id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16088 Fetch model archive structures and plot PAE values gerardo.tauriello@… Tom Goddard "Gerardo contributed code to fetch Model Archive structures and plot PAE files derived from some simpler ChimeraX Recipes code. Would be nice to add this into the ChimeraX distribution. From: Gerardo Tauriello Subject: [chimerax-users] Re: [EXTERN] Re: Support for _ma_qa_metric_local_pairwise to display PAE matrices stored in ModelArchive Date: October 8, 2024 at 3:45:16 AM PDT To: Tom Goddard Cc: ""chimerax-users@cgl.ucsf.edu"" Dear Tom, First of all: thank you very much for that recipe. Seems to work great. As I was motivated to learn how to script ChimeraX, I extended the recipe (new file attached) to better support data as stored in ModelArchive (MA). It now includes the following: Preference for pairwise metric of type PAE (instead of blindly picking the first one) and some info from the metadata on the chosen metric Handling of PAE files as accompanying data. It can handle additional files stored locally in the same folder as the main ModelCIF file or files stored remotely and it can handle files stored within ZIP files (as used in all cases in MA) An additional ""modelarchive open"" command to fetch files directly from MA given an MA ID and add PAE if available. Example usages for the two cases mentioned in my original post: ""modelarchive open ma-dm-hisrep-003"" and ""modelarchive open ma-bak-cepc-0944"" One observation when looking at sparsely populated PAE matrices as in ma-bak-cepc-0944: the mouse-over text which displays the score does not match the display. In ma-bak-cepc-0944 only inter-chain scores are available between chains A and B and the display shows that on the top right, while the mouse-over shows values in the bottom-left. I have no reason to believe that this is specific to ModelCIF and so I think that all PAE matrices suffer from the same display issue. This is barely noticeable as PAE matrices are almost symmetric but very much visible in this case. In terms of handling other pairwise scores beyond AlphaFold PAE. I tried to see how this looks in ma-bak-cepc-0944 which has an additional score of type contact probability (value in [0,1]). If I load it with ""modelcif pae #2 metric_id 4 default_score 0"" it works ok and the only thing preventing me from using it, is that the display is very PAE centric with the used titles and color scale. Just being able to set a color scale which depends on the range of data in the matrix would already make this a useful workaround... 😉 Regards, Gerardo " enhancement closed moderate Input/Output fixed Elaine Meng Eric Pettersen all ChimeraX