There are two alternate locations for the atoms in residue 45. If you open 6xg5 and use this command, it reports two atoms are selected:
select :45.a@ca
You can't see that there are two copies of the backbone atoms because they are almost exactly on top of each other, but you can see more clearly that the sidechain ring has two positions:
You can more clearly understand which atoms have alternate locations by looking in the text of the PDB file with text-editing program, or by using ChimeraX and its tools instead of Chimera, as mentioned earlier.
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 Apr 5, 2026, at 9:01 AM, SHUBHRAJYOTI PANDA via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Thanks a lot. The following code is working fine.
> distance :31.A@CA :45.A@CA.A i
>
> Thanks & Regards
> Shubhrajyoti Panda
> Phone: +91-7001855842
> Email: panda.jyoti.shubhra@gmail.com
> On Sun, 5 Apr 2026, 21:16 SHUBHRAJYOTI PANDA, <panda.jyoti.shubhra@gmail.com> wrote:
> Thank you for your response. But I have used one chain and when I am selecting 45 it shows only one atom. I do not find aby other atom.
>
> Thanks & Regards
> Shubhrajyoti Panda
> Phone: +91-7001855842
> Email: panda.jyoti.shubhra@gmail.com
> On Sun, 5 Apr 2026, 20:46 Elaine Meng, <meng@cgl.ucsf.edu> wrote:
>
> > On Apr 5, 2026, at 8:10 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
> >
> > Hello,
> > The most common reason for this type of confusion is that the PDB input file has "alternate locations" (more than one position) for at least one of those atoms.
> >
> > In this case, PDB 6xg5, residue 45 has two alternate locations, meaning two copies of each of its atoms. You need to decide which one to use and delete the other one. There is an option in Dock Prep to delete the lower-occupancy alternate location, as mentioned in this previous post:
> > <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2023-April/019110.html>
>
> Or instead of deleting one or the other, you can specify directly in the distance command which one you wanted, e.g.
>
> distance :31.A@CA :45.A@CA.A
>
> ... where the last .A says to use alternate location A
> >
> > (If you were using ChimeraX instead of Chimera, it automatically only uses one alternate location for a residue at a time, and you can easily see which residues have alternate locations using the ChimeraX Altloc Explorer tool and delete extra ones with the "altlocs clean" command)
> >
> > 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 Apr 5, 2026, at 7:34 AM, SHUBHRAJYOTI PANDA via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
> >>
> >> Dear,
> >> This is Shubhrajyoti Panda, research scholar at Birla Institute of Technology, Hyderabad. I am using 6XG5 PDB ID for my work. But in this particular protein I want to show the distance between particular residues. But when I am going to show manually or through command it is showing the following error.
> >> Distance between PHE 31.A CA and GLY 15.A CA: 15.891
> >> Distance between PHE 31.A CA and MET 16.A CA: 19.088
> >> Distance between PHE 31.A CA and ALA 19.A CA: 15.571
> >> Distance between PHE 31.A CA and ILE 14.A CA: 14.072
> >> Error while sourcing chimera_distances.cmd, line 14:
> >>
> >> "distance :31.A@CA :45.A@CA"
> >>
> >> Exactly two atoms/axes/planes must be selected. You selected 3.
> >>
> >> But in the protein structure there is only one 45th number residue. But I could not understand why it is showing selected 3 repeatedly. Kindly help me.
> >>
> >>
> >> Thanks & Regards
> >> Shubhrajyoti Panda
> >> Phone: +91-7001855842
> >> Email: panda.jyoti.shubhra@gmail.com
> >> _______________________________________________
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> >
> >
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