Answers.Body: <p>to me your 2 strings seem different, no N in first molecule.</p>
  <p>Here pictures, I used a PDB version of the original mmCIF file</p>
  <p>but dindt use the RCSB PDB available one, imported .cif into</p>
  <p>Biopython and parsed the resulting Struct object [so there could be
  mistakes].</p>
  <p>so chain N --&gt; A and chain U --&gt; E</p>
  <p><a href="https://i.sstatic.net/wVXug.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/wVXug.png" alt="enter image description here" /></a></p>
  <p><a href="https://i.sstatic.net/Q1FrI.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Q1FrI.png" alt="enter image description here" /></a></p>
  <p>as per in my comment:</p>
  <blockquote>
  <p>Mmmhhh be sure that each of the 3 modeled ligands correspond to the full one, could be that the density is poor and pdb shows only what is really ((??) there and not what they soaked the crystal with, actually 1N7 is CHAPSO I believe a detergent</p>
  </blockquote>
  <p>... I could be wrong though, this mmCIF format is driving me crazy</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-05T15:26:05.150Z
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Answers.UserDisplayName: pippo1980
Body: <p>I've just used <em>Open Babel</em> to convert <em>.sdf</em> and <em>.mol2</em> files to <em>SMARTS</em>, and I'm a bit surprised the output can be different for the same structure. It's confusing me that one structure, one piece of information can be different depending on the file format in which it was saved.</p>
  <p>I converted a ligand <em>1N7</em> in <a href="https://i.sstatic.net/16iaJ.png" rel="nofollow noreferrer">two available formats (<em>.sdf</em> and <em>.mol2</em>)</a>  of the <em>7RDX</em> structure from <em>RSCB PDB</em> for chain <em>N</em>, and also for chain <em>U</em>.
  After the conversion, the <em>SMARTS</em> strings for the ligand in both chains are not the same for both input files types (i.e. the difference between the same ligand, from the same chain, just in two different formats available to download from RSCB PDB):</p>
  <h1>example no. 1:</h1>
  <p>[additional <code>@H</code> added in places, some square brackets added]</p>
  <pre><code>$ cat ./7rdx_N_1N7_from_mol2.smi
  
  C1[C@@]2(C)[C@@H](C[C@@H](C1)O)[C][C]([C]1[C@H]3[C@]([C@H](C[C]21)O)([C@H](CC3)[C]([C])[C][C])C)O   1N7
  
  $ cat ./7rdx_N_1N7_from_sdf.smi
  
  C1[C@@]2(C)[C@@H](C[C@@H](C1)O)C[C@H]([C@H]1[C@H]3[C@]([C@H](C[C@H]21)O)([C@H](CC3)[C@H](C)CC)C)O   1N7
  
  </code></pre>
  <h1>example no. 2:</h1>
  <p>[some square brackets added]</p>
  <pre><code>$ cat ./7rdx_U_1N7_from_mol2.smi
  
  C1[C@@]2(C)[C@@H](C[C@@H](C1)O)C[C@H]([C@H]1[C@H]3[C@]([C@H](C[C@H]21)O)([C@H](CC3)[C@H](C)CCC(=O)NC[C][C][N+]([C])([C])[C])C)O 1N7
  
  $ cat ./7rdx_U_1N7_from_sdf.smi
  
  C1[C@@]2(C)[C@@H](C[C@@H](C1)O)C[C@H]([C@H]1[C@H]3[C@]([C@H](C[C@H]21)O)([C@H](CC3)[C@H](C)CCC(=O)NCCC[N+](C)(C)C)C)O   1N7
  
  </code></pre>
  <p>In both examples, the structures look quite similar to each other, but the difference is a little worrisome, because there is no chance to check every output by hand.</p>
  <p>Is it a normal behaviour during the conversion?<br />
  Is it related to a different notation in the input files?<br />
  Which input format is better?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-02T19:59:18.340Z
Comments.Text: Mmmhhh be sure that each of the 3 modeled ligands correspond to the full one, could be that the density is poor and pdb shows only what is really ((??) there and not what they soaked the crystal with, actually 1N7 is CHAPSO I believe a detergent
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-02T20:01:04.777Z
Comments.Text: Prior to grid freezing, 3-([3-cholamidopropyl]dimethylammonio)-2-hydroxy-1-propanesulfonate (CHAPSO, Anatrace) was added to the sample (8 mM final), resulting in a final complex concentration of 8 μM. The final buffer condition for the cryo-EM sample was 20 mM HEPES pH 8.0, 150 mM K-Acetate,10 mM MgCl2, 2 mM DTT, 1 mM ADP, 1 mM AlF3, 8 mM CHAPSO.
Comments.UserDisplayName: pippo1980
Tags: <pdb>
Title: Why are conversion output SMARTS strings are not the same for different file types of the same structure?
ThreadText: # Why are conversion output SMARTS strings are not the same for different file types of the same structure?
  
