Opened 4 years ago

Closed 12 months ago

#5493 closed defect (limitation)

H-bonds nowhere near nucleic acid depictions

Reported by: vishal.sahu@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Greg Couch) 

The following bug report has been submitted:
Platform:        Linux-5.11.0-38-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
ChimeraX, on using hb with the helical structure shows hydrogen bonds as shown in the image, since the display is quite distorted interpretation and visualization may result wrong. Please look into it as hydrogen bonds should start at some atom and end at some atom. Attaching image for your kind perusal. 

With thanks 

V K Sahu
JRF

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/lig_5c04e69d7e8b6.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/lig_5c04e69d7e8b6.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Name: 1KD5B.pdb  
  
Chain information for lig_5c04e69d7e8b6.pdb #1  
---  
Chain | Description  
B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/rec_5c04e69d7e8b6.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/rec_5c04e69d7e8b6.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Name: 1KD5A.pdb  
  
Chain information for rec_5c04e69d7e8b6.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_1.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 1  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -509.12  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 0.64  
  
Chain information for model_1.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_2.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_2.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 2  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -384.80  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 6.20  
  
Chain information for model_2.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_3.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_3.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 3  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -369.96  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 14.53  
  
Chain information for model_3.pdb #5  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_4.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_4.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 4  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -360.71  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 6.88  
  
Chain information for model_4.pdb #6  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_5.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_5.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 5  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -352.17  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 6.08  
  
Chain information for model_5.pdb #7  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_6.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_6.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 6  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -342.71  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 4.73  
  
Chain information for model_6.pdb #8  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_7.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_7.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 7  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -336.42  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 16.81  
  
Chain information for model_7.pdb #9  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_8.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_8.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 8  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -334.81  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 6.10  
  
Chain information for model_8.pdb #10  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_9.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_9.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 9  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -324.97  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 8.79  
  
Chain information for model_9.pdb #11  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_10.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_10.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 10  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -317.08  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 7.05  
  
Chain information for model_10.pdb #12  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_11.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_11.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 11  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -311.14  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 21.61  
  
Chain information for model_11.pdb #13  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_12.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_12.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 12  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -309.84  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 8.40  
  
Chain information for model_12.pdb #14  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_13.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_13.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 13  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -300.89  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 14.25  
  
Chain information for model_13.pdb #15  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_14.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_14.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 14  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -295.65  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 21.52  
  
Chain information for model_14.pdb #16  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_15.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_15.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 15  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -293.94  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 26.17  
  
Chain information for model_15.pdb #17  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_16.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_16.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 16  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -292.61  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 15.58  
  
Chain information for model_16.pdb #18  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_17.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_17.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 17  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -290.78  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 24.10  
  
Chain information for model_17.pdb #19  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_18.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_18.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 18  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -287.46  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 20.47  
  
Chain information for model_18.pdb #20  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_19.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_19.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 19  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -286.74  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 24.54  
  
Chain information for model_19.pdb #21  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_20.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_20.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 20  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -283.47  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 5.38  
  
Chain information for model_20.pdb #22  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_21.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_21.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 21  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -283.30  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 24.58  
  
Chain information for model_21.pdb #23  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_22.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_22.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 22  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -279.60  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 25.89  
  
Chain information for model_22.pdb #24  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_23.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_23.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 23  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -277.85  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 6.74  
  
Chain information for model_23.pdb #25  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_24.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_24.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 24  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -276.48  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 6.09  
  
Chain information for model_24.pdb #26  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_25.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_25.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 25  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -275.50  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 11.30  
  
Chain information for model_25.pdb #27  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_26.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_26.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 26  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -274.90  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 10.58  
  
Chain information for model_26.pdb #28  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_27.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_27.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 27  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -273.47  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 23.42  
  
Chain information for model_27.pdb #29  
---  
Chain | Description  
A B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_28.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_28.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 28  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -272.96  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 9.51  
  
Chain information for model_28.pdb #30  
---  
Chain | Description  
A B | No description available  
  

> select #2

230 atoms, 256 bonds, 11 residues, 1 model selected  

> color sel red

> close #3-99

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/5c04e69d7e8b6/model_94.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/5c04e69d7e8b6/model_94.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 94  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_5c04e69d7e8b6.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -229.18  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 12.14  
  
Chain information for model_94.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> hbonds #3

58 hydrogen bonds found  

> hbonds #3 reveal true showDist true

58 hydrogen bonds found  

> show sel atoms

> select

920 atoms, 1024 bonds, 58 pseudobonds, 44 residues, 5 models selected  

> show sel & #2-3 atoms

> hide sel & #2-3 atoms

> hide sel & #2-3 atoms

> show sel & #2-3 atoms

> hide sel & #2-3 cartoons

> show sel & #2-3 cartoons

> hide sel & #2-3 cartoons

> style sel & #2-3 stick

Changed 690 atom styles  

> style sel & #2-3 sphere

Changed 690 atom styles  

> style sel & #2-3 ball

Changed 690 atom styles  

> style sel & #2-3 sphere

Changed 690 atom styles  

> show sel & #2-3 cartoons

> show sel & #2-3 atoms

> hide sel & #2-3 atoms

> hide sel & #2-3 cartoons

> close

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/lig_5c04e69d7e8b6.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/lig_5c04e69d7e8b6.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Name: 1KD5B.pdb  
  
Chain information for lig_5c04e69d7e8b6.pdb #1  
---  
Chain | Description  
B | No description available  
  

> open /mnt/DataDrive/MDD/PROJ001/Demo-Results-
> HNADock/all_results/rec_5c04e69d7e8b6.pdb

Summary of feedback from opening /mnt/DataDrive/MDD/PROJ001/Demo-Results-
HNADock/all_results/rec_5c04e69d7e8b6.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Name: 1KD5A.pdb  
  
Chain information for rec_5c04e69d7e8b6.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hbonds #3 reveal true showDist true

Atom specifier selects no atoms  

> hbonds #1 reveal true showDist true

26 hydrogen bonds found  

> view




OpenGL version: 4.6 (Core Profile) Mesa 21.0.3
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel
Manufacturer: HP
Model: HP Desktop Pro G1 MT
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz
Cache Size: 9216 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           11Gi       4.3Gi       203Mi       888Mi       7.1Gi       6.1Gi
	Swap:          31Gi       1.5Gi        29Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop) [8086:3e92]	
	DeviceName: Onboard - Video	
	Subsystem: Hewlett-Packard Company UHD Graphics 630 (Desktop) [103c:843c]
Locale: ('en_IN', 'ISO8859-1')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0
File attachment: double-helix-interaction-issue.png

double-helix-interaction-issue.png​

Attachments (1)

double-helix-interaction-issue.png​ (166.3 KB ) - added by vishal.sahu@… 4 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by vishal.sahu@…, 4 years ago

Attachment: double-helix-interaction-issue.png​ added

Added by email2trac

comment:1 by pett, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Depiction
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → H-bonds nowhere near nucleic acid depictions

comment:2 by Greg Couch, 12 months ago

Description: modified (diff)
Resolution: → limitation
Status: assigned → closed

Getting the hydrogen bonds to move to positions on the abstract representations is not going to happen anytime soon. If you want to depict the h-bonds, switch to the filled ring representation.

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