# Calculation of Collision Cross Section (CCS) **URL:** \ **Category:** General Discussion\ **Created:** [May 12, 2026, 2:30pm UTC](https://discuss.avogadro.cc/t/calculation-of-collision-cross-section-ccs/7442 "2026-05-12T14:30:43Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Alex14](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/a/3ab097/32.png) [@Alex14](https://discuss.avogadro.cc/u/Alex14)\ **Post date:** [May 12, 2026, 2:30pm UTC](https://discuss.avogadro.cc/t/calculation-of-collision-cross-section-ccs/7442/1 "2026-05-12T14:30:43Z")
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 ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [May 12, 2026, 10:16pm UTC](https://discuss.avogadro.cc/t/calculation-of-collision-cross-section-ccs/7442/2 "2026-05-12T22:16:33Z")
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. > **[GitHub - DasSusanta/snakemake\_ccs](https://github.com/DasSusanta/snakemake_ccs)** > > Contribute to DasSusanta/snakemake\_ccs development by creating an account on GitHub. 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.) ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [May 12, 2026, 10:17pm UTC](https://discuss.avogadro.cc/t/calculation-of-collision-cross-section-ccs/7442/3 "2026-05-12T22:17:55Z")
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 > **[GitHub - mitkeng/peas: A user-friendly application for precise...](https://github.com/mitkeng/peas)** > > A user-friendly application for precise conformation sampling ---
**Author:** ![Alex14](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/a/3ab097/32.png) [@Alex14](https://discuss.avogadro.cc/u/Alex14)\ **Post date:** [May 13, 2026, 5:54am UTC](https://discuss.avogadro.cc/t/calculation-of-collision-cross-section-ccs/7442/4 "2026-05-13T05:54:12Z")
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. ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [May 13, 2026, 2:01pm UTC](https://discuss.avogadro.cc/t/calculation-of-collision-cross-section-ccs/7442/5 "2026-05-13T14:01:57Z")
> [@Alex14](#): > > 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 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. ---
**Author:** ![Alex14](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/a/3ab097/32.png) [@Alex14](https://discuss.avogadro.cc/u/Alex14)\ **Post date:** [May 14, 2026, 8:52am UTC](https://discuss.avogadro.cc/t/calculation-of-collision-cross-section-ccs/7442/6 "2026-05-14T08:52:38Z")
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 \<[noreply@mail.avogadro.cc](mailto:noreply@mail.avogadro.cc)\>: ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [May 15, 2026, 12:24pm UTC](https://discuss.avogadro.cc/t/calculation-of-collision-cross-section-ccs/7442/7 "2026-05-15T12:24:48Z")
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). ---
**Author:** ![Alex14](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/a/3ab097/32.png) [@Alex14](https://discuss.avogadro.cc/u/Alex14)\ **Post date:** [May 15, 2026, 5:17pm UTC](https://discuss.avogadro.cc/t/calculation-of-collision-cross-section-ccs/7442/8 "2026-05-15T17:17:07Z")
Thank you, Geoff, I will ask Waters. Best regards, Nice weekend, Aleks. пт, 15 мая 2026 г. в 14:35, Geoff Hutchison \<[noreply@mail.avogadro.cc](mailto:noreply@mail.avogadro.cc)\>: