Opened 6 years ago

Last modified 4 years ago

#3011 feedback defect

Disconnected hydrogens in 6rhz

Reported by: lpravda@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen)

In entry 6rhz, the following hydrogens have no bonds:

/B CLA 1238 H122
/B CLA 1238 H13
/B CLA 1238 H203

In the PDB form of the entry, they are bonded to the nearby carbon. I don't know if this is an issue with ChimeraX mmCIF reader or with the mmCIF entry itself... 

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
not really a protaonation issue. probably a source code formatting issue?

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6rhz fromDatabase pdbe_updated

Summary of feedback from opening 6rhz fetched from pdbe_updated  
---  
note |  
  
  
| Summary of feedback from opening
/Users/lpravda/Downloads/ChimeraX/pdbe_updated/6rhz.cif  
  
---  
  
  
  
  
warning | Atom H1 is not in the residue template for MET #1 in chain J  
  
  
  
  
  
6rhz title:  
Structure of a minimal photosystem I from a green alga [more info...]  
  
Chain information for 6rhz #1  
---  
Chain | Description  
1 | Chlorophyll a-b binding protein, chloroplastic  
2 | Chlorophyll a-b binding protein, Lhca2  
3 | Chlorophyll a-b binding protein, chloroplastic  
4 | Chlorophyll a-b binding protein, Lhca4  
A | Photosystem I P700 chlorophyll a apoprotein A1  
B | Photosystem I P700 chlorophyll a apoprotein A2  
C | Photosystem I iron-sulfur center  
D | Photosystem I reaction center subunit II, PsaD  
E | Photosystem I reaction center subunit IV, PsaE  
F | Photosystem I reaction center subunit III, PsaF  
J | Photosystem I reaction center subunit IX  
  
Non-standard residues in 6rhz #1  
---  
BCR — β-carotene  
CHL — chlorophyll B  
CL0 — chlorophyll A isomer  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol, lutein)  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)  
  
  

Invalid "hbond" argument: Expected true or false (or 1 or 0)  

> addh hbond true

Summary of feedback from adding hydrogens to 6rhz #1  
---  
warning | Unknown hybridization for atom (S4) of residue type SF4; not adding
hydrogens to it  
notes | Termini for 6rhz (#1) chain 1 determined from SEQRES records  
Termini for 6rhz (#1) chain 2 determined from SEQRES records  
Termini for 6rhz (#1) chain 3 determined from SEQRES records  
Termini for 6rhz (#1) chain 4 determined from SEQRES records  
Termini for 6rhz (#1) chain A determined from SEQRES records  
6 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /1 GLN 32, /2 ASP 63, /3 TYR
73, /4 ASP 123, /A VAL 13, /B PHE 6, /C ALA 2, /D PRO 69, /E GLU 65, /F ASP
78, /J MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /1 VAL 228, /2 ILE 270, /3 THR
282, /4 PHE 333, /A GLY 751, /B GLY 735, /C TYR 81, /D PRO 209, /E LYS 128, /F
SER 240, /J SER 40  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /1 VAL 228  
Missing OXT added to C-terminal residue /2 ILE 270  
Missing OXT added to C-terminal residue /3 THR 282  
Missing OXT added to C-terminal residue /4 PHE 333  
Missing OXT added to C-terminal residue /C TYR 81  
4 messages similar to the above omitted  
2001 hydrogen bonds  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 171, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/hbond.py", line 748, in add_hydrogens  
_attach_hydrogens(a, altloc_hpos_info, bonding_info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/hbond.py", line 893, in _attach_hydrogens  
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 855, in add_altloc_hyds  
pos, bonding_info, alt_loc)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 881, in new_hydrogen  
new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema),
"H",  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 1003, in _h_name  
while find_atom("%s%s" % (h_name, to_h36(h_num, h_digits))):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 943, in to_h36  
decimal_limit = eval('9' * max_digits)  
File "<string>", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File "", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 943, in to_h36  
decimal_limit = eval('9' * max_digits)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (13)

comment:1 by Eric Pettersen, 6 years ago

Cc: Eric Pettersen added
Component: Unassigned → Input/Output
Description: modified (diff)
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Disconnected hydrogens in 6rhz

Reported by Lucas Pravda

comment:2 by Greg Couch, 6 years ago

Question, when I hide all atoms, then "show /B:1238; view", I see two disjoint residues. Shouldn't they be separate residues?

comment:3 by Eric Pettersen, 6 years ago

It's a chlorophyll that's missing some atoms. Click on the CLA link in the log to see the full residue.

comment:4 by Eric Pettersen, 6 years ago

Correction, the "chlorophyll A" link

comment:5 by Greg Couch, 6 years ago

For residue /B:1238, the CCD entry for CLA says that:

H13 is connected to C13
H122 is connected to C12
H203 is connected to C20

Those hydrogens exist but the carbons are not there, so the hydrogens aren't connected.

