Bad mmCIF → CRYST1 translation

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6rc202304072249 (2023-04-07 22:49:08 UTC)
Description
Really appreciate the new translation of CRYST1-related metadata from mmCIF to PDB, but something isn't quite right - for 8g99 it adds an errant "?" to the end of the line. Doesn't stop the resulting PDB file from opening in ChimeraX (but it does give a warning - see the log), but Phenix for example balks and refuses to go forward until it's fixed or the line is removed entirely.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.6rc202304072249 (2023-04-07)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8g99

8g99 title:  
Partial auto-inhibitory complex of Xenopus laevis DNA polymerase alpha-primase
[more info...]  
  
Chain information for 8g99 #1  
---  
Chain | Description | UniProt  
A | DNA polymerase alpha catalytic subunit | DPOLA_XENLA 335-1458  
B | DNA polymerase alpha subunit B | Q6DCZ1_XENLA 1-598  
C | DNA primase large subunit | A0A1L8G3G3_XENLA 1-513  
  
Non-standard residues in 8g99 #1  
---  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> save 8g99.pdb #1

> open 8g99.pdb

Summary of feedback from opening 8g99.pdb  
---  
warning | Ignored bad PDB record found on line 324  
CRYST1 1.00 1.00 1.00 90.00 90.00 90.00 P 1 ?  
  
Chain information for 8g99.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> ui tool show Shell




OpenGL version: 3.3.0 NVIDIA 528.24
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

Installed Packages:
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    ChimeraX-gltf: 1.0
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[Eric Pettersen]

Apparently the Z_PDB field of the cell table for this entry was '?'. Now outputs a blank instead.

[Tristan Croll]

I did another reply to this ticket by email yesterday, but something's gone wrong - got an email bounce today with the message:

The response from the remote server was:
451 4.3.2 Please try again later

Anyway, here's what I wanted to say:

Seems the spacing of entries in the CRYST1 line is off as well (quite a few packages - including the Clipper plugin - get really finicky about this, so it's important to get right). Format specification is at ​https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1.

As output from ChimeraX:
CRYST1 1.00 1.00 1.00 90.00 90.00 90.00 P 1 ?
As found in the official 8g99 PDB file:
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1

[Tristan Croll]

Seems the spacing of entries in the CRYST1 line is off as well (quite a few
packages - including the Clipper plugin - get really finicky about this, so
it's important to get right). Format specification is at
https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1
.

As output from ChimeraX:
CRYST1     1.00     1.00     1.00  90.00  90.00  90.00         P 1   ?
As found in the official 8g99 PDB file:
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1


On Fri, Apr 14, 2023 at 12:51 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Eric Pettersen]

Not sure what I was thinking, but I had the printf format for the space group as "%12s" (right justified in 12 columns) rather than " %-11s" (space, then left justified in 11 columns).

[Eric Pettersen]

Fixed, in case that wasn't obvious.