VMD-L Mailing List

From: vermaasj (vermaasj_at_msu.edu)
Date: Thu Dec 10 2020 - 09:47:00 CST

Probably. The PDB format has fixed widths, where the residue id can be no longer than 4 characters. You probably have more than 9999 residues, which means that VMD gets creative, and uses hexadecimal notation for the residue ID (0-f representing 0-16). This brings the total addressable space to 65535 residues. I typically only see this in solvent, where the residue numbers are pretty meaningless anyway.

-Josh

From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu>
Date: Wednesday, December 9, 2020 at 11:13 PM
To: Roshan Shrestha <roshanpra_at_gmail.com>
Cc: Vmd l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: confusing about the residue number
no these residue numbers are not present in the original pdb file but when we have loaded trajectory for making pdb for the selected atoms, these confusing residue numbers have been obtained.
should we ignore them?

On Thu, Dec 10, 2020 at 10:49 AM Roshan Shrestha <roshanpra_at_gmail.com<mailto:roshanpra_at_gmail.com>> wrote:
Dear Ashma,
                       Were these residue numbers already present in the original pdb file?

Best regards

On Thu, 10 Dec 2020, 10:45 Ashma Khan, <ashmakhan200_at_gmail.com<mailto:ashmakhan200_at_gmail.com>> wrote:
Dear all,
We are writing the name OW and within 5 of protein in selected atoms and save coordinates in the pdb format and in the pdb file, there are residue numbers 34f5, 370e, 38a7, 3aef , 2930, 2967. 2930 and 2967 are clear but 34f5, 370e, 38a7 are confusing.
Anybody can help me regarding this what are these confusing numbers and how to understand it 

--
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh
--
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh