VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Aug 01 2020 - 12:04:20 CDT

On Jan 09 2018 11:25:28 CST John Stone wrote, inter alia, "if the PSF
doesn't explicitly include a disulfide bond, VMD will not display it,
end of story."

I have a protein with three disulfide bonds, correctly patched when
building psf/pdb with vmd in text mode. All three bonds can be identified
in the psf file, although they are not displayed by VMD in bond
representation. All that can be seen from the display is that the S-S
distance is 2.05A in all three cases.

I remember vaguely that I already had similar problems in the past, relying
on the identification of the S-S bonds from the psf file.

Is that anything I am missing when loading psf/pdb?

thanks
francesco pietra