CIF vs. PDB deposition

[coutandin@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202101220441 (2021-01-22 04:41:35 UTC)
Description
I open a pdb and save it as cif. Validating both the pdb and the cif at
https://validate-rcsb-2.wwpdb.org/ gives no issues for the pdb file but several issues for the cif file (see below). 
I am providing the pdb file so you can reproduce the problem.
As the protein data bank prefers cif over pdb it would be great to have that problem solved.

The following planarity outliers were identified
Plane outliers
Model/Chain/Number/Residue
Region not planar
1/A/177/ARG
SIDE CHAIN

The following bond angles were found to be significantly different from the expected bond angle.
Bond angle outliers
Model/chain
Number/Residue/Atom
Number/Residue/Atom
Number/Residue/Atom
Expected bond angle (°)
Measured bond angle (°)
1/A
168/ARG/NE
168/ARG/CZ
168/ARG/NH1
120.3 ± 0.5
123.5
1/A
338/ARG/NE
338/ARG/CZ
338/ARG/NH1
120.3 ± 0.5
124.4
1/A
338/ARG/NE
338/ARG/CZ
338/ARG/NH2
120.3 ± 0.5
117.2
1/A
358/ARG/NE
358/ARG/CZ
358/ARG/NH1
120.3 ± 0.5
123.9
1/A
449/ARG/NE
449/ARG/CZ
449/ARG/NH1
120.3 ± 0.5
124.5
1/A
504/ARG/NE
504/ARG/CZ
504/ARG/NH1
120.3 ± 0.5
123.6
1/B
168/ARG/NE
168/ARG/CZ
168/ARG/NH1
120.3 ± 0.5
123.3
1/B
177/ARG/NE
177/ARG/CZ
177/ARG/NH2
120.3 ± 0.5
123.9
1/B
197/ARG/NE
197/ARG/CZ
197/ARG/NH1
120.3 ± 0.5
124.5
1/B
359/ARG/NE
359/ARG/CZ
359/ARG/NH1
120.3 ± 0.5
123.7
1/B
449/ARG/NE
449/ARG/CZ
449/ARG/NH1
120.3 ± 0.5
124.7
1/B
506/ARG/NE
506/ARG/CZ
506/ARG/NH1
120.3 ± 0.5
123.4
1/B
583/ARG/NE
583/ARG/CZ
583/ARG/NH1
120.3 ± 0.5
124.5
1/B
583/ARG/NE
583/ARG/CZ
583/ARG/NH2
120.3 ± 0.5
117.3
1/C
32/ARG/NE
32/ARG/CZ
32/ARG/NH1
120.3 ± 0.5
125.3
1/C
32/ARG/NE
32/ARG/CZ
32/ARG/NH2
120.3 ± 0.5
116.1
1/C
36/ARG/NE
36/ARG/CZ
36/ARG/NH1
120.3 ± 0.5
124.5
1/K
518/ARG/NE
518/ARG/CZ
518/ARG/NH1
120.3 ± 0.5
123.5

The following atoms were found to be less than 2.2 Å apart and are considered too close unless they are covalently bonded.
Clashes
Model/Chain/Number/Residue
Atom
Model/Chain/Number/Residue
Atom
Distance between the atoms
1/B/418/GLU
OE1
1/C/127/SER
HG
1.55
1/B/61/ASP
OD1
1/B/63/SER
HG
1.59
1/B/34/SER
HG
1/B/393/GLU
OE1
1.60



Log:
UCSF ChimeraX version: 1.2.dev202101220441 (2021-01-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/daniel/Box/emdb_pdb_deposition/fixed/2-C_LOBE-1_fixed2.pdb

Chain information for 2-C_LOBE-1_fixed2.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
K | No description available  
  

> save /Users/daniel/Box/emdb_pdb_deposition/fixed/2-C_LOBE-1_fixed2.cif

Not saving entity_poly_seq for non-authoritative sequences  




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File attachment: 2-C_LOBE-1_fixed2.pdb

2-C_LOBE-1_fixed2.pdb​

[coutandin@…]

Added by email2trac

[Greg Couch]

tl;dr -- mostly a PDB validator bug.

There are lots of issues here.

I hope you filed a bug with the PDB's validator. The mmCIF coordinates should be exactly the same as the PDB ones. So if the angles are bad in one, then they should be bad in the other.

ChimeraX's mmCIF output is not complete. For example, sheet information is lost because ChimeraX does not preserve that information from PDB files nor mmCIF files. The PDB comments are not translated. If you want to convert a PDB file into a mmCIF one, you should use the PDB's MAXIT software suite. Not sure how well it works for PDB files that aren't deposition ready.

And ideally your PDB file would have SEQRES records with the actual sequence. That is critical information needed to write mmCIF files so that different mmCIF readers will generate the same connectivity. This is what Phenix's mmtbx.prepare_pdb_deposition tool does. You can fake it by saving the mmCIF file with "save filename.cif bestGuess true". If there were no gaps in your chains and no sheets, then it would be okay. But you have both.