Question regarding saving protein-ligand and docking in Chimera
Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam [cid:42d36ba9-f8f9-4ae7-9884-45480afe5dc2] [cid:6467c35e-bbaa-44c4-9a56-8b329bc8f3c1]
Dear Maryam, You did not show the error so I don't know what happened. (1) Make sure you do not include model #3 ("search volume") because that is not an atomic model. Also you probably do not want to include #0 because that is the ligand in the original undocked position. (2) Make sure you have permission to write files in the location you are trying to save to. (3) Pymol can open more than one file at the same time. Why not just save docked positions of the ligand (#2) to one file "relative to model" #1 which is the receptor. The "relative to" option will make sure they are in the right position when you open the receptor from a separate file, which could be the same PDB file that you originally opened in Chimera, Ebour.pdb. I.e. in Pymol just open "Ebour.pdb" and then also open the PDB file of docked ligand positions that you saved from Chimera. Also I don't know if Pymol likes it when you save multiple positions to one PDB file. It might only show the first one instead of all of the positions. In that case you might try saving the docked ligand positions as Mol2 from Chimera instead of as PDB. (4) You may know that Chimera has a ViewDock tool for convenient analysis of the docking results. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...> However, maybe you are more familiar with Pymol and want to use it instead, which is fine, but as I mentioned above, I don't know what kind of input is best for the docking analysis in that program and I can't give detailed advice. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 2, 2020, at 3:35 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam <image.png> <image.png>
Hi Elaine, Thank you for getting back to me. I went through your recommentation #3 and it worked for me. The only thing is that looks like the first position of ligand (#2.1) is saved with PDB. So I saved in Mol2, but not sure if Mol2 save all configurations in single file? So to analyze the docking results should I consider all 10 configurations? In principle I do not understand what does the 10 configurations, proposed in docking results, mean? Best, Maryam ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 2, 2020 4:13 PM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera Dear Maryam, You did not show the error so I don't know what happened. (1) Make sure you do not include model #3 ("search volume") because that is not an atomic model. Also you probably do not want to include #0 because that is the ligand in the original undocked position. (2) Make sure you have permission to write files in the location you are trying to save to. (3) Pymol can open more than one file at the same time. Why not just save docked positions of the ligand (#2) to one file "relative to model" #1 which is the receptor. The "relative to" option will make sure they are in the right position when you open the receptor from a separate file, which could be the same PDB file that you originally opened in Chimera, Ebour.pdb. I.e. in Pymol just open "Ebour.pdb" and then also open the PDB file of docked ligand positions that you saved from Chimera. Also I don't know if Pymol likes it when you save multiple positions to one PDB file. It might only show the first one instead of all of the positions. In that case you might try saving the docked ligand positions as Mol2 from Chimera instead of as PDB. (4) You may know that Chimera has a ViewDock tool for convenient analysis of the docking results. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...> However, maybe you are more familiar with Pymol and want to use it instead, which is fine, but as I mentioned above, I don't know what kind of input is best for the docking analysis in that program and I can't give detailed advice. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 2, 2020, at 3:35 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam <image.png> <image.png>
Hi Maryam, I am guessing that like I said before, Pymol is only showing the first one when you save more than one to the same file. In that case don't save more than one to the same file. Just save each one that you want to a different file. Docking tries many different positions for each compound, and so the output may have many different positions for each compound, but they have different "score" values for which one is best. The Autodock Vina tool in Chimera is not recommended for most research purposes because it does not try very many different positions and so you may never find the real best one. This is mentioned in the Chimera help page for this tool, shown by clicking its Help button or looking at the copy on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> It is beyond the scope of this mailing list to teach general principles of docking, however. There are many textbooks, papers, online tutorials for different docking programs, etc. to learn about this area. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2020, at 11:48 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaine, Thank you for getting back to me. I went through your recommentation #3 and it worked for me. The only thing is that looks like the first position of ligand (#2.1) is saved with PDB. So I saved in Mol2, but not sure if Mol2 save all configurations in single file? So to analyze the docking results should I consider all 10 configurations? In principle I do not understand what does the 10 configurations, proposed in docking results, mean? Best, Maryam From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 2, 2020 4:13 PM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Dear Maryam, You did not show the error so I don't know what happened.
