Hi Everyone!
There is a new update for the experimental drug design group. Bug reports can be filed here or in the discord chat room.
1) Add color to change ligand so that it stands out better
2) Grab full residue during MMFF minimization - bug found by Wbertro
3) Molecular mass/weight text needs to be changed - Wbertro
4) Show limits for Rule of Five Filter in View Panel
5) Highlight important interactions in protein that can be used to guide designs (hydrogen bonds, salt bridges, cation-pi, pi-pi)
In general, more stability was added to designing small molecules and error catching.
-free_radical
One other note of interest. The score function has been more tuned for designs that are specific for HIV protease.
There was no puzzle in the experiment area
Hi dbuske,
There should be a puzzle in the Science Puzzle named HIV Test Case1-reup. Do you see it?
Shake is slow
Filters work nice and view bonds to ligand and filter view are ok.
No crash so far, but I didn't do anything manual yet.
Try it !
Hi Bruno,
A couple of questions for you.
1) Are you running local or global shake?
2) Are you using the puzzle HIV Test Case 1.1a or HIV Test Case-reup?
-Wberto and I are having trouble getting HIV Test Case-reup to work. It crashes for me and him anytime we change anything.
3) Are you running Windows or OSX?
Shake will always be slow when you first edit the small molecule and run shake for the first time. This is because it has to build the conformations for the small molecule at the time of shaking. Unfortunately, there is no way to get around this, unless I add an option to not build the conformations. This would make shake work in the old way, but the small molecule would not "shake".
1) global shake for the first time was extremely long (but if we know it, it's no problem, we can work on another client). I didnt' check when using recipes that include local shakes but recipes seem to work normally (I don't stay behind my computer when recipes are running). Where I am now: no hand move, simple shake 1-2 hours then wiggle backbone then shake 30 minutes 20 hours ago, quickfix (= local shakes, wiggles and idealizes) during 1 hour, then default tvdl enhanced DRW (including random cuts and idealizes) during 19 hours, still going 2-3 hours before I come back to home and see the computer.
2) HIV Test Case 1-reup : http://fold.it/portal/node/2002809
3) OSX
It finally crashed after > 30 hours eDRW but this is not abnormal on my mac. Now running a GAB recipe to see what happens.
Client: 20160919-41a9da0ffb-win_x86-experimental
core.chemical.gasteiger.GasteigerAtomTypeSet: Error when getting all gasteiger atom types for Carbon with 4 bonds.
core.chemical.gasteiger.GasteigerAtomTypeSet: Search string 'C54' not found in non-aromatic database having 91 entries.
core.chemical.gasteiger.GasteigerAtomTypeSet: Cannot find appropriate gasteiger type for atom C5
ERROR: Cannot find appropriate gasteiger type for atom.
ERROR:: Exit from: ......\source\src\core\chemical\gasteiger\GasteigerAtomTyper.cc line: 1176
UNHANDLED EXCEPTION
1: RaiseException +88 bytes (no line)
2: alIsAuxiliaryEffectSlot +283154 bytes (no line)
3: library_main +37032471 bytes (no line)
4: library_main +35895026 bytes (no line)
5: library_main +4521712 bytes (no line)
6: library_main +5204481 bytes (no line)
7: library_main +5209262 bytes (no line)
8: library_main +4404143 bytes (no line)
9: library_main +3973953 bytes (no line)
10: library_main +3458150 bytes (no line)
11: library_main +3264634 bytes (no line)
12: library_main +4908395 bytes (no line)
13: library_main +332360 bytes (no line)
14: library_main +3263900 bytes (no line)
15: library_main +4913283 bytes (no line)
16: library_main +4903391 bytes (no line)
17: gapfnScSendMessage +818 bytes (no line)
18: GetThreadDesktop +215 bytes (no line)
19: GetClientRect +197 bytes (no line)
20: CallWindowProcW +27 bytes (no line)
21: wglSwapBuffers +730 bytes (no line)
22: gapfnScSendMessage +818 bytes (no line)
23: GetThreadDesktop +215 bytes (no line)
24: CharPrevW +319 bytes (no line)
25: DispatchMessageA +15 bytes (no line)
26: library_main +4911621 bytes (no line)
27: library_main +3031726 bytes (no line)
28: library_main +16713 bytes (no line)
29: library_main +21 bytes (no line)
30: no symbol (no line)
31: no symbol (no line)
32: no symbol (no line)
33: BaseThreadInitThunk +18 bytes (no line)
34: RtlInitializeExceptionChain +99 bytes (no line)
35: RtlInitializeExceptionChain +54 bytes (no line)
that was for the re-up puzzle.
