ISOLDE not listing clashes

[andong.li@…]

The following bug report has been submitted:
Platform:        Linux-5.13.0-40-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
ISOLDE unable to resolve clashes for simulation but no clashes are displayed in validation tab.

Log:
> set selectionWidth 4

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/whitelab2/Desktop/Tony/NapBAsym/All_Isolde/Isolde6/Asym_Ad_test4.cif

Summary of feedback from opening
/home/whitelab2/Desktop/Tony/NapBAsym/All_Isolde/Isolde6/Asym_Ad_test4.cif  
---  
warnings | Unknown polymer entity '1' near line 377  
Unknown polymer entity '2' near line 155227  
Unknown polymer entity '3' near line 172436  
Unknown polymer entity '4' near line 177096  
Unknown polymer entity '5' near line 192199  
1 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Asym_Ad_test4.cif #1  
---  
Chain | Description  
A AA AB AC AD AE AF AG AH AI AJ AK AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ
Aa Ac Ad Ah Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax Ay Az B BB BC BD BE
BF BH BJ BK BL C D E F G H I J K L M N O P Q R S T U V W Y Z a b c d e f g i j
k l m o p q r s t u y z | ?  
Ab X h n | ?  
Ae v | ?  
Af Ag w x | ?  
Ai BA BI BM | ?  
BG | ?  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for Asym_Ad_test4.cif  
---  
Chain | Description  
1.2/A 1.2/AA 1.2/AB 1.2/AC 1.2/AD 1.2/AE 1.2/AF 1.2/AG 1.2/AH 1.2/AI 1.2/AJ
1.2/AK 1.2/AM 1.2/AN 1.2/AO 1.2/AP 1.2/AQ 1.2/AR 1.2/AS 1.2/AT 1.2/AU 1.2/AV
1.2/AW 1.2/AX 1.2/AY 1.2/AZ 1.2/Aa 1.2/Ac 1.2/Ad 1.2/Ah 1.2/Aj 1.2/Ak 1.2/Al
1.2/Am 1.2/An 1.2/Ao 1.2/Ap 1.2/Aq 1.2/Ar 1.2/As 1.2/At 1.2/Au 1.2/Av 1.2/Aw
1.2/Ax 1.2/Ay 1.2/Az 1.2/B 1.2/BB 1.2/BC 1.2/BD 1.2/BE 1.2/BF 1.2/BH 1.2/BJ
1.2/BK 1.2/BL 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L
1.2/M 1.2/N 1.2/O 1.2/P 1.2/Q 1.2/R 1.2/S 1.2/T 1.2/U 1.2/V 1.2/W 1.2/Y 1.2/Z
1.2/a 1.2/b 1.2/c 1.2/d 1.2/e 1.2/f 1.2/g 1.2/i 1.2/j 1.2/k 1.2/l 1.2/m 1.2/o
1.2/p 1.2/q 1.2/r 1.2/s 1.2/t 1.2/u 1.2/y 1.2/z | ?  
1.2/Ab 1.2/X 1.2/h 1.2/n | ?  
1.2/Ae 1.2/v | ?  
1.2/Af 1.2/Ag 1.2/w 1.2/x | ?  
1.2/Ai 1.2/BA 1.2/BI 1.2/BM | ?  
1.2/BG | ?  
  

> open
> /home/whitelab2/Desktop/Tony/NapBAsym/All_Isolde/NapoleonB_sharpened_map.ccp4

Opened NapoleonB_sharpened_map.ccp4 as #2, grid size 800,800,800, pixel 1.45,
shown at step 1, values float32  

> clipper associate #2 toModel #1

Opened NapoleonB_sharpened_map.ccp4 as #1.1.1.1, grid size 800,800,800, pixel
1.45, shown at step 1, values float32  

> select /Ad

5736 atoms, 5783 bonds, 99 pseudobonds, 366 residues, 2 models selected  

> isolde sim start sel

ISOLDE: started sim  
ISOLDE: paused sim  




OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: NVIDIA RTX A6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7049GP-TRT
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 64 Intel(R) Xeon(R) Gold 6226R CPU @ 2.90GHz
Cache Size: 22528 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          376Gi       7.1Gi       353Gi        50Mi        16Gi       367Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	DeviceName: ASPEED Video AST2500	
	Subsystem: Super Micro Computer Inc ASPEED Graphics Family [15d9:096d]
Locale: ('en_US', 'UTF-8')
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[pett]

Reported by "Tony"

[andong.li@…]

Hello,

I was wondering if there's additional information I can provide to help
with resolving this issue?

Thank you,
Tony

On Thu, May 5, 2022 at 6:23 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

Sorry for not responding earlier - it's been a bit of a tumultuous time. When a simulation is running, the Clashes widget doesn't actually list distance-based clashes, but atoms that are experiencing out-of-range forces. The problem is that the widget filters out the "fixed" atoms (those that are present in the simulation to maintain context, but aren't allowed to move). OpenMM still calculates forces between those atoms, so if two or more are clashing badly there will be out-of-range forces in the mix (even though they have no practical effect). My code for catching those and launching the clash warning is *supposed* to filter out such cases - but it would appear I've done something wrong there. Will take another look, but in the meantime, here's what you can do:

• in some cases (where the clashes are bad but not catastrophic) you can simply escape by running a brief simulation on the whole protein. With no atoms fixed, the minimiser has a much better chance at finding a way out.

• look at the clash widget *without* a simulation running. Under these circumstances it uses ChimeraX's distance-based clash detection, which should be much more informative. The most problematic clashes will be at or near the top of the list. Click on a clash, and see what you can do to improve it. In many cases that's as simple as choosing a different rotamer; in others you might need to use the isolde ignore command to temporarily exclude a few residues from simulations allowing you to move others out of the way.

In general, the only clashes that need to be treated manually like that are those where there is no simple downhill gradient for the minimiser to push them down - where two atoms are almost perfectly overlapping, or where things are so entangled that pushing nonbonded interactions apart would involve drastically stretching or compressing bonds.

Hope this helps!

Tristan

[Tristan Croll]

Abandoned the use of forces as a proxy for clashes - the Clashes table now always displays distance-based clashes calculated using the ChimeraX clashes tool.