Surface representation of protein-ligand interactions
Dear ChimeraX users! I am working on the surface representation of the protein-ligand contacts. Here is my script: # load pdb of the complex and keep inly the 1st model open pdb.pdb close #1.2-end #calculate electrostatic surface coulombic protein key true #change view of the ligand size ligand atomRadius +.8 color #1.1 & ligand & C gold style ligand sphere #protein-ligand contacts hbonds #1.1 & ligand reveal true log true contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange ~label ligand hide #1 & protein bonds hide #1 & protein pseudobonds Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand? i've tried: transparency 20 surface, but it change the transparency for whole surface 2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ? 3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange Many thanks in advance! Cheers Enrico
P.S. First, please ignore my question regarding surface transparency since I've just found it! just additional question about contacts contacts #1.1 & ligand why sometimes I could see on the displayed layer the same residue two times? Does it mean two possible interactions with the ligand ? May I suppress the replicas from the contacts layer? Cheers, Enrico вт, 18 янв. 2022 г. в 10:06, Enrico Martinez <jmsstarlight@gmail.com>:
Dear ChimeraX users! I am working on the surface representation of the protein-ligand contacts. Here is my script:
# load pdb of the complex and keep inly the 1st model open pdb.pdb close #1.2-end
#calculate electrostatic surface coulombic protein key true
#change view of the ligand size ligand atomRadius +.8 color #1.1 & ligand & C gold style ligand sphere
#protein-ligand contacts hbonds #1.1 & ligand reveal true log true contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange ~label ligand hide #1 & protein bonds hide #1 & protein pseudobonds
Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand?
i've tried: transparency 20 surface, but it change the transparency for whole surface
2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ?
3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange
Many thanks in advance! Cheers Enrico
On Jan 18, 2022, at 3:08 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
P.S. First, please ignore my question regarding surface transparency since I've just found it! just additional question about contacts contacts #1.1 & ligand why sometimes I could see on the displayed layer the same residue two times? Does it mean two possible interactions with the ligand ? May I suppress the replicas from the contacts layer?
I don't understand what you mean by displayed layer. Graphics window? List of results in the Log? The contacts command works on atoms, whereas residues have multiple atoms -- so if there are multiple atoms in the residue that contact the ligand, you will see multiple lines. If you mean the same two atoms are listed twice in the Log for H-bonds, it means it could be donor->acceptor or acceptor<-donor. You can only control the atomic parameters, there is no option to only draw one line per residue.
Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand?
(you already figured this out, as you said above)
2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ?
See "set subdivision" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#subdivision> ... or "graphics quality" and its "atomTriangles" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality>
3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange
You should check the help for the command you are already using. E.g. just use command "help contacts" to see the help page for "contacts". You can specify the VDW surface contact cutoff with the "overlapCutoff" option, or if you don't care about the different atomic sizes and only want to use center-center distances, see the "distanceOnly" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Thank you very much Elaine! Regarding my first question (about the displayed layer of the amino-acids involved in the contact with the ligand): I mean the displayed names (like Glu-199) in the graphical windows (what I see on the screen-shot!), which resulted from the command "contacts". So some amino acids are mentioned tvisely in the same graphical visualization. P.S. may I attach a PNG file directly to the message ?? Cheers, Enrico вт, 18 янв. 2022 г. в 19:41, Elaine Meng <meng@cgl.ucsf.edu>:
On Jan 18, 2022, at 3:08 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
P.S. First, please ignore my question regarding surface transparency since I've just found it! just additional question about contacts contacts #1.1 & ligand why sometimes I could see on the displayed layer the same residue two times? Does it mean two possible interactions with the ligand ? May I suppress the replicas from the contacts layer?
I don't understand what you mean by displayed layer. Graphics window? List of results in the Log? The contacts command works on atoms, whereas residues have multiple atoms -- so if there are multiple atoms in the residue that contact the ligand, you will see multiple lines. If you mean the same two atoms are listed twice in the Log for H-bonds, it means it could be donor->acceptor or acceptor<-donor. You can only control the atomic parameters, there is no option to only draw one line per residue.
Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand?
(you already figured this out, as you said above)
2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ?
See "set subdivision" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#subdivision> ... or "graphics quality" and its "atomTriangles" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality>
3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange
You should check the help for the command you are already using. E.g. just use command "help contacts" to see the help page for "contacts". You can specify the VDW surface contact cutoff with the "overlapCutoff" option, or if you don't care about the different atomic sizes and only want to use center-center distances, see the "distanceOnly" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
As far as I know, there would only be one label for the same residue. Maybe you have open/displayed more than one Glu-199, possibly in different chains or different models. So if it is multiple models, make sure you close or at least hide any extra models. If it is multiple chains in the same model, then specify only the chain you want to label in the labeling command. Yes you can attach images, sessions, etc. to messages sent here. Elaine
On Jan 19, 2022, at 3:27 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine! Regarding my first question (about the displayed layer of the amino-acids involved in the contact with the ligand): I mean the displayed names (like Glu-199) in the graphical windows (what I see on the screen-shot!), which resulted from the command "contacts". So some amino acids are mentioned tvisely in the same graphical visualization. P.S. may I attach a PNG file directly to the message ?? Cheers, Enrico
Please see the picture enclosed (as you see there is a duplicate name of glu-166). I've just checked my script- there is always one model used for the visualization, so I believe it may be due to my pdb. Actually to produce this pdb I fused dockins poses with pdb of protein. Since I did flexible docking the side chain of Glu-166 is present in each frame of the ligand and the backbone of the same residue is in each frame of the protein (now everything within the same multi-model PDB file). I've just check in pym**l and it recognizes the contacts without the duplications, so may be as a trick I have to hide backbones in chimeraX ? The second question about labels: as you may see on the screenshot there are two labels placed using: 2dlab create title text "DOLCE (pdb XRAY), rep 1th" color red font gothic xpos .02 ypos .99 size 40 2dlab create title2 text "Created by Enrico Martinez, 2022" color indigo font Avenir xpos .02 ypos .02 size 33 I can not understand why they are always in the middle of the image (on Y coordinates!) since the first label should be always on the top (xpos .02 ypos .99 size 40) and the second one in the bottom (xpos .02 ypos .02 size 33). At least I see it like this in chimeraX gui. The same is for the electrostatic diagram (-10.. 10), which emerges in the central part of the image ... Many thanks in advance! Enrico ср, 19 янв. 2022 г. в 21:13, Elaine Meng <meng@cgl.ucsf.edu>:
As far as I know, there would only be one label for the same residue. Maybe you have open/displayed more than one Glu-199, possibly in different chains or different models. So if it is multiple models, make sure you close or at least hide any extra models. If it is multiple chains in the same model, then specify only the chain you want to label in the labeling command.
Yes you can attach images, sessions, etc. to messages sent here. Elaine
On Jan 19, 2022, at 3:27 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine! Regarding my first question (about the displayed layer of the amino-acids involved in the contact with the ligand): I mean the displayed names (like Glu-199) in the graphical windows (what I see on the screen-shot!), which resulted from the command "contacts". So some amino acids are mentioned tvisely in the same graphical visualization. P.S. may I attach a PNG file directly to the message ?? Cheers, Enrico
Hello, There is something weird about your PDB file so that ChimeraX thinks there are two residues that are both Glu-166. Since I don't know exactly what is weird about it, I don't know you would fix it, but maybe your idea of hiding the backbone would work. As for the 2D labels, I have never had this problem. It uses the xpos and ypos I give in the command. However, I am always using it interactively (not in batch mode) and I always save an image that has the same aspect ratio as the graphics window of the display. So my only idea is that maybe you are saving an image with different aspect ratio than your graphics window (e.g. graphics window is horizontal rectangle but the image you are saving is a square). I would not recommend saving a different aspect ratio. If you want a square image then make the graphics window square beforehand, e.g. with "windowsize" command. However, that applies to interactive use. I don't know if/how it works in nogui. But maybe you are using the GUI even though scripting it like a batch mode. I don't have gothic font and it looks from the image you sent that you do not have it either. You can see the list of possible fonts in ChimeraX with command "2dlabels listfonts" (on the same machine you are making the images, of course). See 2dlabels help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.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 Jan 20, 2022, at 1:35 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Please see the picture enclosed (as you see there is a duplicate name of glu-166). I've just checked my script- there is always one model used for the visualization, so I believe it may be due to my pdb. Actually to produce this pdb I fused dockins poses with pdb of protein. Since I did flexible docking the side chain of Glu-166 is present in each frame of the ligand and the backbone of the same residue is in each frame of the protein (now everything within the same multi-model PDB file). I've just check in pym**l and it recognizes the contacts without the duplications, so may be as a trick I have to hide backbones in chimeraX ?
