Inter-molecular H-bonds between water molecules not displayed in per-frame script
Hi, I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below: Water molecules are residues :159-162 I would be very grateful for any assistance. :) sg ################################################ #################### # per-frame H-bond repr bs :158 color hot pink :158 color byhet :158 # disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162 disp :WAT # select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select select :90 ################################################
Hi George, I see at least one definite problem and suspect an additional problem. It is impossible to tell for sure without having your data, which you should usually include with such a question to allow your problem to be reproduced so we don’t have to waste time guessing. (1) The definite problem is that your “hbonds” command isn't using the selection in any way. It simply acts on all atoms, which is fine if that’s what you want it to do. But based on your description, it is not actually working on all atoms, so there must be some misunderstanding or incomplete description of what’s happening. To limit “hbonds” to the selection, you’d need the “selRestrict” option. See “hbonds” documentation for the possible values of that option: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> It’s possible that hbonds is working on those waters but that they aren’t displayed due to suspected problem #2, below. To force undisplayed items to be displayed if they are involved in H-bonds, you’d use the hbonds option “reveal true” … but that might accrete more and more displayed residues throughout your trajectory, so I’m not sure you would want it. “intermodel” and “intramodel” are both default true so you don’t have to put them in your command. Also, you don’t need to display the same stuff at every frame since presumably it was displayed in the previous frame. You would just display it once at the beginning before running your per-frame script. (2) The suspected secondary problem is that “:159-162” may not actually specify the waters, because if they don’t have a chain ID, Chimera automatically processes them into chain “water”. Thus they may not be displayed by your first “disp” command that list residue numbers, but they will be displayed by the second one, “disp :WAT”. Your select command may not be selecting them (try typing it in the command line to see) and in that case you’d need something like: select :1-158:159-162.water - OR - select :1-158:159-162.* - OR - select :1-158:wat (where the latter would select all residues named WAT, so you’d only use that if there weren’t other WAT residues you didn’t want to show) The automatic processing into chain “water” was put into Chimera because some data had protein residues and water residues with the same residue numbers, and the added chain ID provided a handle for specifying them independently. 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 May 14, 2015, at 7:42 AM, George Green <soyo.green@gmail.com> wrote:
Hi, I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below:
Water molecules are residues :159-162
I would be very grateful for any assistance. :) sg
################################################ #################### # per-frame H-bond repr bs :158 color hot pink :158 color byhet :158 # disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162 disp :WAT # select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select select :90
################################################
Hi Elaine, Thanks for your detailed reply. Only just saw your email. I will test and check. I think your tips should sort my problem out! Many thanks! On Thu, May 14, 2015 at 5:18 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, I see at least one definite problem and suspect an additional problem. It is impossible to tell for sure without having your data, which you should usually include with such a question to allow your problem to be reproduced so we don’t have to waste time guessing.
(1) The definite problem is that your “hbonds” command isn't using the selection in any way. It simply acts on all atoms, which is fine if that’s what you want it to do. But based on your description, it is not actually working on all atoms, so there must be some misunderstanding or incomplete description of what’s happening. To limit “hbonds” to the selection, you’d need the “selRestrict” option. See “hbonds” documentation for the possible values of that option: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
It’s possible that hbonds is working on those waters but that they aren’t displayed due to suspected problem #2, below. To force undisplayed items to be displayed if they are involved in H-bonds, you’d use the hbonds option “reveal true” … but that might accrete more and more displayed residues throughout your trajectory, so I’m not sure you would want it. “intermodel” and “intramodel” are both default true so you don’t have to put them in your command.
Also, you don’t need to display the same stuff at every frame since presumably it was displayed in the previous frame. You would just display it once at the beginning before running your per-frame script.
(2) The suspected secondary problem is that “:159-162” may not actually specify the waters, because if they don’t have a chain ID, Chimera automatically processes them into chain “water”. Thus they may not be displayed by your first “disp” command that list residue numbers, but they will be displayed by the second one, “disp :WAT”. Your select command may not be selecting them (try typing it in the command line to see) and in that case you’d need something like:
select :1-158:159-162.water - OR - select :1-158:159-162.* - OR - select :1-158:wat (where the latter would select all residues named WAT, so you’d only use that if there weren’t other WAT residues you didn’t want to show)
The automatic processing into chain “water” was put into Chimera because some data had protein residues and water residues with the same residue numbers, and the added chain ID provided a handle for specifying them independently.
