Dear Chimera users! Having already used AUTODOCK plugin of UCSF Chimera (for simple docking of 1 receptor with the ligand and structural examination of binding pocket) I wonder to know whether there is some tool built-in CHIMERA (or ChimeraX) suitable for the manipulating with DLG filles produced by Autodock? Particularly I would be interested to combine several DLG filles with their further reclasterization (in the same manner like it could be found in Autodock-Tools) and examination of particular clusters. I would be helpful for any suggestions! Kind regards Gleb
Hi Gleb, Sorry no, Chimera and ChimeraX cannot directly read or manipulate DLG (docking log) files from AutoDock. In Chimera, the Viewdock tool can read .pdbqt files from Autodock or Autodock Vina (the docking tool used Vina, which as far as I know does not make .dlg files). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html> ChimeraX has a similar tool for viewing docking results, ViewDockX. Again it reads .pdbqt but not .dlg. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html> Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 7, 2020, at 1:30 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera users!
Having already used AUTODOCK plugin of UCSF Chimera (for simple docking of 1 receptor with the ligand and structural examination of binding pocket) I wonder to know whether there is some tool built-in CHIMERA (or ChimeraX) suitable for the manipulating with DLG filles produced by Autodock? Particularly I would be interested to combine several DLG filles with their further reclasterization (in the same manner like it could be found in Autodock-Tools) and examination of particular clusters. I would be helpful for any suggestions! Kind regards Gleb
Thank you so much Elaine! I've just found that it exists in the Autodock-Tools (obviously!) GUI. There are also separate python scripts, which could manipulate with DLG filles (combining, reclustering etc). Anyway it would be definetely cool if one day some plugin for DLG files could be found in Chimera as well (since I prefere it to ADT!). In any case, feel free to contact me, if you need to test it. Sincerely Gleb ср, 7 окт. 2020 г. в 17:14, Elaine Meng <meng@cgl.ucsf.edu>:
Hi Gleb, Sorry no, Chimera and ChimeraX cannot directly read or manipulate DLG (docking log) files from AutoDock.
In Chimera, the Viewdock tool can read .pdbqt files from Autodock or Autodock Vina (the docking tool used Vina, which as far as I know does not make .dlg files). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>
ChimeraX has a similar tool for viewing docking results, ViewDockX. Again it reads .pdbqt but not .dlg. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 7, 2020, at 1:30 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera users!
Having already used AUTODOCK plugin of UCSF Chimera (for simple docking of 1 receptor with the ligand and structural examination of binding pocket) I wonder to know whether there is some tool built-in CHIMERA (or ChimeraX) suitable for the manipulating with DLG filles produced by Autodock? Particularly I would be interested to combine several DLG filles with their further reclasterization (in the same manner like it could be found in Autodock-Tools) and examination of particular clusters. I would be helpful for any suggestions! Kind regards Gleb
participants (3)
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Elaine Meng -
James Starlight -
Jeff Saxon