Insight

What Insight reads from your XML

Insight expects an XML file in the same format PubChem provides. Your XML must have:

PC-Atoms_element — atomic number (e.g. 6 for carbon)
PC-Conformer_x — x coordinates (Å)
PC-Conformer_y — y coordinates (Å)
PC-Conformer_z — z coordinates (Å)

If any of these tags are missing, the upload will fail.

Structure requirements

Use atomic numbers (not element symbols). Example: O = 8, H = 1, C = 6.
Coordinates should be in Angstrom. Insight converts Å → Bohr internally.
All four tag lists should have the same length (one entry per atom).
Tag order should correspond by index: the i-th PC-Element matches the i-th x/y/z.

Example XML

Acetone:


          <PC-Compounds>
            <PC-Atoms_element>
              <PC-Element>8</PC-Element>
              <PC-Element>6</PC-Element>
              <PC-Element>6</PC-Element>
              <PC-Element>6</PC-Element>
              <PC-Element>1</PC-Element>
              <PC-Element>1</PC-Element>
              <PC-Element>1</PC-Element>
              <PC-Element>1</PC-Element>
              <PC-Element>1</PC-Element>
              <PC-Element>1</PC-Element>
            </PC-Atoms_element>

            <PC-Conformer_x>
              <PC-Conformer_x_E>0.0003</PC-Conformer_x_E>
              <PC-Conformer_x_E>0</PC-Conformer_x_E>
              <PC-Conformer_x_E>1.281</PC-Conformer_x_E>
              <PC-Conformer_x_E>-1.2813</PC-Conformer_x_E>
              <PC-Conformer_x_E>1.3279</PC-Conformer_x_E>
              <PC-Conformer_x_E>1.326</PC-Conformer_x_E>
              <PC-Conformer_x_E>2.1351</PC-Conformer_x_E>
              <PC-Conformer_x_E>-2.1352</PC-Conformer_x_E>
              <PC-Conformer_x_E>-1.3284</PC-Conformer_x_E>
              <PC-Conformer_x_E>-1.3266</PC-Conformer_x_E>
            </PC-Conformer_x>

            <PC-Conformer_y>
              <PC-Conformer_y_E>-1.3171</PC-Conformer_y_E>
              <PC-Conformer_y_E>-0.0872</PC-Conformer_y_E>
              <PC-Conformer_y_E>0.7024</PC-Conformer_y_E>
              <PC-Conformer_y_E>0.7019</PC-Conformer_y_E>
              <PC-Conformer_y_E>1.3235</PC-Conformer_y_E>
              <PC-Conformer_y_E>1.3282</PC-Conformer_y_E>
              <PC-Conformer_y_E>0.0196</PC-Conformer_y_E>
              <PC-Conformer_y_E>0.0187</PC-Conformer_y_E>
              <PC-Conformer_y_E>1.323</PC-Conformer_y_E>
              <PC-Conformer_y_E>1.3278</PC-Conformer_y_E>
            </PC-Conformer_y>

            <PC-Conformer_z>
              <PC-Conformer_z_E>-0.0002</PC-Conformer_z_E>
              <PC-Conformer_z_E>0.0006</PC-Conformer_z_E>
              <PC-Conformer_z_E>-0.0002</PC-Conformer_z_E>
              <PC-Conformer_z_E>-0.0002</PC-Conformer_z_E>
              <PC-Conformer_z_E>-0.898</PC-Conformer_z_E>
              <PC-Conformer_z_E>0.8945</PC-Conformer_z_E>
              <PC-Conformer_z_E>0.0027</PC-Conformer_z_E>
              <PC-Conformer_z_E>0.0027</PC-Conformer_z_E>
              <PC-Conformer_z_E>-0.898</PC-Conformer_z_E>
              <PC-Conformer_z_E>0.8945</PC-Conformer_z_E>
            </PC-Conformer_z>
          </PC-Compounds>

Note: These 4 required blocks don't have to be direct children of the root.

How to submit

Drag-and-drop a .xml file anywhere on the page. After it is detected, the Submit Job modal will show filename and atom count. You can also drop a local md_frames.json file to open MD playback without submitting a job.

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