(1) Make sure you do not include model #3 ("search volume") because that is not an atomic model. Also you probably do not want to include #0 because that is the ligand in the original undocked position.
(2) Make sure you have permission to write files in the location you are trying to save to.
(3) Pymol can open more than one file at the same time. Why not just save docked positions of the ligand (#2) to one file "relative to model" #1 which is the receptor. The "relative to" option will make sure they are in the right position when you open the receptor from a separate file, which could be the same PDB file that you originally opened in Chimera, Ebour.pdb. I.e. in Pymol just open "Ebour.pdb" and then also open the PDB file of docked ligand positions that you saved from Chimera. Also I don't know if Pymol likes it when you save multiple positions to one PDB file. It might only show the first one instead of all of the positions. In that case you might try saving the docked ligand positions as Mol2 from Chimera instead of as PDB.
(4) You may know that Chimera has a ViewDock tool for convenient analysis of the docking results. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...>
However, maybe you are more familiar with Pymol and want to use it instead, which is fine, but as I mentioned above, I don't know what kind of input is best for the docking analysis in that program and I can't give detailed advice.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 2, 2020, at 3:35 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam <image.png> <image.png>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine Thank you very much for your reply. I have some more questions, feel free to let me know if my questions are beyond the scope of this mailing list I have some estimation where the ligand should be placed but don’t know how to move the box and the ligand. ( I went through tutorial and it says we can move the box by moving the curser but my my case when I move the curser the whole system rotates so I can not change the position of the box and the ligand before start the docking ) My next question is about the score; when I do the docking the score of docking in output is ~-1.5 to -1. Does it mean if we place the ligand in to that position/orientation the binding site with protein is nit appropriate? How do we define the good score ? My last question is that is there any way to calculate the binding energy of ligands with protein using chimera ? Thank you Maryam ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, September 4, 2020 8:09 AM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera Hi Maryam, I am guessing that like I said before, Pymol is only showing the first one when you save more than one to the same file. In that case don't save more than one to the same file. Just save each one that you want to a different file. Docking tries many different positions for each compound, and so the output may have many different positions for each compound, but they have different "score" values for which one is best. The Autodock Vina tool in Chimera is not recommended for most research purposes because it does not try very many different positions and so you may never find the real best one. This is mentioned in the Chimera help page for this tool, shown by clicking its Help button or looking at the copy on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> It is beyond the scope of this mailing list to teach general principles of docking, however. There are many textbooks, papers, online tutorials for different docking programs, etc. to learn about this area. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2020, at 11:48 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaine, Thank you for getting back to me. I went through your recommentation #3 and it worked for me. The only thing is that looks like the first position of ligand (#2.1) is saved with PDB. So I saved in Mol2, but not sure if Mol2 save all configurations in single file? So to analyze the docking results should I consider all 10 configurations? In principle I do not understand what does the 10 configurations, proposed in docking results, mean? Best, Maryam From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 2, 2020 4:13 PM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Dear Maryam, You did not show the error so I don't know what happened.
(1) Make sure you do not include model #3 ("search volume") because that is not an atomic model. Also you probably do not want to include #0 because that is the ligand in the original undocked position.
(2) Make sure you have permission to write files in the location you are trying to save to.
(3) Pymol can open more than one file at the same time. Why not just save docked positions of the ligand (#2) to one file "relative to model" #1 which is the receptor. The "relative to" option will make sure they are in the right position when you open the receptor from a separate file, which could be the same PDB file that you originally opened in Chimera, Ebour.pdb. I.e. in Pymol just open "Ebour.pdb" and then also open the PDB file of docked ligand positions that you saved from Chimera. Also I don't know if Pymol likes it when you save multiple positions to one PDB file. It might only show the first one instead of all of the positions. In that case you might try saving the docked ligand positions as Mol2 from Chimera instead of as PDB.
