Dear Tom,


Thanks to you and your team for including this in the ChimeraX distribution. I am happy to have it in there and your changes all look very reasonable to me.


Regards,

Gerardo



From: Tom Goddard <goddard@sonic.net>
Sent: Thursday, October 10, 2024 03:54
To: Gerardo Tauriello
Cc: chimerax-users@cgl.ucsf.edu
Subject: Re: [chimerax-users] [EXTERN] Re: Support for _ma_qa_metric_local_pairwise to display PAE matrices stored in ModelArchive
 
Hi Gerardo,

  I decided to replace the metricId option (an integer) with metricName (e.g. "PAE" or "contact probability") since the user likely would not know which integer id to use.  Also in my previous example I gave the command option names with underscore characters, but usually the options names instead use camel case, for example,

modelcif pae #1 metricName "contact probability" defaultScore 0 palette rainbow range 0,1

  Tom


On Oct 8, 2024, at 6:13 PM, Tom Goddard <goddard@sonic.net> wrote:

Hi Gerardo,

  Thanks for adding the Model Archive fetch and improved PAE fetch that can get scores from associated files.  This all looks useful enough that I think it should go into the ChimeraX distribution.  So I added it to the daily build (October 8, 2024 and newer).  Let me know if you don't want your code added to ChimeraX.  I made fetching and opening the Model Archive files use the standard syntax

open ma-bak-cepc-0944 from modelarchive

and it doesn't automatically get the PAE, but I added an option to do that

open ma-bak-cepc-0944 from modelarchive pae true

To handle scores that are not PAE such as probability in the range of 0-1 I added the palette and range options to the "modelcif pae" command, for example,

modelcif pae #1 metric_id 4 default_score 0 palette rainbow range 0,1

For just showing PAE scores after the Model Archive file has been opened you can just use

modelcif pae #1

More details are in the ChimeraX ticket


  Tom