The second question about labels: as you may see on the screenshot there are two labels placed using: 2dlab create title text "DOLCE (pdb XRAY), rep 1th" color red font gothic xpos .02 ypos .99 size 40 2dlab create title2 text "Created by Enrico Martinez, 2022" color indigo font Avenir xpos .02 ypos .02 size 33 I can not understand why they are always in the middle of the image (on Y coordinates!) since the first label should be always on the top (xpos .02 ypos .99 size 40) and the second one in the bottom (xpos .02 ypos .02 size 33). At least I see it like this in chimeraX gui. The same is for the electrostatic diagram (-10.. 10), which emerges in the central part of the image ... Many thanks in advance! Enrico
ср, 19 янв. 2022 г. в 21:13, Elaine Meng <meng@cgl.ucsf.edu>:
As far as I know, there would only be one label for the same residue. Maybe you have open/displayed more than one Glu-199, possibly in different chains or different models. So if it is multiple models, make sure you close or at least hide any extra models. If it is multiple chains in the same model, then specify only the chain you want to label in the labeling command.
Yes you can attach images, sessions, etc. to messages sent here. Elaine
On Jan 19, 2022, at 3:27 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine! Regarding my first question (about the displayed layer of the amino-acids involved in the contact with the ligand): I mean the displayed names (like Glu-199) in the graphical windows (what I see on the screen-shot!), which resulted from the command "contacts". So some amino acids are mentioned tvisely in the same graphical visualization. P.S. may I attach a PNG file directly to the message ?? Cheers, Enrico
<test.png>
Thanks a lot, Elaine! It was exactly due to the mismatch between resolutions. So for the simplicity I have to avoid indication of the resolutions in the save command in order that it could be taken automatically? Cheera Enrico чт, 20 янв. 2022 г. в 21:39, Elaine Meng <meng@cgl.ucsf.edu>:
Hello, There is something weird about your PDB file so that ChimeraX thinks there are two residues that are both Glu-166. Since I don't know exactly what is weird about it, I don't know you would fix it, but maybe your idea of hiding the backbone would work.
As for the 2D labels, I have never had this problem. It uses the xpos and ypos I give in the command. However, I am always using it interactively (not in batch mode) and I always save an image that has the same aspect ratio as the graphics window of the display.
So my only idea is that maybe you are saving an image with different aspect ratio than your graphics window (e.g. graphics window is horizontal rectangle but the image you are saving is a square). I would not recommend saving a different aspect ratio. If you want a square image then make the graphics window square beforehand, e.g. with "windowsize" command. However, that applies to interactive use. I don't know if/how it works in nogui. But maybe you are using the GUI even though scripting it like a batch mode.
I don't have gothic font and it looks from the image you sent that you do not have it either. You can see the list of possible fonts in ChimeraX with command "2dlabels listfonts" (on the same machine you are making the images, of course).
See 2dlabels help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.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 Jan 20, 2022, at 1:35 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Please see the picture enclosed (as you see there is a duplicate name of glu-166). I've just checked my script- there is always one model used for the visualization, so I believe it may be due to my pdb. Actually to produce this pdb I fused dockins poses with pdb of protein. Since I did flexible docking the side chain of Glu-166 is present in each frame of the ligand and the backbone of the same residue is in each frame of the protein (now everything within the same multi-model PDB file). I've just check in pym**l and it recognizes the contacts without the duplications, so may be as a trick I have to hide backbones in chimeraX ?
