VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jan 22 2015 - 03:34:26 CST

Young,

 

you can use the name of the atoms or for ions even the resname. You will
find the correct names in your pdb file. If the names contain + or - signs,
you need to escape these characters in your selection, example: resname
"Na\+". You are right in assuming VMD uses the 1st letter of atom names to
guess their element, how else should it do this? The sodium keyword is just
a macro made for the psf world naming convention. You can define your own
macro for your FF similar to:

 

atomselect macro myions { resname "Na\+ Cl\-" }

 

Afterwards you can simply use "myions" in your selections.

 

Norman Geist.

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
JhonY. I.
Gesendet: Donnerstag, 22. Januar 2015 04:48
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: ion visualization in VMD

 

Hi,
 
I'd like to visualize sodium and chlorine ions in VMD using pdb file.
I used atom name of Na or sodium for sodium ion but It is visualized as if
it is nitrogen or sulfur atom.
It appears that VMD detects the first letter of atom name only.
How can I solve this problem?
 
Thank you very much for your helps in advance.
 
Best
Young