Opened 7 months ago

Closed 7 months ago

Last modified 7 months ago

#17297 closed defect (not a bug)

Split molecule output

Reported by: arangarajan@… Owned by: pett
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202504020144 (2025-04-02 01:44:35 UTC)
Description
when i save models to pdb , it is written out with several types of issues.. one i recently encountered is that each residue was written as a  model and due to this i could not load this pdb into  MOE. I encounter this type of error with written out only a single model or sel  using
save xxx.pdb sel t 
save xxx.pdb #2
i am not able to share the file due to confidentality issues.



Log:
UCSF ChimeraX version: 1.10.dev202504020144 (2025-04-02)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:/AR-9197-structure/PP_Class1/PP_Class1/6OLZ_fit178.pdb

Summary of feedback from opening
D:/AR-9197-structure/PP_Class1/PP_Class1/6OLZ_fit178.pdb  
---  
warnings | Bad residue range for secondary structure: HELIX 36 36 GLU A 9 GLY A 177 1 169  
Bad residue range for secondary structure: HELIX 37 37 ALA A 2 ASP A 206 1 205  
Bad residue range for secondary structure: HELIX 55 55 PRO A 2 ALA A 148 1 147  
Bad residue range for secondary structure: HELIX 59 59 THR A 7 PRO A 109 1 103  
Bad residue range for secondary structure: HELIX 64 64 VAL A 2 LYS A 115 1 114  
35 messages similar to the above omitted  
  
Chain information for 6OLZ_fit178.pdb #1  
---  
Chain | Description  
A | No description available  
A | No description available  
B | No description available  
B | No description available  
  

> open 6olz

6olz title:  
Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like
molecule with PP tRNA [more info...]  
  
Chain information for 6olz #2  
---  
Chain | Description | UniProt  
A | Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN 0-25  
A2 | 28S ribosomal RNA |   
A3 | 5.8S ribosomal RNA |   
A4 | 5S ribosomal RNA |   
AA | 60S ribosomal protein L8 | RL8_HUMAN 2-249  
AB | 60S ribosomal protein L3 | RL3_HUMAN 2-395  
AC | 60S ribosomal protein L4 | RL4_HUMAN 3-365  
AD | 60S ribosomal protein L5 | RL5_HUMAN 4-297  
AE | 60S ribosomal protein L6 | RL6_HUMAN 42-288  
AF | 60S ribosomal protein L7 | RL7_HUMAN 15-248  
AG | 60S ribosomal protein L7a | RL7A_HUMAN 29-262  
AH | 60S ribosomal protein L9 | RL9_HUMAN 1-191  
AI | 60S ribosomal protein L10 | RL10_HUMAN 3-213  
AJ | 60S ribosomal protein L11 | RL11_HUMAN 9-177  
AL | 60S ribosomal protein L13 | RL13_HUMAN 2-206  
AM | 60S ribosomal protein L14 | RL14_HUMAN 2-140  
AN | 60S ribosomal protein L15 | RL15_HUMAN 2-204  
AO | 60S ribosomal protein L13a | RL13A_HUMAN 5-199  
AP | 60S ribosomal protein L17 | RL17_HUMAN 2-154  
AQ | 60S ribosomal protein L18 | RL18_HUMAN 2-188  
AR | 60S ribosomal protein L19 | RL19_HUMAN 2-182  
AS | 60S ribosomal protein L18a | RL18A_HUMAN 1-175  
AT | 60S ribosomal protein L21 | RL21_HUMAN 2-158  
AU | 60S ribosomal protein L22 | RL22_HUMAN 18-116  
AV | 60S ribosomal protein L23 | Q9BTQ7_HUMAN 12-140  
AW | 60S ribosomal protein L24 | RL24_HUMAN 2-122  
AX | 60S ribosomal protein L23a | RL23A_HUMAN 39-155  
AY | 60S ribosomal protein L26 | RL26_HUMAN 1-127  
AZ | 60S ribosomal protein L27 | RL27_HUMAN 3-136  
Aa | 60S ribosomal protein L27a | RL27A_HUMAN 2-148  
Ab | 60S ribosomal protein L29 | RL29_HUMAN 2-119  
Ac | 60S ribosomal protein L30 | RL30_HUMAN 7-109  
Ad | 60S ribosomal protein L31 | RL31_HUMAN 18-123  
Ae | 60S ribosomal protein L32 | RL32_HUMAN 2-130  
Af | 60S ribosomal protein L35a | RL35A_HUMAN 2-110  
Ag | 60S ribosomal protein L34 | RL34_HUMAN 2-115  
Ah | 60S ribosomal protein L35 | RL35_HUMAN 2-123  
Ai | 60S ribosomal protein L36 | RL36_HUMAN 5-101  
Aj | 60S ribosomal protein L37 | RL37_HUMAN 2-85  
Ak | 60S ribosomal protein L38 | RL38_HUMAN 2-70  
Al | 60S ribosomal protein L39 | RL39_HUMAN 2-51  
Am | 60S ribosomal protein L40 | RL40_HUMAN 78-127  
An | 60S ribosomal protein L41 | RL41_HUMAN 1-25  
Ao | 60S ribosomal protein L36a | RL36A_HUMAN 2-106  
Ap | 60S ribosomal protein L37a | RL37A_HUMAN 2-92  
At | 60S ribosomal protein L28 | RL28_HUMAN 2-123  
B1 | 18S ribosomal RNA |   
BA | 40S ribosomal protein SA | RSSA_HUMAN 5-219  
BB | 40S ribosomal protein S3a | RS3A_HUMAN 22-233  
BC | 40S ribosomal protein S2 | RS2_HUMAN 57-278  
BD | 40S ribosomal protein S3 | RS3_HUMAN 2-221  
BE | 40S ribosomal protein S4, Y isoform 1 | RS4Y1_HUMAN 2-258  
BF | 40S ribosomal protein S5 | RS5_HUMAN 15-204  
BG | 40S ribosomal protein S6 | RS6_HUMAN 1-232  
BH | 40S ribosomal protein S7 | RS7_HUMAN 12-194  
BI | 40S ribosomal protein S8 | RS8_HUMAN 2-208  
BJ | 40S ribosomal protein S9 | RS9_HUMAN 2-180  
BK | 40S ribosomal protein S10 | RS10_HUMAN 1-98  
BL | 40S ribosomal protein S11 | RS11_HUMAN 6-158  
BM | 40S ribosomal protein S12 | RS12_HUMAN 11-130  
BN | 40S ribosomal protein S13 | RS13_HUMAN 2-150  
BO | 40S ribosomal protein S14 | RS14_HUMAN 16-151  
BP | 40S ribosomal protein S15 | RS15_HUMAN 12-131  
BQ | 40S ribosomal protein S16 | RS16_HUMAN 8-146  
BR | 40S ribosomal protein S17 | RS17_HUMAN 2-126  
BS | 40S ribosomal protein S18 | RS18_HUMAN 4-142  
BT | 40S ribosomal protein S19 | RS19_HUMAN 2-144  
BU | 40S ribosomal protein S20 | RS20_HUMAN 20-116  
BV | 40S ribosomal protein S21 | RS21_HUMAN 1-81  
BW | 40S ribosomal protein S15a | RS15A_HUMAN 2-130  
BX | 40S ribosomal protein S23 | RS23_HUMAN 2-140  
BY | 40S ribosomal protein S24 | RS24_HUMAN 4-128  
BZ | 40S ribosomal protein S25 | RS25_HUMAN 28-113  
Ba | 40S ribosomal protein S26 | RS26_HUMAN 2-98  
Bb | 40S ribosomal protein S27 | RS27_HUMAN 4-83  
Bc | 40S ribosomal protein S28 | RS28_HUMAN 7-68  
Bd | 40S ribosomal protein S29 | RS29_HUMAN 5-55  
Be | 40S ribosomal protein S30 | E9PR30_HUMAN 3-57  
Bf | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 79-151  
Bg | Receptor of activated protein C kinase 1 | RACK1_HUMAN 2-315  
Bv | tRNA |   
Bx | mRNA |   
  
Non-standard residues in 6olz #2  
---  
MG — magnesium ion  
MVM —
N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide  
ZN — zinc ion  
  

> mmaker #2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6OLZ_fit178.pdb, chain A (#1) with 6olz, chain A2 (#2), sequence
alignment score = 22099.1  
RMSD between 3643 pruned atom pairs is 0.001 angstroms; (across all 3643
pairs: 0.001)  
  

> select #2 /Bv

1625 atoms, 1813 bonds, 77 pseudobonds, 78 residues, 3 models selected  

> ~select

Nothing selected  

> split #2

Split 6olz (#2) into 82 models  
Chain information for 6olz A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 6olz A2 #2.2  
---  
Chain | Description  
A2 | No description available  
  
Chain information for 6olz A3 #2.3  
---  
Chain | Description  
A3 | No description available  
  
Chain information for 6olz A4 #2.4  
---  
Chain | Description  
A4 | No description available  
  
Chain information for 6olz AA #2.5  
---  
Chain | Description  
AA | No description available  
  
Chain information for 6olz AB #2.6  
---  
Chain | Description  
AB | No description available  
  
Chain information for 6olz AC #2.7  
---  
Chain | Description  
AC | No description available  
  
Chain information for 6olz AD #2.8  
---  
Chain | Description  
AD | No description available  
  
Chain information for 6olz AE #2.9  
---  
Chain | Description  
AE | No description available  
  
Chain information for 6olz AF #2.10  
---  
Chain | Description  
AF | No description available  
  
Chain information for 6olz AG #2.11  
---  
Chain | Description  
AG | No description available  
  
Chain information for 6olz AH #2.12  
---  
Chain | Description  
AH | No description available  
  
Chain information for 6olz AI #2.13  
---  
Chain | Description  
AI | No description available  
  
Chain information for 6olz AJ #2.14  
---  
Chain | Description  
AJ | No description available  
  
Chain information for 6olz AL #2.15  
---  
Chain | Description  
AL | No description available  
  
Chain information for 6olz AM #2.16  
---  
Chain | Description  
AM | No description available  
  
Chain information for 6olz AN #2.17  
---  
Chain | Description  
AN | No description available  
  
Chain information for 6olz AO #2.18  
---  
Chain | Description  
AO | No description available  
  
Chain information for 6olz AP #2.19  
---  
Chain | Description  
AP | No description available  
  
Chain information for 6olz AQ #2.20  
---  
Chain | Description  
AQ | No description available  
  
Chain information for 6olz AR #2.21  
---  
Chain | Description  
AR | No description available  
  
Chain information for 6olz AS #2.22  
---  
Chain | Description  
AS | No description available  
  
Chain information for 6olz AT #2.23  
---  
Chain | Description  
AT | No description available  
  
Chain information for 6olz AU #2.24  
---  
Chain | Description  
AU | No description available  
  
Chain information for 6olz AV #2.25  
---  
Chain | Description  
AV | No description available  
  
Chain information for 6olz AW #2.26  
---  
Chain | Description  
AW | No description available  
  
Chain information for 6olz AX #2.27  
---  
Chain | Description  
AX | No description available  
  
Chain information for 6olz AY #2.28  
---  
Chain | Description  
AY | No description available  
  
Chain information for 6olz AZ #2.29  
---  
Chain | Description  
AZ | No description available  
  
Chain information for 6olz Aa #2.30  
---  
Chain | Description  
Aa | No description available  
  
Chain information for 6olz Ab #2.31  
---  
Chain | Description  
Ab | No description available  
  
Chain information for 6olz Ac #2.32  
---  
Chain | Description  
Ac | No description available  
  
