Hi Dmitry,

I had the same problem back in April, see this discussion: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/T3QYY2RX76VFJVXSU2MQI6ZKJ3GJUXQ7/

Here are some answers, from the simplest to the most complicated of your problems:

Standard amino acid residues are sometimes not fully built. For example, in some PDB entries you can find residues truncated to Ala in the coordinates, but with the original residue in the sequence. When this happens, it triggers the "unparameterized residue" warning. In my experience, this is always correctly fixed by clicking on this residue in the list you are presented with and then choosing "rebuild all to template" with the correct template for the standard residue.

Unparameterized ligands (for which you are offered no pre-existing template) are relatively easy to fix for purely organic compounds. I have had good results by using the parametrization tool in ISOLDE, doing it this way: make note of all the unparameterized ligands with their 3-letter code, then for each one:

- open a fresh ChimeraX session

- run: open <ligand 3-letter code> from ccd

- run: addh

- start ISOLDE

- load the model in ISOLDE, it will report that it doesn't have a template and offer to start the parametrization tool, accept

- the parametrization will take a certain amount of time depending on the number of atoms in the compound and the specifications of the computer you are using; be patient!

- once this is complete, I like testing that it worked by running a short simulation and tugging on the molecule (even without a map)

- make sure you save the resulting XML file

Next time you work on a model with this ligand, you need to load the XML file: in ISOLDE's "General" tab, open the "Residue parameterisation" section, click the button "Load residue parameters" and give it the XML file. You have to do this for each ligand present in the model that only has a template that you generated this way. You also need to do it every time you start a new ChimeraX/ISOLDE session.

For compounds with a metal ion, like chlorophylls, this is much less straightforward. Tristan had some recommendations, with varying degrees of "correctness". Turns out, if you are only concerned with being able to tug the molecule in ISOLDE, the quick and dirty way is sufficient.

Fetch the chlorophyll from the CCD like in the directions above, remove the magnesium ion and run the parametrization tool. Then add the magnesium ion back in manually, making sure the charges balance out to overall neutral for the whole molecule. I attached a file I made for CLA (manual edits are indicated by comments). Tristan shared a file for a bacteriochlorophyll (BCL) in the previous discussion, you might be able to download it from the list archive, but I also attached it here.

I hope this helps,

Good luck!

Guillaume