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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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Working with alignments crashes or hangs Firefox #64

Open digitalbio opened 3 years ago

digitalbio commented 3 years ago

I would like students to be able to compare a structure of the SARS-CoV-2 spike protein where the RBD is up and bound to ACE2 and a structure where the RBD is down. Ideally, they could the A key to alternate between the structures and see how the RBD changes conformation.

  1. I found two structures that I could get alignment from in VAST+ - 7KQR and 7A94.
  2. I tried to select the unaligned regions of the chains to show the RBD and color them the same so we could see the movement. This is shown in the image.

But Firefox either crashes or hangs.

Screen Shot 2021-11-21 at 4 10 43 PM
jiywang3 commented 3 years ago

Could you try it without opening the "Seq. & Annotations" window? In this case, the sequence window used a lot of memory because of the number of residues.

digitalbio commented 3 years ago

We need to Sequences and Annotations window open in order to identify the protein chains.

I could have my students view the chain names in the record at the structure database, but that wouldn't tell them which chains are aligned to each other, and some of them work on small laptops, or Windows platforms, so they don't know to have multiple windows open on their screen.

jiywang3 commented 3 years ago

You could use “Defined Sets” and “Aligned Sequences”, but avoid “Seq. & Annotations” when the sequences are long.

digitaltodd commented 3 years ago

Perhaps this is a larger project. It seems to me that if we know there is a performance issue relate to sequence length, that iCn3D should be aware and not display the data. Users won't know when it is ok, or not ok, to view a sequence. Could long sequences be paged in some way to overcome the performance issue?

jiywang3 commented 3 years ago

Yes. If only partial sequence is displayed, the number of html elements corresponding to the residues will decrease. This will use less memory. It also depends on the memory of the user's computer.