Chain information for 6olz Ad #2.33  
---  
Chain | Description  
Ad | No description available  
  
Chain information for 6olz Ae #2.34  
---  
Chain | Description  
Ae | No description available  
  
Chain information for 6olz Af #2.35  
---  
Chain | Description  
Af | No description available  
  
Chain information for 6olz Ag #2.36  
---  
Chain | Description  
Ag | No description available  
  
Chain information for 6olz Ah #2.37  
---  
Chain | Description  
Ah | No description available  
  
Chain information for 6olz Ai #2.38  
---  
Chain | Description  
Ai | No description available  
  
Chain information for 6olz Aj #2.39  
---  
Chain | Description  
Aj | No description available  
  
Chain information for 6olz Ak #2.40  
---  
Chain | Description  
Ak | No description available  
  
Chain information for 6olz Al #2.41  
---  
Chain | Description  
Al | No description available  
  
Chain information for 6olz Am #2.42  
---  
Chain | Description  
Am | No description available  
  
Chain information for 6olz An #2.43  
---  
Chain | Description  
An | No description available  
  
Chain information for 6olz Ao #2.44  
---  
Chain | Description  
Ao | No description available  
  
Chain information for 6olz Ap #2.45  
---  
Chain | Description  
Ap | No description available  
  
Chain information for 6olz At #2.46  
---  
Chain | Description  
At | No description available  
  
Chain information for 6olz B1 #2.47  
---  
Chain | Description  
B1 | No description available  
  
Chain information for 6olz BA #2.48  
---  
Chain | Description  
BA | No description available  
  
Chain information for 6olz BB #2.49  
---  
Chain | Description  
BB | No description available  
  
Chain information for 6olz BC #2.50  
---  
Chain | Description  
BC | No description available  
  
Chain information for 6olz BD #2.51  
---  
Chain | Description  
BD | No description available  
  
Chain information for 6olz BE #2.52  
---  
Chain | Description  
BE | No description available  
  
Chain information for 6olz BF #2.53  
---  
Chain | Description  
BF | No description available  
  
Chain information for 6olz BG #2.54  
---  
Chain | Description  
BG | No description available  
  
Chain information for 6olz BH #2.55  
---  
Chain | Description  
BH | No description available  
  
Chain information for 6olz BI #2.56  
---  
Chain | Description  
BI | No description available  
  
Chain information for 6olz BJ #2.57  
---  
Chain | Description  
BJ | No description available  
  
Chain information for 6olz BK #2.58  
---  
Chain | Description  
BK | No description available  
  
Chain information for 6olz BL #2.59  
---  
Chain | Description  
BL | No description available  
  
Chain information for 6olz BM #2.60  
---  
Chain | Description  
BM | No description available  
  
Chain information for 6olz BN #2.61  
---  
Chain | Description  
BN | No description available  
  
Chain information for 6olz BO #2.62  
---  
Chain | Description  
BO | No description available  
  
Chain information for 6olz BP #2.63  
---  
Chain | Description  
BP | No description available  
  
Chain information for 6olz BQ #2.64  
---  
Chain | Description  
BQ | No description available  
  
Chain information for 6olz BR #2.65  
---  
Chain | Description  
BR | No description available  
  
Chain information for 6olz BS #2.66  
---  
Chain | Description  
BS | No description available  
  
Chain information for 6olz BT #2.67  
---  
Chain | Description  
BT | No description available  
  
Chain information for 6olz BU #2.68  
---  
Chain | Description  
BU | No description available  
  
Chain information for 6olz BV #2.69  
---  
Chain | Description  
BV | No description available  
  
Chain information for 6olz BW #2.70  
---  
Chain | Description  
BW | No description available  
  
Chain information for 6olz BX #2.71  
---  
Chain | Description  
BX | No description available  
  
Chain information for 6olz BY #2.72  
---  
Chain | Description  
BY | No description available  
  
Chain information for 6olz BZ #2.73  
---  
Chain | Description  
BZ | No description available  
  
Chain information for 6olz Ba #2.74  
---  
Chain | Description  
Ba | No description available  
  
Chain information for 6olz Bb #2.75  
---  
Chain | Description  
Bb | No description available  
  
Chain information for 6olz Bc #2.76  
---  
Chain | Description  
Bc | No description available  
  
Chain information for 6olz Bd #2.77  
---  
Chain | Description  
Bd | No description available  
  
Chain information for 6olz Be #2.78  
---  
Chain | Description  
Be | No description available  
  
Chain information for 6olz Bf #2.79  
---  
Chain | Description  
Bf | No description available  
  
Chain information for 6olz Bg #2.80  
---  
Chain | Description  
Bg | No description available  
  
Chain information for 6olz Bv #2.81  
---  
Chain | Description  
Bv | No description available  
  
Chain information for 6olz Bx #2.82  
---  
Chain | Description  
Bx | No description available  
  

> select #2.81

1625 atoms, 1813 bonds, 77 pseudobonds, 78 residues, 3 models selected  

> select ~sel

426805 atoms, 458192 bonds, 5668 pseudobonds, 34738 residues, 108 models
selected  

> hide sel target a

> cartoon

> select ~sel

1625 atoms, 1813 bonds, 77 pseudobonds, 78 residues, 3 models selected  

> hide

> hide target c

> select #2.81

1625 atoms, 1813 bonds, 77 pseudobonds, 78 residues, 3 models selected  

> show sel target c

> save trna-for-fitted-AR-model.pdb selectedOnly true

> close session

> open "C:/Users/Amith Rangarajan/Desktop/trna-for-fitted-AR-model.pdb"

Chain information for trna-for-fitted-AR-model.pdb #1  
---  
Chain | Description  
Bv | No description available  
  
Computing secondary structure  

> close session

> open D:/AR-9197-structure/PP_Class1/PP_Class1/generate-6olz-model.cxc

> open 6OLZ_fit178.pdb

Summary of feedback from opening 6OLZ_fit178.pdb  
---  
warnings | Bad residue range for secondary structure: HELIX 36 36 GLU A 9 GLY A 177 1 169  
Bad residue range for secondary structure: HELIX 37 37 ALA A 2 ASP A 206 1 205  
Bad residue range for secondary structure: HELIX 55 55 PRO A 2 ALA A 148 1 147  
Bad residue range for secondary structure: HELIX 59 59 THR A 7 PRO A 109 1 103  
Bad residue range for secondary structure: HELIX 64 64 VAL A 2 LYS A 115 1 114  
35 messages similar to the above omitted  
  
Chain information for 6OLZ_fit178.pdb #1  
---  
Chain | Description  
A | No description available  
A | No description available  
B | No description available  
B | No description available  
  

> open 6olz

6olz title:  
Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like
molecule with PP tRNA [more info...]  
  
