AddH: trying to bind bonded geometry of atom with no bonds

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-03-12)
Description
structure protonation issue.

Log:
UCSF ChimeraX version: 0.9 (2019-03-12)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/lpravda/assembly.cif.txt

Unrecognized file suffix '.txt'  

Unrecognized file suffix '.txt'  

> open /Users/lpravda/assembly.cif

Summary of feedback from opening /Users/lpravda/assembly.cif  
---  
warnings | Unknown polymer entity '35' near line 8541  
Unknown polymer entity '45' near line 14086  
Unknown polymer entity '60' near line 16754  
notes | Fetching CCD OHX from http://ligand-
expo.rcsb.org/reports/O/OHX/OHX.cif  
Fetching CCD UAM from http://ligand-expo.rcsb.org/reports/U/UAM/UAM.cif  
  
Chain information for assembly.cif #1  
---  
Chain | Description  
5 | 25S ribosomal RNA  
6 | 18S Ribosomal RNA  
7 | 5S ribosomal RNA  
8 | 5.8S ribosomal RNA  
c0 | 40S ribosomal protein S10-A  
c1 | 40S ribosomal protein S11-A  
c2 | 40S ribosomal protein S12  
c3 | 40S ribosomal protein S13  
c4 | 40S ribosomal protein S14-B  
c5 | 40S ribosomal protein S15  
c6 | 40S ribosomal protein S16-A  
c7 | 40S ribosomal protein S17-A  
c8 | 40S ribosomal protein S18-A  
c9 | 40S ribosomal protein S19-A  
d0 | 40S ribosomal protein S20  
d1 | 40S ribosomal protein S21-A  
d2 | 40S ribosomal protein S22-A  
d3 | 40S ribosomal protein S23-A  
d4 | 40S ribosomal protein S24-A  
d5 | 40S ribosomal protein S25-A  
d6 | 40S ribosomal protein S26-B  
d7 | 40S ribosomal protein S27-A  
d8 | 40S ribosomal protein S28-A  
d9 | 40S ribosomal protein S29-A  
e0 | 40S ribosomal protein S30-A  
e1 | Ubiquitin-40S ribosomal protein S31  
l2 | 60S ribosomal protein L2-A  
l3 | 60S ribosomal protein L3  
l4 | 60S ribosomal protein L4-A  
l5 | 60S ribosomal protein L5  
l6 | 60S ribosomal protein L6-A  
l7 | 60S ribosomal protein L7-A  
l8 | 60S ribosomal protein L8-A  
l9 | 60S ribosomal protein L9-A  
m0 | 60S ribosomal protein L10  
m1 | 60S ribosomal protein L11-B  
m2 | 60S ribosomal protein L12  
m3 | 60S ribosomal protein L13-A  
m4 | 60S ribosomal protein L14-A  
m5 | 60S ribosomal protein L15-A  
m6 | 60S ribosomal protein L16-A  
m7 | 60S ribosomal protein L17-A  
m8 | 60S ribosomal protein L18-A  
m9 | 60S ribosomal protein L19-A  
n0 | 60S ribosomal protein L20-A  
n1 | 60S ribosomal protein L21-A  
n2 | 60S ribosomal protein L22-A  
n3 | 60S ribosomal protein L23-A  
n4 | 60S ribosomal protein L24-A  
n5 | 60S ribosomal protein L25  
n6 | 60S ribosomal protein L26-A  
n7 | 60S ribosomal protein L27-A  
n8 | 60S ribosomal protein L28  
n9 | 60S ribosomal protein L29  
o0 | 60S ribosomal protein L30  
o1 | 60S ribosomal protein L31-A  
o2 | 60S ribosomal protein L32  
o3 | 60S ribosomal protein L33-A  
o4 | 60S ribosomal protein L34-A  
o5 | 60S ribosomal protein L35-A  
o6 | 60S ribosomal protein L36-A  
o7 | 60S ribosomal protein L37-A  
o8 | 60S ribosomal protein L38  
o9 | 60S ribosomal protein L39  
p0 | 60S acidic ribosomal protein P0  
p1 p2 | Ribosomal protein P1 alpha, P2 β  
q0 | Ubiquitin-60S ribosomal protein L40  
q1 | 60S ribosomal protein L41-A  
q2 | 60S ribosomal protein L42-A  
q3 | 60S ribosomal protein L43-A  
s0 | 40S ribosomal protein S0-A  
s1 | 40S ribosomal protein S1-A  
s2 | 40S ribosomal protein S2  
s3 | 40S ribosomal protein S3  
s4 | 40S ribosomal protein S4-A  
s5 | 40S ribosomal protein S5  
s6 | 40S ribosomal protein S6-A  
s7 | 40S ribosomal protein S7-A  
s8 | 40S ribosomal protein S8-A  
s9 | 40S ribosomal protein S9-A  
sM | Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1  
sR | Guanine nucleotide-binding protein subunit beta-like protein  
  

> addh hbond true

Summary of feedback from adding hydrogens to assembly.cif #1  
---  
warnings | Not adding hydrogens to /s0 SER 2 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /s0 LEU 3 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /s0 ASP 190 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /s0 THR 192 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /s0 GLN 193 CB because it is missing heavy-atom bond
partners  
129 messages similar to the above omitted  
notes | Termini for assembly.cif (#1) chain o9 determined from SEQRES records  
Termini for assembly.cif (#1) chain n1 determined from SEQRES records  
Termini for assembly.cif (#1) chain l5 determined from SEQRES records  
Termini for assembly.cif (#1) chain m7 determined from SEQRES records  
Termini for assembly.cif (#1) chain n8 determined from SEQRES records  
78 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /o9 ALA 2, /n1 GLY 2, /m7
ALA 2, /n8 PRO 2, /d0 GLN 12, /m2 UNK 9, /l8 ASN 24, /p2 UNK 1, /q2 VAL 2, /l3
SER 2, /s6 MET 1, /d2 THR 2, /o4 ALA 2, /n9 ALA 2, /s5 PHE 20, /o1 LEU 4, /l9
MET 1, /s7 SER 2, /sR ALA 2, /o0 SER 6, /o7 GLY 2, /d3 GLY 2, /m5 GLY 2, /s4
ALA 2, /c0 MET 1, /q3 ALA 2, /q0 ILE 77, /s1 VAL 20, /m1 GLN 6, /d9 GLU 4, /d7
VAL 2, /q1 MET 1, /n4 MET 1, /d4 SER 2, /s9 PRO 2, /s2 GLY 34, /e1 GLY 77, /n3
SER 2, /n7 ALA 2, /l7 THR 22, /e0 ALA 2, /m4 SER 2, /p1 UNK 1, /c9 PRO 2, /n0
MET 1, /8 A 1, /o8 ALA 2, /o5 ALA 2, /l4 SER 2, /o3 ALA 2, /n6 ALA 2, /7 G 1,
/o6 THR 2, /m9 ALA 2, /m8 GLY 2, /o2 ALA 2, /m3 ALA 2, /d6 PRO 2, /m6 VAL 3,
/s0 SER 2, /l2 GLY 2, /c2 ALA 20, /c4 ASN 10, /d8 THR 5, /c8 SER 2, /d1 MET 1,
/c3 GLY 2, /c6 SER 2, /s3 ALA 3, /6 U 1  
Chain-initial residues that are not actual N termini: /l5 GLN 4, /5 U 3, /5 C
491, /5 A 2093, /5 G 2503, /n2 ILE 11, /m0 ALA 2, /m0 LEU 111, /c7 GLY 2, /c7
ARG 95, /s8 GLY 2, /s8 LYS 135, /c0 VAL 87, /c5 ALA 4, /p0 GLY 3, /p0 GLY 184,
/c1 SER 2, /n5 ALA 23, /l6 SER 2, /l6 LYS 128, /sM LYS 23, /sM UNK 119, /d5
GLN 37, /6 C 136, /6 A 673  
Chain-final residues that are actual C termini: /o9 ILE 51, /n1 ILE 160, /l5
GLN 297, /n8 ALA 149, /d0 ASN 121, /l8 ASP 254, /q2 PHE 106, /l3 LEU 387, /5 U
3396, /d2 TYR 130, /o4 LYS 113, /n9 LYS 59, /s5 ARG 225, /n2 TYR 108, /o1 ASP
112, /m0 ALA 221, /l9 LEU 191, /s7 SER 187, /sR ASN 319, /s8 LYS 200, /o0 ALA
105, /o7 ALA 88, /d3 SER 145, /m5 LYS 204, /s4 LEU 261, /c0 THR 98, /q3 ALA
92, /q0 LYS 128, /s1 GLY 235, /m1 LYS 174, /d9 ARG 56, /d7 LYS 82, /q1 LYS 25,
/n4 SER 135, /d4 ASP 135, /s9 GLU 186, /s2 GLN 250, /e1 ALA 152, /n3 VAL 137,
/n7 PHE 136, /l7 ASN 244, /e0 GLN 63, /m4 ALA 138, /p1 UNK 47, /c9 GLU 144,
/n0 TYR 172, /8 U 158, /o8 LEU 78, /o5 ALA 120, /l4 ASP 362, /o3 ILE 107, /n6
GLU 127, /7 U 121, /n5 ILE 142, /o6 HIS 100, /m9 ALA 189, /m8 VAL 186, /o2 LEU
128, /m3 ALA 195, /d6 PRO 98, /l6 PHE 176, /m6 TYR 199, /s0 PRO 207, /l2 GLN
253, /c2 GLN 143, /c4 LEU 137, /sM UNK 174, /d8 ARG 67, /c8 ALA 146, /d1 ARG
87, /d5 THR 105, /c3 ASN 151, /c6 ARG 143, /s3 TYR 225, /6 A 1800  
Chain-final residues that are not actual C termini: /m7 ALA 156, /m2 UNK 163,
/p2 UNK 46, /5 G 443, /5 G 1953, /5 C 2444, /s6 GLU 218, /m0 LEU 103, /c7 ALA
90, /c7 ILE 122, /s8 LYS 123, /c0 GLU 84, /c5 PHE 138, /p0 ALA 107, /p0 ALA
221, /c1 GLY 147, /l6 GLU 109, /sM SER 85, /6 U 132, /6 U 670  
Missing OXT added to C-terminal residue /o9 ILE 51  
Missing OXT added to C-terminal residue /n1 ILE 160  
Missing OXT added to C-terminal residue /l5 GLN 297  
Missing OXT added to C-terminal residue /n8 ALA 149  
Missing OXT added to C-terminal residue /d0 ASN 121  
64 messages similar to the above omitted  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 253, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2617, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 58, in cmd_addh  
add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 166, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/hbond.py", line 243, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/hbond.py", line 489, in find_hbonds  
limited_acceptors, generic_acc_info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/hbond.py", line 784, in _find_acceptors  
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/hbond.py", line 784, in _find_acceptors  
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: assembly.cif.gz

assembly.cif.gz​

[lpravda@…]

Added by email2trac

[Eric Pettersen]

When finding H-bonds, skip donors/acceptors missing heavy-atom bond partners.