[chimerax-users] ChimeraX slower than Chimera at loading maps?

[Brian Hudson]

Hi Tom,

Thank you for your response.  Since we are on a network file system, 
it's possible that ChimeraX may not be the best application for the 
quick visualization that we're looking for.

One thing that I have since noticed, however, is that step of the map 
loading process that appears to be taking significantly longer for 
ChimeraX than Chimera is the "computing histogram" step.

Thanks,

Brian

BRIAN HUDSON, Ph.D.
Biocurator, RCSB Protein Data Bank
Assistant Research Professor, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4941 | E: brian.hudson at rcsb.org

On 9/2/2022 5:04 PM, Tom Goddard wrote:
> Hi Brian,
> 
>    ChimeraX should be the same speed as Chimera for opening maps.  Opening a 4 GB ccp4 map took 1 second including ChimeraX 1.4 startup time on my Mac.  ChimeraX (and Chimera) only display and read a part of a large map (either single plane or subsampled grid) initially so almost any size map should open quickly.  So I guess the script you are timing actually does other things.  There is no way to advise you without knowing what you are actually timing.  It is also possibly you are on an incredibly slow networked file system.  ChimeraX loads maybe 1000 Python files at startup and on a file system that struggles loading many small files it could take a long time. But I expect Chimera is almost as bad as ChimeraX -- Python based software often loads hundreds of small Python code files.
> 
> 	Tom
> 
> 
>> On Sep 2, 2022, at 1:25 PM, Brian Hudson via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>
>> Hi,
>>
>> I have a question about map-loading performance in ChimeraX.
>>
>> We use Chimera for the visualization of EM maps, and have recently loaded ChimeraX 1.3 on our Centos 7 workstations.
>>
>> We frequently run a script that opens Chimera (or ChimeraX) and loads one or more maps.  Running the script for the same 2 Gb CCP4-format map in three different programs, I get the following times for program startup + map loading, i.e., the time from when I run the script at the command line to when the map appears onscreen:
>>
>> Chimera 1.12	13 seconds
>> ChimeraX 0.1	25 seconds
>> ChimeraX 1.3	66 seconds
>>
>> This isn't exactly the direction I had hoped performance would trend, and was wondering if there was anything that could be done within ChimeraX 1.3 to speed the process along a little.
>>
>> Thanks,
>>
>> Brian
>>
>> -- 
>> BRIAN HUDSON, Ph.D.
>> Biocurator, RCSB Protein Data Bank
>> Assistant Research Professor, Institute for Quantitative Biomedicine
>> Rutgers, The State University of New Jersey
>> 174 Frelinghuysen Road, Piscataway NJ 08854
>> P: 848.445.4941 | E: brian.hudson at rcsb.org
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu
>> Manage subscription:
>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>>
>