Chain information for 6olz #2  
---  
Chain | Description | UniProt  
A | Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN 0-25  
A2 | 28S ribosomal RNA |   
A3 | 5.8S ribosomal RNA |   
A4 | 5S ribosomal RNA |   
AA | 60S ribosomal protein L8 | RL8_HUMAN 2-249  
AB | 60S ribosomal protein L3 | RL3_HUMAN 2-395  
AC | 60S ribosomal protein L4 | RL4_HUMAN 3-365  
AD | 60S ribosomal protein L5 | RL5_HUMAN 4-297  
AE | 60S ribosomal protein L6 | RL6_HUMAN 42-288  
AF | 60S ribosomal protein L7 | RL7_HUMAN 15-248  
AG | 60S ribosomal protein L7a | RL7A_HUMAN 29-262  
AH | 60S ribosomal protein L9 | RL9_HUMAN 1-191  
AI | 60S ribosomal protein L10 | RL10_HUMAN 3-213  
AJ | 60S ribosomal protein L11 | RL11_HUMAN 9-177  
AL | 60S ribosomal protein L13 | RL13_HUMAN 2-206  
AM | 60S ribosomal protein L14 | RL14_HUMAN 2-140  
AN | 60S ribosomal protein L15 | RL15_HUMAN 2-204  
AO | 60S ribosomal protein L13a | RL13A_HUMAN 5-199  
AP | 60S ribosomal protein L17 | RL17_HUMAN 2-154  
AQ | 60S ribosomal protein L18 | RL18_HUMAN 2-188  
AR | 60S ribosomal protein L19 | RL19_HUMAN 2-182  
AS | 60S ribosomal protein L18a | RL18A_HUMAN 1-175  
AT | 60S ribosomal protein L21 | RL21_HUMAN 2-158  
AU | 60S ribosomal protein L22 | RL22_HUMAN 18-116  
AV | 60S ribosomal protein L23 | Q9BTQ7_HUMAN 12-140  
AW | 60S ribosomal protein L24 | RL24_HUMAN 2-122  
AX | 60S ribosomal protein L23a | RL23A_HUMAN 39-155  
AY | 60S ribosomal protein L26 | RL26_HUMAN 1-127  
AZ | 60S ribosomal protein L27 | RL27_HUMAN 3-136  
Aa | 60S ribosomal protein L27a | RL27A_HUMAN 2-148  
Ab | 60S ribosomal protein L29 | RL29_HUMAN 2-119  
Ac | 60S ribosomal protein L30 | RL30_HUMAN 7-109  
Ad | 60S ribosomal protein L31 | RL31_HUMAN 18-123  
Ae | 60S ribosomal protein L32 | RL32_HUMAN 2-130  
Af | 60S ribosomal protein L35a | RL35A_HUMAN 2-110  
Ag | 60S ribosomal protein L34 | RL34_HUMAN 2-115  
Ah | 60S ribosomal protein L35 | RL35_HUMAN 2-123  
Ai | 60S ribosomal protein L36 | RL36_HUMAN 5-101  
Aj | 60S ribosomal protein L37 | RL37_HUMAN 2-85  
Ak | 60S ribosomal protein L38 | RL38_HUMAN 2-70  
Al | 60S ribosomal protein L39 | RL39_HUMAN 2-51  
Am | 60S ribosomal protein L40 | RL40_HUMAN 78-127  
An | 60S ribosomal protein L41 | RL41_HUMAN 1-25  
Ao | 60S ribosomal protein L36a | RL36A_HUMAN 2-106  
Ap | 60S ribosomal protein L37a | RL37A_HUMAN 2-92  
At | 60S ribosomal protein L28 | RL28_HUMAN 2-123  
B1 | 18S ribosomal RNA |   
BA | 40S ribosomal protein SA | RSSA_HUMAN 5-219  
BB | 40S ribosomal protein S3a | RS3A_HUMAN 22-233  
BC | 40S ribosomal protein S2 | RS2_HUMAN 57-278  
BD | 40S ribosomal protein S3 | RS3_HUMAN 2-221  
BE | 40S ribosomal protein S4, Y isoform 1 | RS4Y1_HUMAN 2-258  
BF | 40S ribosomal protein S5 | RS5_HUMAN 15-204  
BG | 40S ribosomal protein S6 | RS6_HUMAN 1-232  
BH | 40S ribosomal protein S7 | RS7_HUMAN 12-194  
BI | 40S ribosomal protein S8 | RS8_HUMAN 2-208  
BJ | 40S ribosomal protein S9 | RS9_HUMAN 2-180  
BK | 40S ribosomal protein S10 | RS10_HUMAN 1-98  
BL | 40S ribosomal protein S11 | RS11_HUMAN 6-158  
BM | 40S ribosomal protein S12 | RS12_HUMAN 11-130  
BN | 40S ribosomal protein S13 | RS13_HUMAN 2-150  
BO | 40S ribosomal protein S14 | RS14_HUMAN 16-151  
BP | 40S ribosomal protein S15 | RS15_HUMAN 12-131  
BQ | 40S ribosomal protein S16 | RS16_HUMAN 8-146  
BR | 40S ribosomal protein S17 | RS17_HUMAN 2-126  
BS | 40S ribosomal protein S18 | RS18_HUMAN 4-142  
BT | 40S ribosomal protein S19 | RS19_HUMAN 2-144  
BU | 40S ribosomal protein S20 | RS20_HUMAN 20-116  
BV | 40S ribosomal protein S21 | RS21_HUMAN 1-81  
BW | 40S ribosomal protein S15a | RS15A_HUMAN 2-130  
BX | 40S ribosomal protein S23 | RS23_HUMAN 2-140  
BY | 40S ribosomal protein S24 | RS24_HUMAN 4-128  
BZ | 40S ribosomal protein S25 | RS25_HUMAN 28-113  
Ba | 40S ribosomal protein S26 | RS26_HUMAN 2-98  
Bb | 40S ribosomal protein S27 | RS27_HUMAN 4-83  
Bc | 40S ribosomal protein S28 | RS28_HUMAN 7-68  
Bd | 40S ribosomal protein S29 | RS29_HUMAN 5-55  
Be | 40S ribosomal protein S30 | E9PR30_HUMAN 3-57  
Bf | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 79-151  
Bg | Receptor of activated protein C kinase 1 | RACK1_HUMAN 2-315  
Bv | tRNA |   
Bx | mRNA |   
  