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 May 14, 2015, at 7:42 AM, George Green <soyo.green@gmail.com> wrote:
Hi, I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below:
Water molecules are residues :159-162
I would be very grateful for any assistance. :) sg
################################################ #################### # per-frame H-bond repr bs :158 color hot pink :158 color byhet :158 # disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162 disp :WAT # select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select select :90
################################################
Hi, Just one other question if I could trouble you? Is it possible to have two colors of H-bond in the per-frame script. That way I could highlight bonds of particular importance (red), while the ones that maintain a steady structure are yellow. That would help draw the users eye and save wordy annotations. I tried the following to no avail. I suspect that maybe this is not possible? If you could offer any guidance, I would be much obliged. :) ########### select :1-158; hbonds line 5 color gold ; ~select select :64,80,76,50,21; hbonds selrestrict both retainCurrent true line 5 color red ; ~select ############ On Sun, May 17, 2015 at 3:13 AM, George Green <soyo.green@gmail.com> wrote:
Hi Elaine,
Thanks for your detailed reply. Only just saw your email. I will test and check. I think your tips should sort my problem out!
Many thanks!
On Thu, May 14, 2015 at 5:18 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, I see at least one definite problem and suspect an additional problem. It is impossible to tell for sure without having your data, which you should usually include with such a question to allow your problem to be reproduced so we don’t have to waste time guessing.
(1) The definite problem is that your “hbonds” command isn't using the selection in any way. It simply acts on all atoms, which is fine if that’s what you want it to do. But based on your description, it is not actually working on all atoms, so there must be some misunderstanding or incomplete description of what’s happening. To limit “hbonds” to the selection, you’d need the “selRestrict” option. See “hbonds” documentation for the possible values of that option: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
It’s possible that hbonds is working on those waters but that they aren’t displayed due to suspected problem #2, below. To force undisplayed items to be displayed if they are involved in H-bonds, you’d use the hbonds option “reveal true” … but that might accrete more and more displayed residues throughout your trajectory, so I’m not sure you would want it. “intermodel” and “intramodel” are both default true so you don’t have to put them in your command.
Also, you don’t need to display the same stuff at every frame since presumably it was displayed in the previous frame. You would just display it once at the beginning before running your per-frame script.
(2) The suspected secondary problem is that “:159-162” may not actually specify the waters, because if they don’t have a chain ID, Chimera automatically processes them into chain “water”. Thus they may not be displayed by your first “disp” command that list residue numbers, but they will be displayed by the second one, “disp :WAT”. Your select command may not be selecting them (try typing it in the command line to see) and in that case you’d need something like:
select :1-158:159-162.water - OR - select :1-158:159-162.* - OR - select :1-158:wat (where the latter would select all residues named WAT, so you’d only use that if there weren’t other WAT residues you didn’t want to show)
The automatic processing into chain “water” was put into Chimera because some data had protein residues and water residues with the same residue numbers, and the added chain ID provided a handle for specifying them independently.
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 May 14, 2015, at 7:42 AM, George Green <soyo.green@gmail.com> wrote:
Hi, I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below:
Water molecules are residues :159-162
I would be very grateful for any assistance. :) sg
################################################ #################### # per-frame H-bond repr bs :158 color hot pink :158 color byhet :158 # disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162 disp :WAT # select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select select :90
################################################
Hi George, With “retain true” you could have both the old and new H-bonds in the same place, but only see the old colors if the new ones are “underneath.” Instead I would say just use “hbonds” one time per frame and then re-color the desired lines with “setattr”, for example something like: hb line 5 color gold setattr p color red :64,80,76,50,21 The latter command sets the “color” attribute of pseudobonds to red, affecting only the pseudobonds between atoms of the specified residues. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2015, at 11:47 AM, George Green <soyo.green@gmail.com> wrote:
Hi, Just one other question if I could trouble you? Is it possible to have two colors of H-bond in the per-frame script. That way I could highlight bonds of particular importance (red), while the ones that maintain a steady structure are yellow. That would help draw the users eye and save wordy annotations. I tried the following to no avail. I suspect that maybe this is not possible? If you could offer any guidance, I would be much obliged. :)
########### select :1-158; hbonds line 5 color gold ; ~select select :64,80,76,50,21; hbonds selrestrict both retainCurrent true line 5 color red ; ~select ############
That's great! thanks v much. Its much appreciated. :) On Tue, May 19, 2015 at 8:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, With “retain true” you could have both the old and new H-bonds in the same place, but only see the old colors if the new ones are “underneath.”
