VMD-L Mailing List

From: Sung M Hong (hong109_at_purdue.edu)
Date: Fri Oct 25 2013 - 19:17:49 CDT

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