The second question about labels: as you may see on the screenshot there are two labels placed using: 2dlab create title text "DOLCE (pdb XRAY), rep 1th" color red font gothic xpos .02 ypos .99 size 40 2dlab create title2 text "Created by Enrico Martinez, 2022" color indigo font Avenir xpos .02 ypos .02 size 33 I can not understand why they are always in the middle of the image (on Y coordinates!) since the first label should be always on the top (xpos .02 ypos .99 size 40) and the second one in the bottom (xpos .02 ypos .02 size 33). At least I see it like this in chimeraX gui. The same is for the electrostatic diagram (-10.. 10), which emerges in the central part of the image ... Many thanks in advance! Enrico
ср, 19 янв. 2022 г. в 21:13, Elaine Meng <meng@cgl.ucsf.edu>:
As far as I know, there would only be one label for the same residue. Maybe you have open/displayed more than one Glu-199, possibly in different chains or different models. So if it is multiple models, make sure you close or at least hide any extra models. If it is multiple chains in the same model, then specify only the chain you want to label in the labeling command.
Yes you can attach images, sessions, etc. to messages sent here. Elaine
On Jan 19, 2022, at 3:27 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine! Regarding my first question (about the displayed layer of the amino-acids involved in the contact with the ligand): I mean the displayed names (like Glu-199) in the graphical windows (what I see on the screen-shot!), which resulted from the command "contacts". So some amino acids are mentioned tvisely in the same graphical visualization. P.S. may I attach a PNG file directly to the message ?? Cheers, Enrico
<test.png>
Different resolution should not be a problem, only different height/width ratio. So if your window is 500 x 700 pixels, you could save anything with 5 x 7 ratio (1000 x 1400, 750 x 1050, etc.). You can adjust the size of the window with "windowsize". In "save" command just give either "width" (which will automatically fix height) or "height" (which will automatically fix width), but do not give both unless they match the ratio of your window. I explained all of these before, but maybe it was not clear. see help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/windowsize.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image> Elaine
On Jan 21, 2022, at 1:02 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thanks a lot, Elaine! It was exactly due to the mismatch between resolutions. So for the simplicity I have to avoid indication of the resolutions in the save command in order that it could be taken automatically? Cheera Enrico
чт, 20 янв. 2022 г. в 21:39, Elaine Meng <meng@cgl.ucsf.edu>:
Hello, There is something weird about your PDB file so that ChimeraX thinks there are two residues that are both Glu-166. Since I don't know exactly what is weird about it, I don't know you would fix it, but maybe your idea of hiding the backbone would work.
As for the 2D labels, I have never had this problem. It uses the xpos and ypos I give in the command. However, I am always using it interactively (not in batch mode) and I always save an image that has the same aspect ratio as the graphics window of the display.
So my only idea is that maybe you are saving an image with different aspect ratio than your graphics window (e.g. graphics window is horizontal rectangle but the image you are saving is a square). I would not recommend saving a different aspect ratio. If you want a square image then make the graphics window square beforehand, e.g. with "windowsize" command. However, that applies to interactive use. I don't know if/how it works in nogui. But maybe you are using the GUI even though scripting it like a batch mode.
I don't have gothic font and it looks from the image you sent that you do not have it either. You can see the list of possible fonts in ChimeraX with command "2dlabels listfonts" (on the same machine you are making the images, of course).
See 2dlabels help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.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 Jan 20, 2022, at 1:35 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Please see the picture enclosed (as you see there is a duplicate name of glu-166). I've just checked my script- there is always one model used for the visualization, so I believe it may be due to my pdb. Actually to produce this pdb I fused dockins poses with pdb of protein. Since I did flexible docking the side chain of Glu-166 is present in each frame of the ligand and the backbone of the same residue is in each frame of the protein (now everything within the same multi-model PDB file). I've just check in pym**l and it recognizes the contacts without the duplications, so may be as a trick I have to hide backbones in chimeraX ?
