VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 25 2013 - 20:52:32 CDT

Hi,
  You might want to use the VMD "altloc" selection to control which
one of the conformations you're dealing with (PDB alternate location
identifier). If you look in the "Selections" tab of the graphical
representations window, and highlight the "altloc" keyword from the
list, it shows that this PDB entry has altloc identifiers A through F.
You can pick just the atoms that are in all conformations with the
selection macro 'conformationall', which picks atoms that have no
PDB altloc identifier tag. To view the atoms with altloc tag "A",
you can use the selection 'altloc "A"'. To view all atoms that
are involved in conformation "A", you can use the "conformationA"
macro that's defined by default for VMD. The selection text associated
with the "conformationA" macro is actually:
  altloc "" or altloc "A"

To get a better understanding about these altloc tags, you'll want
to read the documentation at the PDB web site.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 25, 2013 at 08:17:49PM -0400, Sung M Hong wrote:
> Hi,
>
> I have a question about the visualize PDB with VMD.
>
> When I visualized crystal structure of Bchl a protein, (PDB ID: 3ENI) I found two different geometries for (assumed to be) same atom.
>
> Here is quick snap shoot of the one of the section.
>
> http://s21.postimg.org/uaul55qkn/3eni_issue.jpg
>
> When I look inside of PDB, I found this,
>
> HETATM 5824 C1CABCL A 376 19.018 -5.914 0.007 0.47 18.97 C
> HETATM 5825 C1CBBCL A 376 19.012 -5.947 -0.051 0.53 19.35 C
> HETATM 5826 C2CABCL A 376 17.573 -5.878 0.399 0.47 18.47 C
> HETATM 5827 C2CBBCL A 376 17.560 -5.963 0.312 0.53 19.33 C
> HETATM 5828 C3CABCL A 376 17.411 -7.165 1.234 0.47 18.21 C
> HETATM 5829 C3CBBCL A 376 17.325 -7.471 0.523 0.53 19.80 C
>
> So, it seems like there is some duplicates, named A and B at (C1C BCL) section.
>
> Though, the problem that I am currently having is that there is another terms like C and D.
>
> HETATM 5846 CADCBCL A 376 23.074 -12.173 1.781 0.37 19.19 C
> HETATM 5847 CADDBCL A 376 23.115 -12.079 2.062 0.63 23.00 C
> HETATM 5848 OBDCBCL A 376 23.109 -13.418 1.905 0.37 19.25 O
> HETATM 5849 OBDDBCL A 376 23.204 -13.208 2.588 0.63 23.04 O
> HETATM 5850 CBDCBCL A 376 24.365 -11.349 1.488 0.37 18.27 C
> HETATM 5851 CBDDBCL A 376 24.344 -11.384 1.409 0.63 24.04 C
>
> I found out that A and B is not related (assumed) to C and D.
>
> May I have some help to fix this issue?
>
> Thank you,
> SungMin Hong 

-- 
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