MolecularDynamicsViewer

[waleed.sabir@…]

Hello,

I have a question.

I have downloaded MolecularDynamicsViewer. When I try to use it I get “Please register the custom scheme 'kmd' via QWebEngineUrlScheme::registerScheme() before installing the custom scheme handler.”

What exactly should I do, how should I proceed?

Thank you,
Waleed Sabir

[Eric Pettersen]

Hi Waleed,

I think the error is relatively harmless and that you can proceed to use the tool afterward, for reference for the author (Kyle Diller), to fix the error the following code would need to be added to the bundle's bundle_info.xml file:

<Providers>

<Provider name="kmd" manager="url_schemes"/>

</Providers>

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[waleed.sabir@…]

I see thanks for letting me know.

I have a follow up. I don’t understand how to use the moleculardynamicsviewer. I have a series of pdbs of different frames. Does it all need to be one pdb? If so how do I do this.

My file comes from Yasara where there are sim files.

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Tuesday, October 1, 2024 at 12:58 PM
To: kdiller99@gmail.com <kdiller99@gmail.com>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Sabir, Waleed (NIH/NEI) [F] <waleed.sabir@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #16051: MolecularDynamicsViewer
#16051: MolecularDynamicsViewer
-------------------------------------+-------------------------
          Reporter:  waleed.sabir@…  |      Owner:  Kyle Diller
              Type:  defect          |     Status:  assigned
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+-------------------------
Changes (by pett):

 * cc: pett (added)
 * component:  Unassigned => Third Party
 * owner:  (none) => Kyle Diller
 * platform:   => all
 * project:   => ChimeraX
 * status:  new => assigned

Comment:

 Hi Waleed,
         I think the error is relatively harmless and that you can proceed
 to use the tool afterward, for reference for the author (Kyle Diller), to
 fix the error the following code would need to be added to the bundle's
 bundle_info.xml file:

   <Providers>
     <Provider name="kmd" manager="url_schemes"/>
   </Providers>

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F16051%23comment%3A1&data=05%7C02%7Cwaleed.sabir%40nih.gov%7Cf2eee629666e47db055608dce23a54f7%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638633987372794988%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=%2F7NagnL96iGnBzjFcsA3I6EDUYi0CzN5O2VgwN2TQIE%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16051#comment:1>>
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[Eric Pettersen]

As far as I know, the MolecularDynamicsViewer only accepts multi-MODEL PDB files.

[Kyle Diller]

I added the Providers tag to the bundle_info.xml.
That should fix the issue of the warning.

The tool only works with multi-MODEL PDB files since that was what I was
working with at the time.

-Kyle

On Wed, Oct 2, 2024 at 12:08 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>

[Eric Pettersen]

Due to database problems, this comment from Waleed did not make it into the ticket:

I see thank you.