for your assistance
Much appreciated
arthur
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-02-16 12:47 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question
Hi Arthur, Unfortunately "ribbackbone" only applies to the whole model. However, it is merely an "enabler" allowing backbone atoms and ribbon to be shown at the same time, if the atoms and ribbon both happen to be displayed for the same residue. You can still hide (~display) any atoms you don't want to see and hide ribbon (~ribbon) of any residue whose ribbon segment you don't want to see.
So you would have to use "ribbackbone #0.1" or something like that on the whole model, but then hide all the atoms you don't want, say "~disp #0.1" to hide all atoms, and then to show all atoms of glycines 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for example, if they are in chain A of model #0.1).
Again, you can use Selection Inspector instead of commands for many things, although commands are better for doing things with specific residue numbers. 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 2, 2016, at 9:33 AM, A G Szabo <agszabo@bell.net> wrote:
You have been very helpful in explaining different items that use the command line.
I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc.
So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number.
I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model.
Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K.
The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec
I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1.
So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly.
Thank you
Arthur G. Szabo
_______________________________________________ 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
Elaine Thank you for your assistance once again. If you ever have need of some supportive comments in order to ensure grant support I would be very willing to provide it. arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-05-16 5:26 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] showing backbone for some residues and not others Hi Arthur, You are right, you have hit one of the limitations of Chimera: it is not possible to have ribbackbone on only part of a model, and when it is turned on you can only show the “real” positions of the backbone atoms which may appear as detached from the ribbon. Two possibilities are to show the CA as a bigger ball so that the detachment is not so obvious, or to use the cardinal spline for the ribbon which goes through the real CA atom positions, as mentioned earlier. This issue of CA floating away from the ribbon and the ways to (try to) solve it are discussed in the manual here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset> Selection Inspector is simply a dialog that shows the settings of the things you have selected currently, and allows you to change their settings by choosing or entering different values. If using this dialog, you don’t have to remember the commands. For example, instead of using “ribbackbone” command you can just select any atom in the model and use the Selection Inspector: in that dialog “Inspect: Molecule model” and then change its setting “ribbon hides backbone atoms” between true and false. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> Similarly, then I don’t have to explain the commands to change the ribbon from B-spline to cardinal spline… Instead, using the Selection Inspector and inspecting “Molecule model” you can change the settings for “ribbon spline” and “ribbon (cardinal) smoothing”. Best, 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 5, 2016, at 1:54 PM, A G Szabo <agszabo@bell.net> wrote:
Elaine
Your message was helpful as it taught me how to specify residues within one chain out of a large number of chains, i.e. Chain #0.1: Res#.K That is Chain #0.1.K and res#.
However, after trying a number of command ideas, I do not think it is possible to do what I would like to do.
I know how to hide all the chains in the data base, and visualize the individual the ribbons of the chains that I want. I visualize the ribbons for Chain #0.1 E, and #0.1 K. PDB 2LMN
I then go to "Tools" ; "Sequence" and select two chain sequences. I select a residue, Met 35 on #0.1 E, and then, "Actions" ; "Atoms/bonds" ; "Show". The side chain Met 35 pops up on Chain #0.1 E. then "ball and stick" (no problem so far have done this many times) the side chain of Met 35 shows as balls and sticks. If I color the atoms of Met35 a color different from the ribbon, the CA atom is nicely embedded in the ribbon.
I also know that when I use the command line and enter "disp #0.1:35.E" I can achieve the same result without having to highlight the residue in the sequence of that chain. I can visualize several residues using the same command style.
If I use the command line and enter "ribbackbone", the backbone atoms of Met 35 are displayed.
When one visualizes four or five side chains on a chain, the presence of the backbone atoms starts to clutter up the image. The backbone atoms do not add to the information regarding the inter or intramolecular interactions that one would like to display between the different side chains.
I then use your suggestion and enter the command "~disp #0.1:35.E @N,C,O,H"
The backbone atoms of Met 35 disappear, BUT the rest of the side chain remains sitting above the ribbon. There is a gap between the side chain and the ribbon.
Further to this imaging, I would like select and visualize some Gly residues on part of Chain #0.1K. Met35 of Chain #0.1E interacts with these Gly residues. With "ribbackbone" in effect the Gly residues show up as the five backbone atoms, C, N, O, and 2 H atoms.
That would be fine but the esthetically it doesn't look good with the Met35 side chain and others just hanging there not attached to ribbon, and if I turn "ribbackbone" off in order to get CA of Met35 in the ribbon, then the Gly residues no longer have any atoms visualized and disappear into the ribbon..
I have tried various permutations, such as "disp #0.1:33.K,37.K,38.K @N,C,O,H" hoping that I might be able to visualize the Gly residues, it doesn't work.
So that leads me back to my original statement that I don't think I can achieve the image that I would like to present.
A suggestion would be if one could apply "ribbackbone" only to a specific chain in the model instead of to the entire model.