Instead I would say just use “hbonds” one time per frame and then re-color the desired lines with “setattr”, for example something like:
hb line 5 color gold setattr p color red :64,80,76,50,21
The latter command sets the “color” attribute of pseudobonds to red, affecting only the pseudobonds between atoms of the specified residues. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2015, at 11:47 AM, George Green <soyo.green@gmail.com> wrote:
Hi, Just one other question if I could trouble you? Is it possible to have two colors of H-bond in the per-frame script. That way I could highlight bonds of particular importance (red), while the ones that maintain a steady structure are yellow. That would help draw the users eye and save wordy annotations. I tried the following to no avail. I suspect that maybe this is not possible? If you could offer any guidance, I would be much obliged. :)
########### select :1-158; hbonds line 5 color gold ; ~select select :64,80,76,50,21; hbonds selrestrict both retainCurrent true line 5 color red ; ~select ############
Hi, Know this has been a while, but just came back to it after a long while. Got most of your suggestions working, but cannot get water-water hbonds going. After some investigation, I think this could be due to the fact that I'm using TIP4-EW water. Reason is that I got water-water hbonds working with TIP3 and after trying lots of permutations cannot get this going. My current per-frame script command for showing Hbonds is: select :159-165.*; hbonds line 5 color gold selRestrict any reveal true; ~select setattr p color gold :159-165.*; setattr g lineType 1 This works fine in that hbonds between water and protein/ligand residues are shown, but none between the water which is a problem. Any advice would be greatly appreciated. :) On Tue, May 19, 2015 at 8:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, With “retain true” you could have both the old and new H-bonds in the same place, but only see the old colors if the new ones are “underneath.”
Instead I would say just use “hbonds” one time per frame and then re-color the desired lines with “setattr”, for example something like:
hb line 5 color gold setattr p color red :64,80,76,50,21
The latter command sets the “color” attribute of pseudobonds to red, affecting only the pseudobonds between atoms of the specified residues. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2015, at 11:47 AM, George Green <soyo.green@gmail.com> wrote:
Hi, Just one other question if I could trouble you? Is it possible to have two colors of H-bond in the per-frame script. That way I could highlight bonds of particular importance (red), while the ones that maintain a steady structure are yellow. That would help draw the users eye and save wordy annotations. I tried the following to no avail. I suspect that maybe this is not possible? If you could offer any guidance, I would be much obliged. :)
########### select :1-158; hbonds line 5 color gold ; ~select select :64,80,76,50,21; hbonds selrestrict both retainCurrent true line 5 color red ; ~select ############
Hi George, Unfortunately the TIP4EW atoms are not recognized as H-bonding. You would have to delete the 4th point and remove the H1-H2 bond for them to be recognized as such. For example, commands: del @epw ~bond @h1,h2 Then running FindHBond or its command works, at least for me. 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 Nov 20, 2015, at 5:29 PM, George Green <soyo.green@gmail.com> wrote:
Hi, Know this has been a while, but just came back to it after a long while. Got most of your suggestions working, but cannot get water-water hbonds going. After some investigation, I think this could be due to the fact that I'm using TIP4-EW water. Reason is that I got water-water hbonds working with TIP3 and after trying lots of permutations cannot get this going.
My current per-frame script command for showing Hbonds is: select :159-165.*; hbonds line 5 color gold selRestrict any reveal true; ~select setattr p color gold :159-165.*; setattr g lineType 1
This works fine in that hbonds between water and protein/ligand residues are shown, but none between the water which is a problem.
Any advice would be greatly appreciated. :)
AWESOME!!!!!! :) :) :) Thanks v much. this was doing my head in for the last hour or so!!! On Sat, Nov 21, 2015 at 1:40 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, Unfortunately the TIP4EW atoms are not recognized as H-bonding. You would have to delete the 4th point and remove the H1-H2 bond for them to be recognized as such. For example, commands:
del @epw ~bond @h1,h2
Then running FindHBond or its command works, at least for me. 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 Nov 20, 2015, at 5:29 PM, George Green <soyo.green@gmail.com> wrote:
Hi, Know this has been a while, but just came back to it after a long while. Got most of your suggestions working, but cannot get water-water hbonds going. After some investigation, I think this could be due to the fact that I'm using TIP4-EW water. Reason is that I got water-water hbonds working with TIP3 and after trying lots of permutations cannot get this going.
My current per-frame script command for showing Hbonds is: select :159-165.*; hbonds line 5 color gold selRestrict any reveal true; ~select setattr p color gold :159-165.*; setattr g lineType 1
This works fine in that hbonds between water and protein/ligand residues are shown, but none between the water which is a problem.
Any advice would be greatly appreciated. :)
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Elaine Meng -
George Green