VMD-L Mailing List

From: Ashma Khan (ashmakhan200_at_gmail.com)
Date: Thu Dec 10 2020 - 10:07:56 CST

thank you for your suggestion

On Thu, Dec 10, 2020 at 9:17 PM vermaasj <vermaasj_at_msu.edu> wrote:

> 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>
> 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> 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
> 

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