Thanks your assistance, I am learning more and more about nuances of Chimera, which I recommend as a very user friendly package especially if you use the menu section. One thing I have had trouble understanding is the "Inspect Selection" menu that is available under "Actions". You have suggested that I use that on a couple of occasions, but it is a bit unfathomable. Tried to check it out in the Help sections but was unable to make any progress in understanding it.
Best regards
arthur
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-02-16 3:38 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: showing backbone for some residues and not others
Hi Arthur, I believe I understand completely, but I can only repeat my suggestions from before. You would use "ribbackbone" to allow both ribbon and backbone atoms, and then use "disp" to show the atoms you want to see and "~disp" to hide the atoms you don't want to see. Don't know what you mean by "didn't work".
The exact disp and ~disp commands depend on the models, chains, residues,.. in your structure.
Here is an example with PDB entry 2gbp, pretending I want to see all atoms of residues 40-50 but sidechain only of residues 20-30; everything in that structure is chain A:
open 2gbp ribbackbone ~disp disp #0:40-50.A disp #0:20-30.A & with CA/C1'
The last part of the last line means sidechains only. However, another way to the same result is to display all atoms of those residues but then hide their backbone atoms like we talked about before:
disp #0:20-30.A ~disp #0:20-30.A@n,c,o,h
Still one more step if you don't want fake CA-CA bonds between adjacent residues for which you are showing sidechain only:
setattr m autochain false
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 2, 2016, at 11:21 AM, A G Szabo <agszabo@bell.net> wrote:
Elaine
The essential issue is that all of the Atoms of Gly are part of the backbone. So in order to visualize those atoms one has to turn them on with ribbackbone. But visualizing the backbone atoms of other residues with longer side chains clutters up the image, and I would rather have the backbone atoms of such amino acids turned off.
I sent you a power point attachment with the structure I am working with. This is the partial structure of a beta sheet amyloid made up of the same peptide all in a stack. So in order to show the key intramolecular interactions in one of the peptides in the stack one can show the selected residues. Only issue is that one cannot visualize Gly in any meaningful way unless ribbackbone is turned on.
Thanks for your assistance
Much appreciated
arthur
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-02-16 12:47 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question
Hi Arthur, Unfortunately "ribbackbone" only applies to the whole model. However, it is merely an "enabler" allowing backbone atoms and ribbon to be shown at the same time, if the atoms and ribbon both happen to be displayed for the same residue. You can still hide (~display) any atoms you don't want to see and hide ribbon (~ribbon) of any residue whose ribbon segment you don't want to see.
So you would have to use "ribbackbone #0.1" or something like that on the whole model, but then hide all the atoms you don't want, say "~disp #0.1" to hide all atoms, and then to show all atoms of glycines 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for example, if they are in chain A of model #0.1).
Again, you can use Selection Inspector instead of commands for many things, although commands are better for doing things with specific residue numbers. 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 2, 2016, at 9:33 AM, A G Szabo <agszabo@bell.net> wrote:
You have been very helpful in explaining different items that use the command line.
I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc.
So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number.
I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model.
Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K.
The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec
I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1.
So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly.
Thank you
Arthur G. Szabo
_______________________________________________ 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
Hi Arthur, I remembered one more “trick” — instead of using ribbackbone on a single structure, you could open the same structure twice: In one copy of the structure, show ribbons, and show the residues for which you want to see only the sidechains attached to the ribbon (no ribbackbone). In the other copy of the structure, do not show any ribbons. Show only the atoms of residues for which you want to show backbone atoms. The atoms from the second copy could still be floating away from the ribbon of the first copy, but at least the sidechain-only residues (also from the first copy) would be attached to the ribbon. Best, Elaine
On Dec 5, 2016, at 3:12 PM, A G Szabo <agszabo@bell.net> wrote:
Elaine
Thank you for your assistance once again. If you ever have need of some supportive comments in order to ensure grant support I would be very willing to provide it.
arthur
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-05-16 5:26 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] showing backbone for some residues and not others
Hi Arthur, You are right, you have hit one of the limitations of Chimera: it is not possible to have ribbackbone on only part of a model, and when it is turned on you can only show the “real” positions of the backbone atoms which may appear as detached from the ribbon.
Two possibilities are to show the CA as a bigger ball so that the detachment is not so obvious, or to use the cardinal spline for the ribbon which goes through the real CA atom positions, as mentioned earlier.
This issue of CA floating away from the ribbon and the ways to (try to) solve it are discussed in the manual here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>
Selection Inspector is simply a dialog that shows the settings of the things you have selected currently, and allows you to change their settings by choosing or entering different values. If using this dialog, you don’t have to remember the commands. For example, instead of using “ribbackbone” command you can just select any atom in the model and use the Selection Inspector: in that dialog “Inspect: Molecule model” and then change its setting “ribbon hides backbone atoms” between true and false.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
Similarly, then I don’t have to explain the commands to change the ribbon from B-spline to cardinal spline… Instead, using the Selection Inspector and inspecting “Molecule model” you can change the settings for “ribbon spline” and “ribbon (cardinal) smoothing”.
Best, Elaine
participants (2)
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A G Szabo -
Elaine Meng