Hi Mikkel
In the actual PDB standard, the “C” column in “DOPCA” is supposed to be blank, separating the limited-to-3-character residue name from the limited-to-1-character chain ID.  These limits are obviously constraining so many non-standard PDB files conscript that blank column for either a 4-character residue name or a 2-character chain ID and ChimeraX has to guess which one it is.  The criteria ChimeraX has been using is that if that character is the same for all residues of a chain, then it’s part of a 2-character chain ID, otherwise it’s part of a 4-character residue name, which is why for your file the residue name winds up being “DOP” with a chain ID of “CA”.
I have now tweaked that criteria so that if there is exactly one residue in a chain it instead assumes a 4-character residue name instead of a 2-character chain ID, which gets things working for the file you provided.  That change will be in the daily build (not the 1.8 release candidate) starting tomorrow.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Jun 6, 2024, at 6:14 AM, Mikkel Dahl Andreasen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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

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