Edwin Rojas-Unable to access toolbox to download

[emrojas@…]

To ChimeraX team:

My name is Edwin, a chemistry graduate student at UAB. I am trying to do energy minimizations for my homology model I generated. I am having trouble obtaining the ISOLDE plug-in. I followed the instructions in https://isolde.cimr.cam.ac.uk/download/ and have ChimeraX 1.3 on my Windows computer. I am getting this error, attached. Not sure what the issue is.

Thanks for your time!

Regards,

Edwin M. Rojas
NIH/NIDCR Ruth L. Kirschstein Fellow
DMD/PhD Program | School of Dentistry
Velu Group | Department of Chemistry
UAB | The University of Alabama at Birmingham

Capture.PNG​

[emrojas@…]

Added by email2trac

[pett]

Hi Edwin,

The toolshed was down until around 15 minutes ago. Could you try again? It may take several seconds to respond.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[emrojas@…]

It works now and I was able to install the plug-in, thanks for responding so quickly!

Best,

Edwin M. Rojas
NIH/NIDCR Ruth L. Kirschstein Fellow
DMD/PhD Program | School of Dentistry
Velu Group | Department of Chemistry
UAB | The University of Alabama at Birmingham

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, January 19, 2022 8:03:39 PM
Cc: Rojas, Edwin M <emrojas@uab.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #5968: Edwin Rojas-Unable to access toolbox to download

#5968: Edwin Rojas-Unable to access toolbox to download
--------------------------------+------------------------
          Reporter:  emrojas@…  |      Owner:  Greg Couch
              Type:  defect     |     Status:  feedback
          Priority:  normal     |  Milestone:
         Component:  Tool Shed  |    Version:
        Resolution:             |   Keywords:
        Blocked By:             |   Blocking:
Notify when closed:             |   Platform:  all
           Project:  ChimeraX   |
--------------------------------+------------------------
Changes (by pett):

 * status:  assigned => feedback


Comment:

 Hi Edwin,
         The toolshed was down until around 15 minutes ago.  Could you try
 again?  It may take several seconds to respond.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5968#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[pett]

Great! Glad it worked for you.

--Eric

[emrojas@…]

Eric,

By chance could you point me to the right direction to where I can learn energy minimization using ChimeraX with ISOLDE? Thanks and sorry if it is a very obvious answer.

Edwin M. Rojas
NIH/NIDCR Ruth L. Kirschstein Fellow
DMD/PhD Program | School of Dentistry
Velu Group | Department of Chemistry
UAB | The University of Alabama at Birmingham

From: ChimeraX<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, January 19, 2022 8:20 PM
Cc: Rojas, Edwin M<mailto:emrojas@uab.edu>; gregc@cgl.ucsf.edu<mailto:gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #5968: Edwin Rojas-Unable to access toolbox to download

#5968: Edwin Rojas-Unable to access toolbox to download
--------------------------------+------------------------
          Reporter:  emrojas@…  |      Owner:  Greg Couch
              Type:  defect     |     Status:  feedback
          Priority:  normal     |  Milestone:
         Component:  Tool Shed  |    Version:
        Resolution:             |   Keywords:
        Blocked By:             |   Blocking:
Notify when closed:             |   Platform:  all
           Project:  ChimeraX   |
--------------------------------+------------------------

Comment (by pett):

 Great!  Glad it worked for you.

 --Eric

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5968#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[pett]

Hi Edwin,

I'm not really sure how to do *just* minimization in ISOLDE -- in ISOLDE minimization is just kind of a stage in the process of running molecular dynamics in the context of a map. I've cc'ed ISOLDE's author, Tristan Croll, here and he might have a better answer.
If *all* you want to do is minimize your structure, you might consider using our older Chimera program (www.cgl.ucsf.edu/chimera). In that program you minimize by using the Tools→Structure Editing→Minimize Structure menu entry.

--Eric

[Tristan Croll]

First, a caveat: ISOLDE isn't really built to be run in the absence of a density map, and will warn you as such when you start a simulation - the implicit solvent environment is an imperfect replacement for real modelling with explicit water and ions. That being said, simply turning the simulation temperature down to zero Kelvin is an easy way to effective minimisation - there's an automatic LBFGS minimisation that happens every time you start a simulation (that's just meant to get things to the point where dynamics can stably start), and then the physics should do the rest. Of course you'll need to have added hydrogens with addh first, and really serious clashes will cause it issues (but those would be a strong sign that such a model isn't reliable enough to be used in the absence of experimental data anyway). There's currently no running indicator of convergence for this scenario, so you'd just have to watch it to see when things stop moving.

-- Tristan
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 20 January 2022 02:48
Cc: emrojas@uab.edu <emrojas@uab.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5968: Edwin Rojas-Unable to access toolbox to download

#5968: Edwin Rojas-Unable to access toolbox to download
--------------------------------+--------------------
          Reporter:  emrojas@…  |      Owner:  pett
              Type:  defect     |     Status:  closed
          Priority:  normal     |  Milestone:
         Component:  Tool Shed  |    Version:
        Resolution:  fixed      |   Keywords:
        Blocked By:             |   Blocking:
Notify when closed:             |   Platform:  all
           Project:  ChimeraX   |
--------------------------------+--------------------
Changes (by pett):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 Hi Edwin,
         I'm not really sure how to do *just* minimization in ISOLDE -- in
 ISOLDE minimization is just kind of a stage in the process of running
 molecular dynamics in the context of a map.  I've cc'ed ISOLDE's author,
 Tristan Croll, here and he might have a better answer.
         If *all* you want to do is minimize your structure, you might
 consider using our older Chimera program (www.cgl.ucsf.edu/chimera<http://www.cgl.ucsf.edu/chimera>).  In
 that program you minimize by using the Tools→Structure Editing→Minimize
 Structure menu entry.

 --Eric

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5968#comment:8>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker