ligand tools cause crash on puzzle 1422

Case number:845829-2004105
Topic:Crash/Hang
Opened by:LociOiling
Status:Closed
Type:Bug
Opened on:Monday, August 28, 2017 - 04:49
Last modified:Tuesday, July 31, 2018 - 20:57

On puzzle 1422, using the selection interface, select the ligand at segment 107. Several ligand tools become visible on the toolbar.

The Ligand Design tool (L) displays a message "Cant design ligand" [sic] when clicked. (Perhaps the message could be "Ligand design not available" if there's a problem with contractions, or better yet, don't display the tool.)

The Ligand Queue tool (Q) crashes the client when clicked. Both debug.txt and log.txt contain a message "Encountered molecule which cannot properly be represented in RDKit" in this case.

The Ligand Properties tool (V) displays the "Small-Molecule Properties" window. (Simply "Small Molecule Properties" would be a better title.) The IsoSurface option appears to work, displaying an adjustable isosurface of the protein. Clicking the "Cation Pi Interactions" or "Pi Pi Interactions" checkbox crashes the client, again with the "RDKit" message. The "Small-Molecule Color" option does not cause a crash, but it colors the designable sections of the protein, and not the ligand. All colors seem to be yellow-green, including "cyan" and "magenta". Selecting one of the "Small-Molecule Color" options automatically selects "Ligand Specific" coloring in the regular View Options. It appears that "Small-Molecule Color" is actually redundant.

The Reaction Design tool (R) produces the message "Reaction Based Design not available for this puzzle!". The hyphen removed from the previous window title could be used here, as in "Reaction-based design not available". Better yet, don't display the tool in this case.

The MMFF Wiggle tool (M) crashes the client, again with the "RDKit" message. (It also sounds kind of rude, but maybe that's a plus.)

In summary, most of the ligand tools displayed cause a crash or do nothing. The adjustable isosurface on the Ligand Properties tool might actually be useful, however.

(Mon, 08/28/2017 - 04:49  |  3 comments)


jflat06's picture
User offline. Last seen 1 hour 19 min ago. Offline
Joined: 09/29/2010
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Thanks for pointing this out. It looks like some of the drug-design related tools are being enabled unintentionally - we'll get a fix out for this soon.

rmoretti's picture
User offline. Last seen 3 hours 49 min ago. Offline
Joined: 01/15/2010
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The most recent release should have fixes to most of these issues: both in not enabling ligand design tools when they shouldn't be, and also the fixes to most of the other issues you mention (when the ligand design tools are enabled).

By the way, MMFF is the acronym for the Merck Molecular Force Field, a small-molecule-centric energy function/scoring system.

LociOiling's picture
User offline. Last seen 2 hours 59 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
Status: Open » Closed

Old, closing.

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