(4) You may know that Chimera has a ViewDock tool for convenient analysis of the docking results. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...>
However, maybe you are more familiar with Pymol and want to use it instead, which is fine, but as I mentioned above, I don't know what kind of input is best for the docking analysis in that program and I can't give detailed advice.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 2, 2020, at 3:35 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam <image.png> <image.png>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Maryam, There is no simple answer as to what score is good enough. However, since this tool does not try very many positions, it is quite likely that it will NOT find the best one. You should probably use some other docking program or web server directly (not using Chimera). See this recent post for some possibilities of other docking software to use: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017126.html> You might ask “well why is this tool in Chimera, then?” You can see a longer answer in the bottom half of this message: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-July/015992.html> If you really want to keep using this tool, the instructions of how to move the box are in the Help page. You can change which mouse button is assigned. I think the default is "button 2" which means middle mouse button (trackpad + option on Mac). You were probably using button 1 (left mouse button or trackpad without other key) if you were only rotating the whole structure. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> No, Chimera does not calculate binding energy of ligands. Best, Elaine
On Sep 4, 2020, at 9:12 AM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaine Thank you very much for your reply. I have some more questions, feel free to let me know if my questions are beyond the scope of this mailing list I have some estimation where the ligand should be placed but don’t know how to move the box and the ligand. ( I went through tutorial and it says we can move the box by moving the curser but my my case when I move the curser the whole system rotates so I can not change the position of the box and the ligand before start the docking ) My next question is about the score; when I do the docking the score of docking in output is ~-1.5 to -1. Does it mean if we place the ligand in to that position/orientation the binding site with protein is nit appropriate? How do we define the good score ?
My last question is that is there any way to calculate the binding energy of ligands with protein using chimera ? Thank you Maryam From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, September 4, 2020 8:09 AM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Hi Maryam, I am guessing that like I said before, Pymol is only showing the first one when you save more than one to the same file. In that case don't save more than one to the same file. Just save each one that you want to a different file.
Docking tries many different positions for each compound, and so the output may have many different positions for each compound, but they have different "score" values for which one is best. The Autodock Vina tool in Chimera is not recommended for most research purposes because it does not try very many different positions and so you may never find the real best one. This is mentioned in the Chimera help page for this tool, shown by clicking its Help button or looking at the copy on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
It is beyond the scope of this mailing list to teach general principles of docking, however. There are many textbooks, papers, online tutorials for different docking programs, etc. to learn about this area. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2020, at 11:48 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaine, Thank you for getting back to me. I went through your recommentation #3 and it worked for me. The only thing is that looks like the first position of ligand (#2.1) is saved with PDB. So I saved in Mol2, but not sure if Mol2 save all configurations in single file? So to analyze the docking results should I consider all 10 configurations? In principle I do not understand what does the 10 configurations, proposed in docking results, mean? Best, Maryam From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 2, 2020 4:13 PM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Dear Maryam, You did not show the error so I don't know what happened.
(1) Make sure you do not include model #3 ("search volume") because that is not an atomic model. Also you probably do not want to include #0 because that is the ligand in the original undocked position.
(2) Make sure you have permission to write files in the location you are trying to save to.
(3) Pymol can open more than one file at the same time. Why not just save docked positions of the ligand (#2) to one file "relative to model" #1 which is the receptor. The "relative to" option will make sure they are in the right position when you open the receptor from a separate file, which could be the same PDB file that you originally opened in Chimera, Ebour.pdb. I.e. in Pymol just open "Ebour.pdb" and then also open the PDB file of docked ligand positions that you saved from Chimera. Also I don't know if Pymol likes it when you save multiple positions to one PDB file. It might only show the first one instead of all of the positions. In that case you might try saving the docked ligand positions as Mol2 from Chimera instead of as PDB.
(4) You may know that Chimera has a ViewDock tool for convenient analysis of the docking results. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...>
However, maybe you are more familiar with Pymol and want to use it instead, which is fine, but as I mentioned above, I don't know what kind of input is best for the docking analysis in that program and I can't give detailed advice.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 2, 2020, at 3:35 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam <image.png> <image.png>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaina, Is there any way to decrease the distance of protein with ligand in Chimera before or after doing the docking? Thank you Maryam ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, September 4, 2020 9:30 AM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera Hi Maryam, There is no simple answer as to what score is good enough. However, since this tool does not try very many positions, it is quite likely that it will NOT find the best one. You should probably use some other docking program or web server directly (not using Chimera). See this recent post for some possibilities of other docking software to use: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017126.html> You might ask “well why is this tool in Chimera, then?” You can see a longer answer in the bottom half of this message: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-July/015992.html> If you really want to keep using this tool, the instructions of how to move the box are in the Help page. You can change which mouse button is assigned. I think the default is "button 2" which means middle mouse button (trackpad + option on Mac). You were probably using button 1 (left mouse button or trackpad without other key) if you were only rotating the whole structure. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> No, Chimera does not calculate binding energy of ligands. Best, Elaine
On Sep 4, 2020, at 9:12 AM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaine Thank you very much for your reply. I have some more questions, feel free to let me know if my questions are beyond the scope of this mailing list I have some estimation where the ligand should be placed but don’t know how to move the box and the ligand. ( I went through tutorial and it says we can move the box by moving the curser but my my case when I move the curser the whole system rotates so I can not change the position of the box and the ligand before start the docking ) My next question is about the score; when I do the docking the score of docking in output is ~-1.5 to -1. Does it mean if we place the ligand in to that position/orientation the binding site with protein is nit appropriate? How do we define the good score ?
My last question is that is there any way to calculate the binding energy of ligands with protein using chimera ? Thank you Maryam From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, September 4, 2020 8:09 AM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Hi Maryam, I am guessing that like I said before, Pymol is only showing the first one when you save more than one to the same file. In that case don't save more than one to the same file. Just save each one that you want to a different file.
Docking tries many different positions for each compound, and so the output may have many different positions for each compound, but they have different "score" values for which one is best. The Autodock Vina tool in Chimera is not recommended for most research purposes because it does not try very many different positions and so you may never find the real best one. This is mentioned in the Chimera help page for this tool, shown by clicking its Help button or looking at the copy on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
It is beyond the scope of this mailing list to teach general principles of docking, however. There are many textbooks, papers, online tutorials for different docking programs, etc. to learn about this area. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2020, at 11:48 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaine, Thank you for getting back to me. I went through your recommentation #3 and it worked for me. The only thing is that looks like the first position of ligand (#2.1) is saved with PDB. So I saved in Mol2, but not sure if Mol2 save all configurations in single file? So to analyze the docking results should I consider all 10 configurations? In principle I do not understand what does the 10 configurations, proposed in docking results, mean? Best, Maryam From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 2, 2020 4:13 PM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Dear Maryam, You did not show the error so I don't know what happened.
(1) Make sure you do not include model #3 ("search volume") because that is not an atomic model. Also you probably do not want to include #0 because that is the ligand in the original undocked position.
(2) Make sure you have permission to write files in the location you are trying to save to.
(3) Pymol can open more than one file at the same time. Why not just save docked positions of the ligand (#2) to one file "relative to model" #1 which is the receptor. The "relative to" option will make sure they are in the right position when you open the receptor from a separate file, which could be the same PDB file that you originally opened in Chimera, Ebour.pdb. I.e. in Pymol just open "Ebour.pdb" and then also open the PDB file of docked ligand positions that you saved from Chimera. Also I don't know if Pymol likes it when you save multiple positions to one PDB file. It might only show the first one instead of all of the positions. In that case you might try saving the docked ligand positions as Mol2 from Chimera instead of as PDB.
(4) You may know that Chimera has a ViewDock tool for convenient analysis of the docking results. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...>
However, maybe you are more familiar with Pymol and want to use it instead, which is fine, but as I mentioned above, I don't know what kind of input is best for the docking analysis in that program and I can't give detailed advice.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 2, 2020, at 3:35 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam <image.png> <image.png>
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Hi Maryam, In Chimera, yes you can move one structure relative to another manually, as explained here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> However, most molecular docking programs (including Autodock Vina) do not care about the starting position of the ligand relative to the receptor, so moving it around first is not expected to give significantly different results. Instead of trying to dock in Chimera, maybe you should take a look at some easy-to-use web servers, for example: Swissdock <http://www.swissdock.ch/> Webina <https://durrantlab.pitt.edu/webina/> I hope this helps, Elaine
On Sep 11, 2020, at 12:35 AM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaina,
Is there any way to decrease the distance of protein with ligand in Chimera before or after doing the docking? Thank you Maryam
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, September 4, 2020 9:30 AM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Hi Maryam, There is no simple answer as to what score is good enough. However, since this tool does not try very many positions, it is quite likely that it will NOT find the best one. You should probably use some other docking program or web server directly (not using Chimera). See this recent post for some possibilities of other docking software to use: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017126.html>
You might ask “well why is this tool in Chimera, then?” You can see a longer answer in the bottom half of this message: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-July/015992.html>
If you really want to keep using this tool, the instructions of how to move the box are in the Help page. You can change which mouse button is assigned. I think the default is "button 2" which means middle mouse button (trackpad + option on Mac). You were probably using button 1 (left mouse button or trackpad without other key) if you were only rotating the whole structure. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
No, Chimera does not calculate binding energy of ligands.
Best, Elaine
On Sep 4, 2020, at 9:12 AM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaine Thank you very much for your reply. I have some more questions, feel free to let me know if my questions are beyond the scope of this mailing list I have some estimation where the ligand should be placed but don’t know how to move the box and the ligand. ( I went through tutorial and it says we can move the box by moving the curser but my my case when I move the curser the whole system rotates so I can not change the position of the box and the ligand before start the docking ) My next question is about the score; when I do the docking the score of docking in output is ~-1.5 to -1. Does it mean if we place the ligand in to that position/orientation the binding site with protein is nit appropriate? How do we define the good score ?
My last question is that is there any way to calculate the binding energy of ligands with protein using chimera ? Thank you Maryam From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, September 4, 2020 8:09 AM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Hi Maryam, I am guessing that like I said before, Pymol is only showing the first one when you save more than one to the same file. In that case don't save more than one to the same file. Just save each one that you want to a different file.
Docking tries many different positions for each compound, and so the output may have many different positions for each compound, but they have different "score" values for which one is best. The Autodock Vina tool in Chimera is not recommended for most research purposes because it does not try very many different positions and so you may never find the real best one. This is mentioned in the Chimera help page for this tool, shown by clicking its Help button or looking at the copy on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
It is beyond the scope of this mailing list to teach general principles of docking, however. There are many textbooks, papers, online tutorials for different docking programs, etc. to learn about this area. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2020, at 11:48 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaine, Thank you for getting back to me. I went through your recommentation #3 and it worked for me. The only thing is that looks like the first position of ligand (#2.1) is saved with PDB. So I saved in Mol2, but not sure if Mol2 save all configurations in single file? So to analyze the docking results should I consider all 10 configurations? In principle I do not understand what does the 10 configurations, proposed in docking results, mean? Best, Maryam From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 2, 2020 4:13 PM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Dear Maryam, You did not show the error so I don't know what happened.
(1) Make sure you do not include model #3 ("search volume") because that is not an atomic model. Also you probably do not want to include #0 because that is the ligand in the original undocked position.
(2) Make sure you have permission to write files in the location you are trying to save to.
(3) Pymol can open more than one file at the same time. Why not just save docked positions of the ligand (#2) to one file "relative to model" #1 which is the receptor. The "relative to" option will make sure they are in the right position when you open the receptor from a separate file, which could be the same PDB file that you originally opened in Chimera, Ebour.pdb. I.e. in Pymol just open "Ebour.pdb" and then also open the PDB file of docked ligand positions that you saved from Chimera. Also I don't know if Pymol likes it when you save multiple positions to one PDB file. It might only show the first one instead of all of the positions. In that case you might try saving the docked ligand positions as Mol2 from Chimera instead of as PDB.
(4) You may know that Chimera has a ViewDock tool for convenient analysis of the docking results. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...>
However, maybe you are more familiar with Pymol and want to use it instead, which is fine, but as I mentioned above, I don't know what kind of input is best for the docking analysis in that program and I can't give detailed advice.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 2, 2020, at 3:35 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam <image.png> <image.png>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Hi Elaine, Thank you for your reply. Yes sure I am going to try other docking methods. Best Maryam ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, September 11, 2020 9:15 AM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera Hi Maryam, In Chimera, yes you can move one structure relative to another manually, as explained here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> However, most molecular docking programs (including Autodock Vina) do not care about the starting position of the ligand relative to the receptor, so moving it around first is not expected to give significantly different results. Instead of trying to dock in Chimera, maybe you should take a look at some easy-to-use web servers, for example: Swissdock <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.swissdock.ch_&d=DwIF... > Webina <https://urldefense.proofpoint.com/v2/url?u=https-3A__durrantlab.pitt.edu_web... > I hope this helps, Elaine
On Sep 11, 2020, at 12:35 AM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaina,
Is there any way to decrease the distance of protein with ligand in Chimera before or after doing the docking? Thank you Maryam
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, September 4, 2020 9:30 AM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Hi Maryam, There is no simple answer as to what score is good enough. However, since this tool does not try very many positions, it is quite likely that it will NOT find the best one. You should probably use some other docking program or web server directly (not using Chimera). See this recent post for some possibilities of other docking software to use: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017126.html>
You might ask “well why is this tool in Chimera, then?” You can see a longer answer in the bottom half of this message: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-July/015992.html>
If you really want to keep using this tool, the instructions of how to move the box are in the Help page. You can change which mouse button is assigned. I think the default is "button 2" which means middle mouse button (trackpad + option on Mac). You were probably using button 1 (left mouse button or trackpad without other key) if you were only rotating the whole structure. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
No, Chimera does not calculate binding energy of ligands.
Best, Elaine
On Sep 4, 2020, at 9:12 AM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaine Thank you very much for your reply. I have some more questions, feel free to let me know if my questions are beyond the scope of this mailing list I have some estimation where the ligand should be placed but don’t know how to move the box and the ligand. ( I went through tutorial and it says we can move the box by moving the curser but my my case when I move the curser the whole system rotates so I can not change the position of the box and the ligand before start the docking ) My next question is about the score; when I do the docking the score of docking in output is ~-1.5 to -1. Does it mean if we place the ligand in to that position/orientation the binding site with protein is nit appropriate? How do we define the good score ?
My last question is that is there any way to calculate the binding energy of ligands with protein using chimera ? Thank you Maryam From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, September 4, 2020 8:09 AM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Hi Maryam, I am guessing that like I said before, Pymol is only showing the first one when you save more than one to the same file. In that case don't save more than one to the same file. Just save each one that you want to a different file.
Docking tries many different positions for each compound, and so the output may have many different positions for each compound, but they have different "score" values for which one is best. The Autodock Vina tool in Chimera is not recommended for most research purposes because it does not try very many different positions and so you may never find the real best one. This is mentioned in the Chimera help page for this tool, shown by clicking its Help button or looking at the copy on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
It is beyond the scope of this mailing list to teach general principles of docking, however. There are many textbooks, papers, online tutorials for different docking programs, etc. to learn about this area. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2020, at 11:48 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Hi Elaine, Thank you for getting back to me. I went through your recommentation #3 and it worked for me. The only thing is that looks like the first position of ligand (#2.1) is saved with PDB. So I saved in Mol2, but not sure if Mol2 save all configurations in single file? So to analyze the docking results should I consider all 10 configurations? In principle I do not understand what does the 10 configurations, proposed in docking results, mean? Best, Maryam From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 2, 2020 4:13 PM To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera
Dear Maryam, You did not show the error so I don't know what happened.
(1) Make sure you do not include model #3 ("search volume") because that is not an atomic model. Also you probably do not want to include #0 because that is the ligand in the original undocked position.
(2) Make sure you have permission to write files in the location you are trying to save to.
(3) Pymol can open more than one file at the same time. Why not just save docked positions of the ligand (#2) to one file "relative to model" #1 which is the receptor. The "relative to" option will make sure they are in the right position when you open the receptor from a separate file, which could be the same PDB file that you originally opened in Chimera, Ebour.pdb. I.e. in Pymol just open "Ebour.pdb" and then also open the PDB file of docked ligand positions that you saved from Chimera. Also I don't know if Pymol likes it when you save multiple positions to one PDB file. It might only show the first one instead of all of the positions. In that case you might try saving the docked ligand positions as Mol2 from Chimera instead of as PDB.
(4) You may know that Chimera has a ViewDock tool for convenient analysis of the docking results. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...>
However, maybe you are more familiar with Pymol and want to use it instead, which is fine, but as I mentioned above, I don't know what kind of input is best for the docking analysis in that program and I can't give detailed advice.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 2, 2020, at 3:35 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam <image.png> <image.png>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (2)
-
Elaine Meng -
Tarazkar, Maryam