<p>The covalent linkages specified in the <code>LINK</code> record in a PDB file should be converted to rows in the mmCIF table <code>struct_conn</code>. If you don't see the linkages when using an mmCIF file, either they were not converted correctly, the visualization program ignores them when reading the mmCIF file, or there is a more subtle problem (one program wrote them in a way that's not understood by the other program). I can't tell what's the exact cause without inspecting the files and testing the programs.</p>
<p>In general, the mmCIF format is more prone to such problems than the PDB format because it's more flexible, more complex and less widely used (and therefore less tested).</p>
<p>(I wrote this as a comment, but I see that mods deleted that comment, so now I expanded it into answer.)</p>

CC BY-SA 4.0
2024-07-24T20:09:48.250Z
2024-07-24T20:09:48.250Z
marcin
<p>I am trying to convert a pdb file to mmcif file format. But the covalent linkages between the ligands are getting broken when I save it in mmcif format. Happens both in Chimerax and pdb_extract.  Any suggestion on how to get around this.</p>

CC BY-SA 4.0
2024-07-23T01:57:00.160Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2024-07-23T07:36:29.150Z
@marcin I created an input linking two ligands in pymol (wrong geometry of course) and got no link like the question says. Both pymol and chimera show the actual link bond between the two ligands thought when loding pdb. Of course without the OP input ... who knows, maybe just a pdb of two linked HETATM ONE and HETATM TWO would suffice as test ?
pippo1980
CC BY-SA 4.0
2024-07-23T08:07:40.567Z
Please provide additional context for your question; this does not seem sufficient to get a useful answer. It would be great if you could also add links to the PDB information that this doesn't work for (or copy-paste into the question).
gringer
CC BY-SA 4.0
2024-07-23T08:28:51.747Z
https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/mmcif/mmcif_guidelines.html  read carefully the Reconstructing Connectivity part ... it could be old nevetheless is informative https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/mmcif/mmcif_guidelines.html#reconstructing-connectivity
pippo1980
<proteins><protein-structure><pdb><structural-biology><chimera>
Conversion of PDB to mmcif results in bond between the ligands getting broken
# Conversion of PDB to mmcif results in bond between the ligands getting broken

(Asked by: username_0 on 2024-07-22)

I am trying to convert a pdb file to mmcif file format. But the covalent linkages between the ligands are getting broken when I save it in mmcif format. Happens both in Chimerax and pdb\_extract. Any suggestion on how to get around this.

**Tags:** proteins, protein-structure, pdb, structural-biology, chimera
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: @marcin I created an input linking two ligands in pymol (wrong geometry of course) and got no link like the question says. Both pymol and chimera show the actual link bond between the two ligands thought when loding pdb. Of course without the OP input ... who knows, maybe just a pdb of two linked HETATM ONE and HETATM TWO would suffice as test ?  
> **username_3**: Please provide additional context for your question; this does not seem sufficient to get a useful answer. It would be great if you could also add links to the PDB information that this doesn't work for (or copy-paste into the question).  
> **username_2**: https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/mmcif/mmcif_guidelines.html  read carefully the Reconstructing Connectivity part ... it could be old nevetheless is informative https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/mmcif/mmcif_guidelines.html#reconstructing-connectivity  

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## 1 answers

### Answer by username_4 on 2024-07-24. Score: 1 | Accepted answer

The covalent linkages specified in the `LINK` record in a PDB file should be converted to rows in the mmCIF table `struct_conn`. If you don't see the linkages when using an mmCIF file, either they were not converted correctly, the visualization program ignores them when reading the mmCIF file, or there is a more subtle problem (one program wrote them in a way that's not understood by the other program). I can't tell what's the exact cause without inspecting the files and testing the programs.

In general, the mmCIF format is more prone to such problems than the PDB format because it's more flexible, more complex and less widely used (and therefore less tested).

(I wrote this as a comment, but I see that mods deleted that comment, so now I expanded it into answer.)


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