Not a bug, that is the expected numbering in that situation. If you want to renumber the residues before saving the PDB file, you can do it with the ChimeraX tool Renumber Residues or the command "renumber," see: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/renumber.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/renumber.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 27, 2024, at 7:47 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
P.S. just one extra question:
I noticed a small bug in the order of amino acids added by the modeller in the case where they are added in the N-terminal positions. For example, if 10 amino acids are added in the first position, they will be numbered in the sequence like -10,-9 ... 0, and than 1,2,3 (for residues that were in the original pdb). Do we need to use a special save command for the generated model something like: save test.pdb #2.1 + some specific options ?
Many thanks in advance
Enrico