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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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Select by Distance is not working with metals #62

Closed digitalbio closed 3 years ago

digitalbio commented 3 years ago

Structure 1UVQ

  1. I clicked on the Zinc in the 3d structure to select it. The yellow halo appeared around it.
  2. Opened Select > by Distance
  3. I used "selected" for the first set, a radius of 4 A, and "non-selected" for the second set, clicked Display Result: The yellow halo disappeared and nothing happened.

What I expected: I expected to see one or two amino acids selected. If I opened Sequences & Annotations, clicked Details, then Interactions, I could see D76 and H81 interact with the Zinc.

Here are the commands that appeared below the structure window:

load mmdb 1UVQ | parameters &mmdbid=1UVQ pickatom 3108(chain: 1UVQ_ZN, residue: ZN, number: 1003, atom: ZN) select zone cutoff 4 | sets selected non-selected | false

digitalbio commented 3 years ago

Also - this process did work with 3R0L. I have a video of the process here [https://youtu.be/XGYWUMAmZX0]

So - I wonder if there's something specific about certain structures.

jiywang3 commented 3 years ago

This was fixed. Thanks for the report.

digitalbio commented 3 years ago

Confirmed. :-)