Non-standard residues in 6olz #2  
---  
MG — magnesium ion  
MVM —
N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide  
ZN — zinc ion  
  

> mmaker #2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6OLZ_fit178.pdb, chain A (#1) with 6olz, chain A2 (#2), sequence
alignment score = 22099.1  
RMSD between 3643 pruned atom pairs is 0.001 angstroms; (across all 3643
pairs: 0.001)  
  

> save 6olz-rotated-for-AR-fitted-model.pdb #2

executed generate-6olz-model.cxc  




OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce RTX 4070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: LENOVO
Model: 83DF
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 34,070,192,128
MaxProcessMemory: 137,438,953,344
CPU: 32 Intel(R) Core(TM) i9-14900HX
OSLanguage: en-US

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    appdirs: 1.4.4
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    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
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    ChimeraX-BugReporter: 1.0.2
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    ChimeraX-CheckWaters: 1.4
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    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
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    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
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    ChimeraX-ImageFormats: 1.2
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    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
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    ChimeraX-Map: 1.3
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    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
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    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
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    ChimeraX-ModelArchive: 1.0
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    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
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    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.1
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
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    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
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    kiwisolver: 1.4.8
    line_profiler: 4.2.0
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    pycollada: 0.8
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    WMI: 1.5.1

Change History (3)

comment:1 by pett, 7 months ago

Component: Unassigned → Input/Output
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Split molecule output

comment:2 by pett, 7 months ago

Resolution: → not a bug
Status: accepted → closed

Hi Amith,

If you use the 'split' command, then yes, each chain is its own model which will be reflected in the output PDB file. If you really need to split the model for some reason, you will need to use the 'combine' command to make it into a single model again before you create your PDB file.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by arangarajan@…, 7 months ago 

Thank you.
I am still not clear on what I should do to fix the issue, I have started a thread on chimerax forum on this same topic.

Best
amith

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Monday, April 7, 2025 11:46 AM
To: Amith Rangarajan <arangarajan@initialtx.com>; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #17297: Split molecule output (was: ChimeraX bug report submission)

#17297: Split molecule output
------------------------------------+----------------------
          Reporter:  arangarajan@\u2026  |      Owner:  pett
              Type:  defect         |     Status:  accepted
          Priority:  normal         |  Milestone:
         Component:  Input/Output   |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+----------------------
Changes (by pett):

 * component:  Unassigned => Input/Output
 * owner:  (none) => pett
 * platform:   => all
 * project:   => ChimeraX
 * status:  new => accepted
 * summary:  ChimeraX bug report submission => Split molecule output
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