Hi Rayees,

Mac Air graphics is pretty slow for running ISOLDE. But Tristan Croll who develops ISOLDE added a nice option "Sim Fidelity" to the ISOLDE panel in the middle -- by default it is set to "High" and setting it to "Quick" will make the simulations run much faster. Here is what Tristan told me about what it does:

"The latest ISOLDE release has new “sim fidelity” radio buttons on the “Sim settings” tab. The “quick” mode (no implicit solvent, nonbonded cutoff tightened to 9 Å) runs about 4x faster on my MacBook Air and still gives reasonable results in good density. Still not *fast*, but I think definitely usable."

This is in ISOLDE 1.2.2. If you need to update ISOLDE use ChimeraX menu Tools / More Tools....

If this is still too slow, I'm afraid it is a limitation. You have to use faster hardware. The realtime dynamics simulations used by ISOLDE need fast graphics - the molecular dynamics is done with OpenMM using OpenCL or CUDA GPU accelerated computation. CUDA is fastest and needs Nvidia graphics and the CUDA driver installed -- Macs don't support Nvidia gpus. The macOS OpenCL implementation is very slow, almost as slow as just running on the CPU.

Tristan has ISOLDE benchmarks on different hardware here

https://isolde.cimr.cam.ac.uk/performance-benchmarks/

Tom

On Jul 22, 2021, at 6:03 PM, Rayees Mattoo rmattoo@stanford.edu wrote:

Hi Tom, Thanks for responding. Actually, I wanted to run ISOLDE from chimeraX and already tried it running on Mac with my 500KDa protein complex. It was very slow, wanted to try on linux machine and ran into the OpenGL problem. Do you have any suggestions how to run ISOLDE faster on mac?

Best Rayees From: Tom Goddard goddard@sonic.net Sent: Thursday, July 22, 2021 5:32 PM To: Rayees Mattoo rmattoo@stanford.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu; chimerax-bugs@cgl.ucsf.edu chimerax-bugs@cgl.ucsf.edu Subject: Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS mojave)?

Hi Rayees,

I guess you have X Windows (XQuartz) running on your Mac and are hoping that X remote display from Linux to the Mac will work with ChimeraX. Unfortunately X Windows remote display of 3D OpenGL graphics has not worked reliably since the days Silicon Graphics computers in the 1990s. It is possible to get it to work between two Linux machines with identical OpenGL drivers. But it would be a near miracle if the XQuartz implementation of X Windows on Mac could handle the OpenGL from a Linux machine.

The sensible approach is to run ChimeraX directly on your MacBook Pro. We don't recommend remote display even when it works because rendering speed is likely to be poor.

Tom

...

On Jul 22, 2021, at 1:31 PM, Rayees Mattoo via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:

Hi, I am trying to access ChimeraX remotley using my mac book pro. The ChimeraX is installed on linux machine. Upon launching, the chimeraX GUI appears and suddenly disappears with the following error message: "ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4, Try updating your graphics driver". My mac currently has macOS mojave version 10.14.6 and it seems it does not have OpenGL graphics version 3.3 required to display chimeraX remotely. Is there any way out to fix the problem? Not sure if updating my macbook to Catalina or BigSur is going to help!

Best Rayees

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