How to view SwissDock output in ViewDockX
On Feb 9, 2021, at 3:56 AM, Michael Weber wrote:
Hi,
... I use SwissDock for molecular docking experiments and there is an explanation on how to examine the output results in Chimera. Unfortunately all those workflows appear not to work in ChimeraX - are there any plans (or even already existing documentation which very well might have escaped my attention) to get these working in ChimeraX as well? Invoking ViewDockX from either the menu >tools>general>ViewDockX or by typing the command after having loaded a PDB structure plus the docked ligands just results in the message "No suitable models found for ViewDockX".
Hi Michael, Although the Swissdock website can output a Chimera session, I believe you can also get the docking results in at least one other format. However, I don't see details about what that is, so it would be helpful if you would provide a sample of what you got (multi-model PDB?) and opened in ChimeraX. Can send it to just me (to share with other developers here) if you don't want it publicly available.
I tried running their example but got a server error on the first attempt, and the second attempt is still running.
My guess is that the ViewDockX tool doesn't know that the Swissdock file you opened could be docking results. However, we would need a sample to figure out exactly why, or if it is possible to fix that. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 9, 2021, at 10:33 AM, Tom Goddard goddard@sonic.net wrote:
On Feb 9, 2021, at 3:56 AM, Michael Weber wrote:
Hi,
... I use SwissDock for molecular docking experiments and there is an explanation on how to examine the output results in Chimera. Unfortunately all those workflows appear not to work in ChimeraX - are there any plans (or even already existing documentation which very well might have escaped my attention) to get these working in ChimeraX as well? Invoking ViewDockX from either the menu >tools>general>ViewDockX or by typing the command after having loaded a PDB structure plus the docked ligands just results in the message "No suitable models found for ViewDockX".
Hi Michael, I was able to get a set of example results from the server. I see that the ligand PDB file just has all the positions strung together in one huge model (does not separate them into individual models). I tried manually editing to add MODEL and ENDMDL records so that they would be read as individual models (edited file of subset of results attached), which did work, but ViewDockX still does not recognize that set of models as docking results nor does it read the scores and other descriptors that are in the REMARK records. I guess the code would need to be modified to support SwissDock output.
Now that I have a set of example results, I can make a "request for enhancement" ticket and attach them. However, our ViewDockX tool developer has retired (snif, sad for us!) and we have very limited manpower, so it may be that you will need to use Chimera to view Swissdock results for a while. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 9, 2021, at 11:09 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Michael, Although the Swissdock website can output a Chimera session, I believe you can also get the docking results in at least one other format. However, I don't see details about what that is, so it would be helpful if you would provide a sample of what you got (multi-model PDB?) and opened in ChimeraX. Can send it to just me (to share with other developers here) if you don't want it publicly available.
I tried running their example but got a server error on the first attempt, and the second attempt is still running.
My guess is that the ViewDockX tool doesn't know that the Swissdock file you opened could be docking results. However, we would need a sample to figure out exactly why, or if it is possible to fix that. Thanks, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 9, 2021, at 3:56 AM, Michael Weber wrote:
Hi, ... I use SwissDock for molecular docking experiments and there is an explanation on how to examine the output results in Chimera. Unfortunately all those workflows appear not to work in ChimeraX - are there any plans (or even already existing documentation which very well might have escaped my attention) to get these working in ChimeraX as well? Invoking ViewDockX from either the menu >tools>general>ViewDockX or by typing the command after having loaded a PDB structure plus the docked ligands just results in the message "No suitable models found for ViewDockX".
Hi Elaine, thanks for the kind support - I saw the "request for enhancement" ticket already. You were quicker than I could respond to the initial mails. :) Michael.
Am 10.02.2021 00:49 schrieb Elaine Meng:
Hi Michael, I was able to get a set of example results from the server. I see that the ligand PDB file just has all the positions strung together in one huge model (does not separate them into individual models). I tried manually editing to add MODEL and ENDMDL records so that they would be read as individual models (edited file of subset of results attached), which did work, but ViewDockX still does not recognize that set of models as docking results nor does it read the scores and other descriptors that are in the REMARK records. I guess the code would need to be modified to support SwissDock output.
Now that I have a set of example results, I can make a "request for enhancement" ticket and attach them. However, our ViewDockX tool developer has retired (snif, sad for us!) and we have very limited manpower, so it may be that you will need to use Chimera to view Swissdock results for a while. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 9, 2021, at 11:09 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Michael, Although the Swissdock website can output a Chimera session, I believe you can also get the docking results in at least one other format. However, I don't see details about what that is, so it would be helpful if you would provide a sample of what you got (multi-model PDB?) and opened in ChimeraX. Can send it to just me (to share with other developers here) if you don't want it publicly available.
I tried running their example but got a server error on the first attempt, and the second attempt is still running.
My guess is that the ViewDockX tool doesn't know that the Swissdock file you opened could be docking results. However, we would need a sample to figure out exactly why, or if it is possible to fix that. Thanks, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 9, 2021, at 3:56 AM, Michael Weber wrote:
Hi, ... I use SwissDock for molecular docking experiments and there is an explanation on how to examine the output results in Chimera. Unfortunately all those workflows appear not to work in ChimeraX - are there any plans (or even already existing documentation which very well might have escaped my attention) to get these working in ChimeraX as well? Invoking ViewDockX from either the menu
tools>general>ViewDockX or by typing the command after having loaded a PDB structure plus the docked ligands just results in the message "No suitable models found for ViewDockX".
participants (3)
-
Elaine Meng -
Michael Weber -
Tom Goddard