Working with alignments crashes or hangs Firefox

[digitalbio]

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.

[jiywang3]

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]

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]

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

[digitaltodd]

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]

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.