Calculation of Collision Cross Section (CCS)

General Discussion
1

Dear experts, may I ask you couple of questions, dedicated to calculation of Collision Cross Section (CCS)?

I downloaded and installed Avogadro 2.0.0.
What is a workflow, how to calculate Collision Cross Section (CCS)? I did not find an Extension dedicated to this type of calculation. Maybe you can suggest some tutorial or a video.

I have options to save my results as .cjson and .cml file. How can I save my molecule in PDB file?

Best regards,

Aleks

2

At the moment, we don’t have code to do that explicitly. I think you want to look into work by the Merz group at Michigan State, e.g.

“Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input”
J. Chem. Inf. Model. 2023, 63, 16, 4995–5000
doi: 10.1021/acs.jcim.3c00890

Their code is open source, although I don’t know if it’s directly maintained. I’d suggest sending a message to Prof. Merz.

In principle, it wouldn’t be too hard to make something like this into an Avogadro plugin, but you’d need good conformers first. (Prof. Merz and I have discussed this a bit at ACS meetings.)

3

Looks like they have a follow-up:

“PEAS: An Application for Autonomous Precision Conformation Sampling”
J. Chem. Inf. Model. 2025, 65, 22, 12161–12167

doi: 10.1021/acs.jcim.5c02104

4

Dear Ghutchis,

Thank you for the fast reply.

I have found a way how to create a pdb. file via Export function, but my software for CCS calculation does not see a structure in created pdb. file.

I am doing like this:

  1. Open or Build your molecule in Avogadro.

  2. Optimize the geometry if necessary to ensure accurate coordinates (e.g., using Extensions > Optimize Geometry).

  3. Navigate to the File menu.

  4. Select Export > Molecule….

  5. In the save dialog box, choose the location and name your file.

  6. Change the Save as type (format) dropdown to PDB (*.pdb).

  7. Click Save

Is the workflow correct?

Thank you in advance,

Aleks.

5

I think you’d need to explain what software you’re using for CCS. For example, does it expect an “official” PDB for a biomolecule? etc.

What you don’t indicate in your workflow is anything about conformer sampling. In a CCS calculation, you ideally want the Boltzmann-averaged ensemble of conformers. Failing that, you’d want to make sure you at least have the lowest energy conformer.

There are some conformer search tools in Avogadro (using Open Babel) or you can use a general conformer search with a program like XTB / CREST.

But your main question is that the software doesn’t recognize the PDB file. For that, we’d need to know the program in question. Avogadro works hard to stick to the PDB specification, but not all programs do.

6

Hi Ghutchis,

We are working with .pdb files with CCSCalc software, which is part of DriftScope3.0 package from Waters.

We have Q-TOF HRMS with Ion Mobility section, and for work we need in-silico values of our objects. We are working with small molecules (up to 4 kDa)

Waters is providing software, however we need a .pdb file.

As for now, after drawing and uploading /pdb files, CCSCalc is calculating everything as 1 sq A, and pointed that 0 structures were found in the file.

Maybe you know any other software for .pdb that we can test.

Best wishes,
Aleks.

13 May 2026 16:12, Geoff Hutchison <[email protected]>:

7

You should obviously ask Waters - I don’t know that software. In general, I’ve seen lots of programs that “read PDB” but the PDB format has a wide variety of variants, and it’s always unclear what they take. For example, they may assume you’re using protein files and expect certain headers.

As I indicated above, the Merz group has open source software for calculating CCS (e.g., the PEAS app).

8

Thank you, Geoff,

I will ask Waters.

Best regards,
Nice weekend, Aleks.

пт, 15 мая 2026 г. в 14:35, Geoff Hutchison <[email protected]>: