Hi, I did a docking experiment from autodock and downloaded the file in chimerax format, when I open it works great and I select the model with highest delta G and visaulise it, but when I save the model as PDB, and open it in pymol only ligand is visible when I open the protein file in the same, although the ligand sits perfectly. I am not able to get a PDB file of the docked structure for ligplot analysis. Any help would be appreciated. Take care Sincerely, Yash Bahl
Hi Yash Bahl, Is the question how to get both models in one PDB file? If you use Chimera menu: File... Save PDB, then in the dialog you can choose more than oen model to save. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> However: I don't use Pymol or ligplot, so I don't know for sure, but I'm guessing they might not use this kind of PDB file with more than one model in it. Instead you may need to combine ligand and receptor into one model before you save to PDB. To combine the ligand and the protein into one model, you can use the Model Panel (open from Favorites menu) "copy/combine" function. You have to choose the two models (the ligand and the protein) on the left side of the Model Panel and then click "copy/combine" button on the right side of the Model Panel. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine> Or, instead of Model Panel, you could use the "combine" command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Then save the new combined model to a PDB file. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 10, 2020, at 3:59 AM, Yash Bahl <yashbahl1999@gmail.com> wrote:
Hi, I did a docking experiment from autodock and downloaded the file in chimerax format, when I open it works great and I select the model with highest delta G and visaulise it, but when I save the model as PDB, and open it in pymol only ligand is visible when I open the protein file in the same, although the ligand sits perfectly. I am not able to get a PDB file of the docked structure for ligplot analysis. Any help would be appreciated. Take care Sincerely, Yash Bahl
Thank you very much. On Sun, May 10, 2020, 22:35 Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yash Bahl, Is the question how to get both models in one PDB file? If you use Chimera menu: File... Save PDB, then in the dialog you can choose more than oen model to save. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
However: I don't use Pymol or ligplot, so I don't know for sure, but I'm guessing they might not use this kind of PDB file with more than one model in it. Instead you may need to combine ligand and receptor into one model before you save to PDB.
To combine the ligand and the protein into one model, you can use the Model Panel (open from Favorites menu) "copy/combine" function. You have to choose the two models (the ligand and the protein) on the left side of the Model Panel and then click "copy/combine" button on the right side of the Model Panel. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>
Or, instead of Model Panel, you could use the "combine" command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
Then save the new combined model to a PDB file.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 10, 2020, at 3:59 AM, Yash Bahl <yashbahl1999@gmail.com> wrote:
Hi, I did a docking experiment from autodock and downloaded the file in chimerax format, when I open it works great and I select the model with highest delta G and visaulise it, but when I save the model as PDB, and open it in pymol only ligand is visible when I open the protein file in the same, although the ligand sits perfectly. I am not able to get a PDB file of the docked structure for ligplot analysis. Any help would be appreciated. Take care Sincerely, Yash Bahl
Hi, But I thought that the Autodock Vina function has been discontinued since April 30th as I have been having trouble docking my compound. Is there any way around this? Thank you Ammar Jastaniah On Sun, May 10, 2020 at 1:22 PM Yash Bahl <yashbahl1999@gmail.com> wrote:
Thank you very much.
On Sun, May 10, 2020, 22:35 Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yash Bahl, Is the question how to get both models in one PDB file? If you use Chimera menu: File... Save PDB, then in the dialog you can choose more than oen model to save. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
However: I don't use Pymol or ligplot, so I don't know for sure, but I'm guessing they might not use this kind of PDB file with more than one model in it. Instead you may need to combine ligand and receptor into one model before you save to PDB.
To combine the ligand and the protein into one model, you can use the Model Panel (open from Favorites menu) "copy/combine" function. You have to choose the two models (the ligand and the protein) on the left side of the Model Panel and then click "copy/combine" button on the right side of the Model Panel. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine
Or, instead of Model Panel, you could use the "combine" command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
Then save the new combined model to a PDB file.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 10, 2020, at 3:59 AM, Yash Bahl <yashbahl1999@gmail.com> wrote:
Hi, I did a docking experiment from autodock and downloaded the file in chimerax format, when I open it works great and I select the model with highest delta G and visaulise it, but when I save the model as PDB, and open it in pymol only ligand is visible when I open the protein file in the same, although the ligand sits perfectly. I am not able to get a PDB file of the docked structure for ligplot analysis. Any help would be appreciated. Take care Sincerely, Yash Bahl
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Hi Ammar, Typically you can use one of many docking programs separately from Chimera: UCSF DOCK, Glide, GOLD, AutoDock, AutoDock Vina, SwissDock, etc. You just have to download that other program (or use a web service) to do the docking, instead of using Chimera. Then, after you get the output file you can use Chimera's ViewDock tool to view and analyze the results. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...> For example, see the Swissdock website, which includes a video of using Chimera to view the results: <http://www.swissdock.ch/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 10, 2020, at 2:36 PM, Ammar Jastaniah <ajasta2@uic.edu> wrote:
Hi,
But I thought that the Autodock Vina function has been discontinued since April 30th as I have been having trouble docking my compound. Is there any way around this?
Thank you
Ammar Jastaniah
On Sun, May 10, 2020 at 1:22 PM Yash Bahl <yashbahl1999@gmail.com> wrote: Thank you very much.
On Sun, May 10, 2020, 22:35 Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Yash Bahl, Is the question how to get both models in one PDB file? If you use Chimera menu: File... Save PDB, then in the dialog you can choose more than oen model to save. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
However: I don't use Pymol or ligplot, so I don't know for sure, but I'm guessing they might not use this kind of PDB file with more than one model in it. Instead you may need to combine ligand and receptor into one model before you save to PDB.
To combine the ligand and the protein into one model, you can use the Model Panel (open from Favorites menu) "copy/combine" function. You have to choose the two models (the ligand and the protein) on the left side of the Model Panel and then click "copy/combine" button on the right side of the Model Panel. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>
Or, instead of Model Panel, you could use the "combine" command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
Then save the new combined model to a PDB file.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 10, 2020, at 3:59 AM, Yash Bahl <yashbahl1999@gmail.com> wrote:
Hi, I did a docking experiment from autodock and downloaded the file in chimerax format, when I open it works great and I select the model with highest delta G and visaulise it, but when I save the model as PDB, and open it in pymol only ligand is visible when I open the protein file in the same, although the ligand sits perfectly. I am not able to get a PDB file of the docked structure for ligplot analysis. Any help would be appreciated. Take care Sincerely, Yash Bahl
Thank you for your help Elaine. Ammar On Mon, May 11, 2020 at 10:55 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ammar, Typically you can use one of many docking programs separately from Chimera: UCSF DOCK, Glide, GOLD, AutoDock, AutoDock Vina, SwissDock, etc. You just have to download that other program (or use a web service) to do the docking, instead of using Chimera.
Then, after you get the output file you can use Chimera's ViewDock tool to view and analyze the results. < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...
For example, see the Swissdock website, which includes a video of using Chimera to view the results: <http://www.swissdock.ch/>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 10, 2020, at 2:36 PM, Ammar Jastaniah <ajasta2@uic.edu> wrote:
Hi,
But I thought that the Autodock Vina function has been discontinued since April 30th as I have been having trouble docking my compound. Is there any way around this?
Thank you
Ammar Jastaniah
On Sun, May 10, 2020 at 1:22 PM Yash Bahl <yashbahl1999@gmail.com> wrote: Thank you very much.
On Sun, May 10, 2020, 22:35 Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Yash Bahl, Is the question how to get both models in one PDB file? If you use Chimera menu: File... Save PDB, then in the dialog you can choose more than oen model to save. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
However: I don't use Pymol or ligplot, so I don't know for sure, but I'm guessing they might not use this kind of PDB file with more than one model in it. Instead you may need to combine ligand and receptor into one model before you save to PDB.
To combine the ligand and the protein into one model, you can use the Model Panel (open from Favorites menu) "copy/combine" function. You have to choose the two models (the ligand and the protein) on the left side of the Model Panel and then click "copy/combine" button on the right side of the Model Panel. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen
< http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>
Or, instead of Model Panel, you could use the "combine" command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
Then save the new combined model to a PDB file.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 10, 2020, at 3:59 AM, Yash Bahl <yashbahl1999@gmail.com> wrote:
Hi, I did a docking experiment from autodock and downloaded the file in chimerax format, when I open it works great and I select the model with highest delta G and visaulise it, but when I save the model as PDB, and open it in pymol only ligand is visible when I open the protein file in the same, although the ligand sits perfectly. I am not able to get a PDB file of the docked structure for ligplot analysis. Any help would be appreciated. Take care Sincerely, Yash Bahl
participants (3)
-
Ammar Jastaniah -
Elaine Meng -
Yash Bahl