  (Asked by: username_0 on 2023-01-02)
  
  I've just used *Open Babel* to convert *.sdf* and *.mol2* files to *SMARTS*, and I'm a bit surprised the output can be different for the same structure. It's confusing me that one structure, one piece of information can be different depending on the file format in which it was saved.
  
  I converted a ligand *1N7* in [two available formats (*.sdf* and *.mol2*)](https://i.sstatic.net/16iaJ.png) of the *7RDX* structure from *RSCB PDB* for chain *N*, and also for chain *U*.
  After the conversion, the *SMARTS* strings for the ligand in both chains are not the same for both input files types (i.e. the difference between the same ligand, from the same chain, just in two different formats available to download from RSCB PDB):
  
  # example no. 1:
  
  [additional `@H` added in places, some square brackets added]
  
  ```
  $ cat ./7rdx_N_1N7_from_mol2.smi
  
  C1[C@@]2(C)[C@@H](C[C@@H](C1)O)[C][C]([C]1[C@H]3[C@]([C@H](C[C]21)O)([C@H](CC3)[C]([C])[C][C])C)O   1N7
  
  $ cat ./7rdx_N_1N7_from_sdf.smi
  
  C1[C@@]2(C)[C@@H](C[C@@H](C1)O)C[C@H]([C@H]1[C@H]3[C@]([C@H](C[C@H]21)O)([C@H](CC3)[C@H](C)CC)C)O   1N7
  
  ```
  
  # example no. 2:
  
  [some square brackets added]
  
  ```
  $ cat ./7rdx_U_1N7_from_mol2.smi
  
  C1[C@@]2(C)[C@@H](C[C@@H](C1)O)C[C@H]([C@H]1[C@H]3[C@]([C@H](C[C@H]21)O)([C@H](CC3)[C@H](C)CCC(=O)NC[C][C][N+]([C])([C])[C])C)O 1N7
  
  $ cat ./7rdx_U_1N7_from_sdf.smi
  
  C1[C@@]2(C)[C@@H](C[C@@H](C1)O)C[C@H]([C@H]1[C@H]3[C@]([C@H](C[C@H]21)O)([C@H](CC3)[C@H](C)CCC(=O)NCCC[N+](C)(C)C)C)O   1N7
  
  ```
  
  In both examples, the structures look quite similar to each other, but the difference is a little worrisome, because there is no chance to check every output by hand.
  
  Is it a normal behaviour during the conversion?  
  Is it related to a different notation in the input files?  
  Which input format is better?
  
  **Tags:** pdb
  
  > **Comments:**
  > **username_1**: Mmmhhh be sure that each of the 3 modeled ligands correspond to the full one, could be that the density is poor and pdb shows only what is really ((??) there and not what they soaked the crystal with, actually 1N7 is CHAPSO I believe a detergent  
  > **username_1**: Prior to grid freezing, 3-([3-cholamidopropyl]dimethylammonio)-2-hydroxy-1-propanesulfonate (CHAPSO, Anatrace) was added to the sample (8 mM final), resulting in a final complex concentration of 8 μM. The final buffer condition for the cryo-EM sample was 20 mM HEPES pH 8.0, 150 mM K-Acetate,10 mM MgCl2, 2 mM DTT, 1 mM ADP, 1 mM AlF3, 8 mM CHAPSO.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-01-05. Score: 1
  
  to me your 2 strings seem different, no N in first molecule.
  
  Here pictures, I used a PDB version of the original mmCIF file
  
  but dindt use the RCSB PDB available one, imported .cif into
  
  Biopython and parsed the resulting Struct object [so there could be
  mistakes].
  
  so chain N --> A and chain U --> E
  
  [![enter image description here](https://i.sstatic.net/wVXug.png)](https://i.sstatic.net/wVXug.png)
  
  [![enter image description here](https://i.sstatic.net/Q1FrI.png)](https://i.sstatic.net/Q1FrI.png)
  
  as per in my comment:
  
  > Mmmhhh be sure that each of the 3 modeled ligands correspond to the full one, could be that the density is poor and pdb shows only what is really ((??) there and not what they soaked the crystal with, actually 1N7 is CHAPSO I believe a detergent
  
  ... I could be wrong though, this mmCIF format is driving me crazy
  
  
  ---
  
  