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ncbi / icn3d

web-based protein structure viewer and analysis tool interactively or in batch mode
https://www.ncbi.nlm.nih.gov/Structure/icn3d
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Confusion with structure alignments #63

Closed digitalbio closed 3 years ago

digitalbio commented 3 years ago

For some structures, I can go to the NCBI structure database, click a chain, select a structure in the VAST results, choose iCn3, and see a structure alignment in iCn3D. The image below shows a case where I did this by using 6M0J and then I chose 7L3NB as the structure.

Screen Shot 2021-11-21 at 1 04 25 PM

If I open iCn3D, and choose Align > Structure to Structure, enter the same PDB IDs, and choose All Matching Molecules Superimposed, I get a message saying that these two structures do not have 3D alignment data.

Screen Shot 2021-11-21 at 1 07 27 PM

I don't understand why I'm getting a different result with iCn3D than I get from the NCBI structure database.

digitalbio commented 3 years ago

Also - when I load aligned structures by using the View 3D Alignment option from VAST, iCn3D is really slow. I'm not sure if this is related.

jiywang3 commented 3 years ago

NCBI structure database has two kinds of alignment: VAST and VAST+. The VAST alignment is typically between two chains as you saw between 6M0J_E and 7L3N_B. The VAST+ alignment is typically between two biological assemblies such as 6M0J and 7L3N. In iCn3D, the option "File > Align > Structure to Structure" uses the VAST+ alignment. The option "File > Align > Multiple Chains" using just chains as inputs uses the VAST alignment. Hope this clarifies the difference a bit.

digitalbio commented 3 years ago

Ok, I'll try that and see if it works.

I was confused because of the error message saying that there wasn't alignment data.

The error message seemed to contradict the results that I saw from VAST.

digitalbio commented 3 years ago

Oh, I haven't used VAST+ much. There's a feature I use in VAST where I search with set of PDB IDs and I've found a way to do that in VAST+.

Do you know, with VAST+, if there's as way I can search with more than one PDB ID? I only seem to be able to make this work with one ID. I tried using comma separated IDs, IDs separated by spaces but neither worked.

Screen Shot 2021-11-21 at 2 50 41 PM
digitalbio commented 3 years ago

I also haven't used VAST+ because when search for alignments, I can find them in the old VAST and I can't find them in VAST+. So, it hasn't seemed very useful.

jiywang3 commented 3 years ago

This help page (https://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html) talks about both VAST and VAST+. I updated the error message to 'These two MMDB IDs [PDB ID 1] and [PDB ID 2] do not have 3D alignment data in the VAST+ database. You can try the VAST alignment by visiting the VAST+ page https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=[PDB ID] (e.g., uid=1KQ2), and clicking "Original VAST"'. The VAST+ page can be used for both VAST+ and VAST search.