[Chimera-users] Re: PDB file breaking down

Hello, I believe this is caused by limitations of the fchk format, namely that it loses some information that is in the original PDB file. It only keeps the atomic coordinates and the element information, and loses the original atom names, residue names, and chain IDs. Chimera cannot tell from reading an fchk file if it is a biopolymer like a peptide or a nucleic acid that could be shown with ribbons. If you need to put the structure through Gaussian, requiring going through the fchk format, I don't think there is any way to avoid this loss of information. I hope this clarifies the situation, 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 Jan 30, 2024, at 10:45 AM, NCdt In Gue Chang via Chimera-users wrote:

Good Afternoon,

I'm currently a master's student using chimera but I have a problem and I was wondering if you guys have a solution for it. When the original PDB file is loaded onto chimera, I can see different alpha and beta chains however, when I run optimization using gaussian program and load the fchk file or pdb file converted from chk file, the chains are gone and I'm left with just atoms. When I convert the chk file to pdb file in gaussian, it does the same and I was wondering if you guys know a solution or tips to bypass this. If you could help me out, it would be great!

Thank you

ASLt / Ens 2 In Gue Chang