[chimerax-users] How to view SwissDock output in ViewDockX

[Michael Weber]

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 at 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".
>>>