Hi Wang, Glad to hear ArtiaX helps showing your subtomogram averaged particles. An important feature of that extension written by Utz Ermel optimizes the display of thousands of particles by not using a separate ChimeraX model for each one. I tried opening 1500 maps of size 20 x 20 x 20 grid points in ChimeraX 1.8 on a Mac Studio M2 Ultra with much less powerful graphics than an Nvidia 4090, displaying all as surfaces, full lighting, and they rotated, zoomed and translated usably fast at 9 frames per second. So I am surprised you had a problem and I don't know why it is slow for you. Tom

On Sep 6, 2024, at 3:01 AM, 王光磊 <wangguanglei20@mails.ucas.ac.cn> wrote:

Hi Tom,

Thank you for your prompt response.

It seems that the performance issue was caused by the excessive number of subtomo maps. In my case, I loaded approximately 1,500 subtomo maps using the subtomo2chimera script, and displayed them in surface mode. This led to ChimeraX freezing for several seconds after any rotation or zoom of the view. Loading an extra tomograph did not affect performance.

I tried using AriaX to load the subtomo maps, and now the scene runs smoothly. Thank you for your advice!

Thanks,

Wang GuangLei

-----原始邮件----- 发件人:"Tom Goddard" <goddard@sonic.net> 发送时间:2024-09-06 03:34:59 (星期五) 收件人: 王光磊 <wangguanglei20@mails.ucas.ac.cn> 抄送: chimerax-users@cgl.ucsf.edu 主题: Re: [chimerax-users] Optimizing ChimeraX Performance for Multiple Subtomo Maps

Hi Wang,

I think your Nvidia 4090 should handle the large tomogram fine, and probably the slowdown is because having 1000-2000 open model of any kind, even if they are small like your subtomo maps, is more than ChimeraX was designed to handle. I am surprised though that rotating the view becomes slow because that should just move the camera which should not depend on the number of models shown. Do I understand correctly that you just open the tomogram and 1000-2000 subtomograms, display them all, and rotate and it updates slowly? How slowly, like 1 frame per second, or does it freeze for ten seconds? What display style do you use for the subtomograms, surface or volumetric?

You might be interested in the ArtiaX ChimeraX extension which is for looking at particles in tomograms. You would get it using ChimeraX menu Tools / More Tools....

Tom

...

On Sep 5, 2024, at 1:15 AM, 王光磊 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I'm using chimerax to display my tomograph and multiple subtomo averages in surface mode. Specifically, I need to visualize a 1440*1022*250 tomograph, along with 1000-2000 subtomo maps, sized at 32x32x32 and 16x16x16. However, loading such a large number of maps has significantly slowed down ChimeraX, particularly when rotating the view. Is there any settings to improve interactive performance or increase hardware utilization? I hope to avoid cropping the tomograph.

My system specifications are as follows:

Dual Intel Xeon 5317 processors@3.00GHz RTX 4090 GPU 128GB RAM Operating System: CentOS Stream 9 GNOME Version: 40.4 GPU Driver Version: 550.54.15 I would greatly appreciate any suggestions.

Thanks,

Wang GuangLei

_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/