That bug appears to be in the atom naming or the CLA CCD entry.

comment:6 by Greg Couch, 6 years ago

Status: assigned → feedback

comment:7 by Greg Couch, 5 years ago

FYI, I've modified ChimeraX to give a warning when this situation occurs.

Out of curiosity, did you report this bug in this entry to the PDB?

in reply to:  8 ; comment:8 by Eric Pettersen, 5 years ago 



Are you asking me or Lukas?  I didn’t.

—Eric

comment:9 by Greg Couch, 5 years ago

Lukas, it's his bug so to speak.

in reply to:  10 ; comment:10 by lpravda@…, 5 years ago 

Hi all,

Sorry for not responding earlier, I flagged this with the data annotation team, if there is anything we could to about that, however, to my knowledge this has not been resolved yet. I will let you know when this is fixed.

Thank you,
Lukas

On 15/05/2020, 20:12, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #3011: Disconnected hydrogens in 6rhz
    -----------------------------------+------------------------
              Reporter:  lpravda@…     |      Owner:  Greg Couch
                  Type:  defect        |     Status:  feedback
              Priority:  normal        |  Milestone:
             Component:  Input/Output  |    Version:
            Resolution:                |   Keywords:
            Blocked By:                |   Blocking:
    Notify when closed:                |   Platform:  all
               Project:  ChimeraX      |
    -----------------------------------+------------------------

    Comment (by Greg Couch):

     Lukas, it's his bug so to speak.

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3011#comment:9>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:11 by Greg Couch, 5 years ago

Thank you LUkas for the update.

I have a related question. What's your opinion of ChimeraX not fixing common mistakes mmCIF files by default? Should it normally be more forgiving? I do want the "PDB" to able to open a submitted mmCIF file and see the mistakes. But that could a special mode, or being more forgiving could be the special mode.

in reply to:  12 ; comment:12 by lpravda@…, 5 years ago 

Hi Greg,

I suppose this is rather a philosophical question. That really depends on who your users are and what the source of the data is. I believe that if the data comes from wwPDB site, you should not experience issues at all (or at least not many). However, when it comes to 3rd party software the situation can be very different. I can imagine all sorts of combination of issues, id duplications, missing fields etc. As far as I can tell wwpdb works closely  with phenix and ccp4 people to get the output of the structure refinement software into the best shape possible, so that we can extract most of the metadata during the annotation process. To make my point data coming from those two resources should be safe to use from syntactical point of view. Semantically there can be all sort of funny content as you all know. Finally, there are all those structure converted from one format to another by different tools or in-house scripts (modelling software from my past experience used to be the worst.), that's a whole different story.

During my phd I spent a couple of weeks in Janet Thornton's lab implementing ligand validation pipeline we developed during my phd into the pdbsum database. The most of the time, I spent not on the actual ligand validation, but on fixing all sorts of possible errors of the pdb files people were uploading, just to get it working with the software. It was a nightmare and definitely not worth it.

So all in all, the question narrows down to who the primary users of ChimeraX are. You may find out that implementing these extra filters and checks, are not worth the effort. You may also find out a few problematic cases worth fixing and then just report the rest. Perhaps even talking to certain method developers to improve their mmcif export would be worth trying (I know, I'm bit unrealistic in here). 

What do you think?

Lukas



On 19/05/2020, 03:09, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #3011: Disconnected hydrogens in 6rhz
    -----------------------------------+------------------------
              Reporter:  lpravda@…     |      Owner:  Greg Couch
                  Type:  defect        |     Status:  feedback
              Priority:  normal        |  Milestone:
             Component:  Input/Output  |    Version:
            Resolution:                |   Keywords:
            Blocked By:                |   Blocking:
    Notify when closed:                |   Platform:  all
               Project:  ChimeraX      |
    -----------------------------------+------------------------

    Comment (by Greg Couch):

     Thank you LUkas for the update.

     I have a related question.  What's your opinion of ChimeraX not fixing
     common mistakes mmCIF files by default?  Should it normally be more
     forgiving?  I do want the "PDB" to able to open a submitted mmCIF file and
     see the mistakes.  But that could a special mode, or being more forgiving
     could be the special mode.

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3011#comment:11>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:13 by Greg Couch, 4 years ago

Hi Lukus, it has been almost 2 years and the bug with disconnected hydrogens in 6rhz hasn't been fixed by the annotation team. Should I report this separately to info@…?

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