The second question about labels: as you may see on the screenshot there are two labels placed using: 2dlab create title text "DOLCE (pdb XRAY), rep 1th" color red font gothic xpos .02 ypos .99 size 40 2dlab create title2 text "Created by Enrico Martinez, 2022" color indigo font Avenir xpos .02 ypos .02 size 33 I can not understand why they are always in the middle of the image (on Y coordinates!) since the first label should be always on the top (xpos .02 ypos .99 size 40) and the second one in the bottom (xpos .02 ypos .02 size 33). At least I see it like this in chimeraX gui. The same is for the electrostatic diagram (-10.. 10), which emerges in the central part of the image ... Many thanks in advance! Enrico
ср, 19 янв. 2022 г. в 21:13, Elaine Meng <meng@cgl.ucsf.edu>:
As far as I know, there would only be one label for the same residue. Maybe you have open/displayed more than one Glu-199, possibly in different chains or different models. So if it is multiple models, make sure you close or at least hide any extra models. If it is multiple chains in the same model, then specify only the chain you want to label in the labeling command.
Yes you can attach images, sessions, etc. to messages sent here. Elaine
On Jan 19, 2022, at 3:27 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine! Regarding my first question (about the displayed layer of the amino-acids involved in the contact with the ligand): I mean the displayed names (like Glu-199) in the graphical windows (what I see on the screen-shot!), which resulted from the command "contacts". So some amino acids are mentioned tvisely in the same graphical visualization. P.S. may I attach a PNG file directly to the message ?? Cheers, Enrico
<test.png>
Right, thank you very much! And yes, I've just double checked the problem with double labels was due to the my pdb so I ould solve it via selection only of the side chains for the labels: label @@display & sideonly height 0.8 color gold Keep in touch Enrico пт, 21 янв. 2022 г. в 17:37, Elaine Meng <meng@cgl.ucsf.edu>:
Different resolution should not be a problem, only different height/width ratio. So if your window is 500 x 700 pixels, you could save anything with 5 x 7 ratio (1000 x 1400, 750 x 1050, etc.).
You can adjust the size of the window with "windowsize". In "save" command just give either "width" (which will automatically fix height) or "height" (which will automatically fix width), but do not give both unless they match the ratio of your window. I explained all of these before, but maybe it was not clear.
see help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/windowsize.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image>
Elaine
On Jan 21, 2022, at 1:02 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thanks a lot, Elaine! It was exactly due to the mismatch between resolutions. So for the simplicity I have to avoid indication of the resolutions in the save command in order that it could be taken automatically? Cheera Enrico
чт, 20 янв. 2022 г. в 21:39, Elaine Meng <meng@cgl.ucsf.edu>:
Hello, There is something weird about your PDB file so that ChimeraX thinks there are two residues that are both Glu-166. Since I don't know exactly what is weird about it, I don't know you would fix it, but maybe your idea of hiding the backbone would work.
As for the 2D labels, I have never had this problem. It uses the xpos and ypos I give in the command. However, I am always using it interactively (not in batch mode) and I always save an image that has the same aspect ratio as the graphics window of the display.
So my only idea is that maybe you are saving an image with different aspect ratio than your graphics window (e.g. graphics window is horizontal rectangle but the image you are saving is a square). I would not recommend saving a different aspect ratio. If you want a square image then make the graphics window square beforehand, e.g. with "windowsize" command. However, that applies to interactive use. I don't know if/how it works in nogui. But maybe you are using the GUI even though scripting it like a batch mode.
I don't have gothic font and it looks from the image you sent that you do not have it either. You can see the list of possible fonts in ChimeraX with command "2dlabels listfonts" (on the same machine you are making the images, of course).
See 2dlabels help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.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 Jan 20, 2022, at 1:35 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Please see the picture enclosed (as you see there is a duplicate name of glu-166). I've just checked my script- there is always one model used for the visualization, so I believe it may be due to my pdb. Actually to produce this pdb I fused dockins poses with pdb of protein. Since I did flexible docking the side chain of Glu-166 is present in each frame of the ligand and the backbone of the same residue is in each frame of the protein (now everything within the same multi-model PDB file). I've just check in pym**l and it recognizes the contacts without the duplications, so may be as a trick I have to hide backbones in chimeraX ?
The second question about labels: as you may see on the screenshot there are two labels placed using: 2dlab create title text "DOLCE (pdb XRAY), rep 1th" color red font gothic xpos .02 ypos .99 size 40 2dlab create title2 text "Created by Enrico Martinez, 2022" color indigo font Avenir xpos .02 ypos .02 size 33 I can not understand why they are always in the middle of the image (on Y coordinates!) since the first label should be always on the top (xpos .02 ypos .99 size 40) and the second one in the bottom (xpos .02 ypos .02 size 33). At least I see it like this in chimeraX gui. The same is for the electrostatic diagram (-10.. 10), which emerges in the central part of the image ... Many thanks in advance! Enrico
ср, 19 янв. 2022 г. в 21:13, Elaine Meng <meng@cgl.ucsf.edu>:
As far as I know, there would only be one label for the same residue. Maybe you have open/displayed more than one Glu-199, possibly in different chains or different models. So if it is multiple models, make sure you close or at least hide any extra models. If it is multiple chains in the same model, then specify only the chain you want to label in the labeling command.
Yes you can attach images, sessions, etc. to messages sent here. Elaine
On Jan 19, 2022, at 3:27 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine! Regarding my first question (about the displayed layer of the amino-acids involved in the contact with the ligand): I mean the displayed names (like Glu-199) in the graphical windows (what I see on the screen-shot!), which resulted from the command "contacts". So some amino acids are mentioned tvisely in the same graphical visualization. P.S. may I attach a PNG file directly to the message ?? Cheers, Enrico
<test.png>
P.S. I also tried increase quality of the representation using the following options: # 100 times more that the default option: set subdivision 100 # 100 times more that the default option: graphics quality 100 # 10 times more that the default option: graphics quality atomTriangles 50000000 save ./test.png however it produced the image with the same quality as it has been before.. Cheers, Enrico вт, 18 янв. 2022 г. в 19:41, Elaine Meng <meng@cgl.ucsf.edu>:
On Jan 18, 2022, at 3:08 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
P.S. First, please ignore my question regarding surface transparency since I've just found it! just additional question about contacts contacts #1.1 & ligand why sometimes I could see on the displayed layer the same residue two times? Does it mean two possible interactions with the ligand ? May I suppress the replicas from the contacts layer?
I don't understand what you mean by displayed layer. Graphics window? List of results in the Log? The contacts command works on atoms, whereas residues have multiple atoms -- so if there are multiple atoms in the residue that contact the ligand, you will see multiple lines. If you mean the same two atoms are listed twice in the Log for H-bonds, it means it could be donor->acceptor or acceptor<-donor. You can only control the atomic parameters, there is no option to only draw one line per residue.
Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand?
(you already figured this out, as you said above)
2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ?
See "set subdivision" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#subdivision> ... or "graphics quality" and its "atomTriangles" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality>
3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange
You should check the help for the command you are already using. E.g. just use command "help contacts" to see the help page for "contacts". You can specify the VDW surface contact cutoff with the "overlapCutoff" option, or if you don't care about the different atomic sizes and only want to use center-center distances, see the "distanceOnly" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
I guess I don't know what you mean by quality, then. If you mean you want higher resolution (more pixels in the image), then just specify width and height in the save image command. see the "save" help for image-saving options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image> Elaine
On Jan 19, 2022, at 6:32 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
P.S. I also tried increase quality of the representation using the following options: # 100 times more that the default option: set subdivision 100 # 100 times more that the default option: graphics quality 100 # 10 times more that the default option: graphics quality atomTriangles 50000000 save ./test.png however it produced the image with the same quality as it has been before.. Cheers, Enrico
вт, 18 янв. 2022 г. в 19:41, Elaine Meng <meng@cgl.ucsf.edu>:
On Jan 18, 2022, at 3:08 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
P.S. First, please ignore my question regarding surface transparency since I've just found it! just additional question about contacts contacts #1.1 & ligand why sometimes I could see on the displayed layer the same residue two times? Does it mean two possible interactions with the ligand ? May I suppress the replicas from the contacts layer?
