Hello

I have a question regarding ChimeraX renaming residues upon loading pdb files. I am specifically referring to a pdb file containing the following lines:

TITLE PLACEHOLDER_TITLE

REMARK PLACEHOLDER_REMARK

CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 1

MODEL 1

ATOM 1 NC3 DOPCA 1 93.725 50.146 69.265 1.00 0.00

ATOM 2 PO4 DOPCA 1 93.471 50.284 66.361 1.00 0.00

ATOM 3 GL1 DOPCA 1 93.591 50.038 63.469 1.00 0.00

ATOM 4 GL2 DOPCA 1 94.818 50.396 63.498 1.00 0.00

ATOM 5 C1A DOPCA 1 93.669 50.374 60.367 1.00 0.00

ATOM 6 D2A DOPCA 1 93.738 49.939 57.365 1.00 0.00

ATOM 7 C3A DOPCA 1 93.390 49.936 54.359 1.00 0.00

ATOM 8 C4A DOPCA 1 93.358 50.194 51.480 1.00 0.00

ATOM 9 C1B DOPCA 1 96.261 50.393 60.395 1.00 0.00

ATOM 10 D2B DOPCA 1 96.060 50.114 57.261 1.00 0.00

ATOM 11 C3B DOPCA 1 96.224 50.032 54.669 1.00 0.00

ATOM 12 C4B DOPCA 1 95.844 50.135 51.528 1.00 0.00

TER

END

When I load this file into ChimeraX using "open file.pdb" it renames the residue name "DOPC" to "DOP". A table appears in the Log regarding "Non-standard residues in file.pdb" wherein it lists "DOP - (DOP)" without mentioning "DOPC". However, when I open another file which contains many different types of molecules, then it does not rename "DOPC" to "DOP", even though the "Non-standard residues in file.pdb" table also appears, though this time with an entry containing "DOPC - (DOPC)".

I have also previously experienced that ChimeraX renames some (not all) of my cholesterol molecules to "CHO" (instead of using the actual residue name which is "CHOL").

I had a look through the documentation for the "open" command, but I couldn't find anything useful about it.

I was wondering why this is happening and if there is a way to prevent it. And just so i am clear, by prevent I don't mean revert (e.g. rename them back to "DOPC" after loading), but actually preventing the initial renaming done by ChimeraX.

Kind regards, Mikkel Dahl Andreasen