I don't understand what you mean by displayed layer. Graphics window? List of results in the Log? The contacts command works on atoms, whereas residues have multiple atoms -- so if there are multiple atoms in the residue that contact the ligand, you will see multiple lines. If you mean the same two atoms are listed twice in the Log for H-bonds, it means it could be donor->acceptor or acceptor<-donor. You can only control the atomic parameters, there is no option to only draw one line per residue.
Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand?
(you already figured this out, as you said above)
2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ?
See "set subdivision" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#subdivision> ... or "graphics quality" and its "atomTriangles" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality>
3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange
You should check the help for the command you are already using. E.g. just use command "help contacts" to see the help page for "contacts". You can specify the VDW surface contact cutoff with the "overlapCutoff" option, or if you don't care about the different atomic sizes and only want to use center-center distances, see the "distanceOnly" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Actually, don't bother using both width and height. Just give one or the other, and then the one you didn't give will be set automatically to match the height/width ratio of the graphics window. That way what you get will match what is shown in the graphics window. Elaine
On Jan 19, 2022, at 12:15 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I guess I don't know what you mean by quality, then. If you mean you want higher resolution (more pixels in the image), then just specify width and height in the save image command.
see the "save" help for image-saving options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image>
Elaine
On Jan 19, 2022, at 6:32 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
P.S. I also tried increase quality of the representation using the following options: # 100 times more that the default option: set subdivision 100 # 100 times more that the default option: graphics quality 100 # 10 times more that the default option: graphics quality atomTriangles 50000000 save ./test.png however it produced the image with the same quality as it has been before.. Cheers, Enrico
вт, 18 янв. 2022 г. в 19:41, Elaine Meng <meng@cgl.ucsf.edu>:
On Jan 18, 2022, at 3:08 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
P.S. First, please ignore my question regarding surface transparency since I've just found it! just additional question about contacts contacts #1.1 & ligand why sometimes I could see on the displayed layer the same residue two times? Does it mean two possible interactions with the ligand ? May I suppress the replicas from the contacts layer?
I don't understand what you mean by displayed layer. Graphics window? List of results in the Log? The contacts command works on atoms, whereas residues have multiple atoms -- so if there are multiple atoms in the residue that contact the ligand, you will see multiple lines. If you mean the same two atoms are listed twice in the Log for H-bonds, it means it could be donor->acceptor or acceptor<-donor. You can only control the atomic parameters, there is no option to only draw one line per residue.
Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand?
(you already figured this out, as you said above)
2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ?
See "set subdivision" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#subdivision> ... or "graphics quality" and its "atomTriangles" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality>
3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange
You should check the help for the command you are already using. E.g. just use command "help contacts" to see the help page for "contacts". You can specify the VDW surface contact cutoff with the "overlapCutoff" option, or if you don't care about the different atomic sizes and only want to use center-center distances, see the "distanceOnly" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you Elaine! May the option supersample also increase quality (I use supersample 4) ? Cheers Enrico ср, 19 янв. 2022 г. в 21:17, Elaine Meng <meng@cgl.ucsf.edu>:
Actually, don't bother using both width and height. Just give one or the other, and then the one you didn't give will be set automatically to match the height/width ratio of the graphics window. That way what you get will match what is shown in the graphics window.
Elaine
On Jan 19, 2022, at 12:15 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I guess I don't know what you mean by quality, then. If you mean you want higher resolution (more pixels in the image), then just specify width and height in the save image command.
see the "save" help for image-saving options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image>
Elaine
On Jan 19, 2022, at 6:32 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
P.S. I also tried increase quality of the representation using the following options: # 100 times more that the default option: set subdivision 100 # 100 times more that the default option: graphics quality 100 # 10 times more that the default option: graphics quality atomTriangles 50000000 save ./test.png however it produced the image with the same quality as it has been before.. Cheers, Enrico
вт, 18 янв. 2022 г. в 19:41, Elaine Meng <meng@cgl.ucsf.edu>:
On Jan 18, 2022, at 3:08 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
P.S. First, please ignore my question regarding surface transparency since I've just found it! just additional question about contacts contacts #1.1 & ligand why sometimes I could see on the displayed layer the same residue two times? Does it mean two possible interactions with the ligand ? May I suppress the replicas from the contacts layer?
I don't understand what you mean by displayed layer. Graphics window? List of results in the Log? The contacts command works on atoms, whereas residues have multiple atoms -- so if there are multiple atoms in the residue that contact the ligand, you will see multiple lines. If you mean the same two atoms are listed twice in the Log for H-bonds, it means it could be donor->acceptor or acceptor<-donor. You can only control the atomic parameters, there is no option to only draw one line per residue.
Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand?
(you already figured this out, as you said above)
2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ?
See "set subdivision" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#subdivision> ... or "graphics quality" and its "atomTriangles" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality>
3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange
You should check the help for the command you are already using. E.g. just use command "help contacts" to see the help page for "contacts". You can specify the VDW surface contact cutoff with the "overlapCutoff" option, or if you don't care about the different atomic sizes and only want to use center-center distances, see the "distanceOnly" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
It depends what you mean by "quality" but yes, it is another way to make the image look smoother. Supersampling is explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image> Best, Elaine
On Jan 20, 2022, at 1:15 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you Elaine! May the option supersample also increase quality (I use supersample 4) ? Cheers Enrico
ср, 19 янв. 2022 г. в 21:17, Elaine Meng <meng@cgl.ucsf.edu>:
Actually, don't bother using both width and height. Just give one or the other, and then the one you didn't give will be set automatically to match the height/width ratio of the graphics window. That way what you get will match what is shown in the graphics window.
Elaine
On Jan 19, 2022, at 12:15 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I guess I don't know what you mean by quality, then. If you mean you want higher resolution (more pixels in the image), then just specify width and height in the save image command.
see the "save" help for image-saving options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image>
Elaine
On Jan 19, 2022, at 6:32 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
P.S. I also tried increase quality of the representation using the following options: # 100 times more that the default option: set subdivision 100 # 100 times more that the default option: graphics quality 100 # 10 times more that the default option: graphics quality atomTriangles 50000000 save ./test.png however it produced the image with the same quality as it has been before.. Cheers, Enrico
вт, 18 янв. 2022 г. в 19:41, Elaine Meng <meng@cgl.ucsf.edu>:
On Jan 18, 2022, at 3:08 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
P.S. First, please ignore my question regarding surface transparency since I've just found it! just additional question about contacts contacts #1.1 & ligand why sometimes I could see on the displayed layer the same residue two times? Does it mean two possible interactions with the ligand ? May I suppress the replicas from the contacts layer?
I don't understand what you mean by displayed layer. Graphics window? List of results in the Log? The contacts command works on atoms, whereas residues have multiple atoms -- so if there are multiple atoms in the residue that contact the ligand, you will see multiple lines. If you mean the same two atoms are listed twice in the Log for H-bonds, it means it could be donor->acceptor or acceptor<-donor. You can only control the atomic parameters, there is no option to only draw one line per residue.
> > Here are my questions: > 1) is it possible to set transparency on the part of the displayed > surface that overlaps (hide) with the part of the displayed ligand?
(you already figured this out, as you said above)
> > 2) how I may improve further sphere representation of the ligand? it > looks very nice but probably there are further modifications ?
See "set subdivision" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#subdivision> ... or "graphics quality" and its "atomTriangles" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality>
> > 3) is it possible to customize the following commands to display > amino-acids that within specified distance within the ligand (I would > like to display only very closer amino-acids): > contacts #1.1 & ligand makePseudobonds false reveal true log true > label @@display height 0.8 color orange >
You should check the help for the command you are already using. E.g. just use command "help contacts" to see the help page for "contacts". You can specify the VDW surface contact cutoff with the "overlapCutoff" option, or if you don't care about the different atomic sizes and only want to use center-center distances, see the "distanceOnly" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Elaine Meng -
Enrico Martinez