From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 11 2003 - 14:49:49 CDT

Hi,
  If you want to upgrade to VMD 1.8, the best plan would be to either
move, rename, or delete your existing VMD 1.7.x install. You do NOT
want to try and install VMD 1.8 on top of an existing VMD 1.7.x
directory, this will likely cause problems as some platforms won't
replace all of the files correctly. If in doubt, delete the old
version before installing the new one. :)

There isn't any way to make labels display with just single letter
codes at this time, we'll take this as a feature request and see
what we can do for future versions. We do plan to make some
improvements in the labelling area soon.

Regarding the sequence highlighting question, can you send me a
picture of what you mean by "yellow cover"? Are you talking about
the highlighted structure? (drawn as yellow colored 'bonds' rep..)

I don't know much about Rasmol's command language so I'm afraid
I can't be of much help here. VMD implements a tiny subset of
the rasmol atom selection commands as VMD atom selection macros.
Here's a brief listing of them taken from the VMD initialization
scripts:

### Rasmol keywords -- note they are all lowercase!
# rasmol sets (the ones that are built into VMD are marked *)
# AT Acidic Acyclic
# Aliphatic Alpha Amino
# Aromatic * Backbone Basic
# Bonded Buried CG
# Charged Cyclic Cystine
# * Helix Hetero Hydrogen
# Hydrophobic Ions Large
# Ligand Medium Neutral
# * Nucleic Polar * Protein
# Purine Pyrimidine Selected
# * Sheet * Sidechain Small
# Solvent Surface * Turn
# * Water

atomselect macro at "resname ADE A THY T"
atomselect macro acidic "resname ASP GLU"
atomselect macro cyclic "resname HIS PHE PRO TRP TYR"
atomselect macro acyclic "protein and not cyclic"
atomselect macro aliphatic "resname ALA GLY ILE LEU VAL"
atomselect macro alpha "protein and name CA"
atomselect macro amino "protein"
atomselect macro aromatic "resname HIS PHE TRP TYR"
atomselect macro basic "resname ARG HIS LYS"
atomselect macro bonded "numbonds > 0"
atomselect macro buried "resname ALA LEU VAL ILE PHE CYS MET TRP"
atomselect macro cg "resname CYT C GUA G"
atomselect macro charged "basic or acidic"
atomselect macro hetero "not (protein or nucleic)"
atomselect macro hydrophobic "resname ALA LEU VAL ILE PRO PHE MET TRP"
atomselect macro small "resname ALA GLY SER"
atomselect macro medium "resname VAL THR ASP ASN PRO CYS ASX PCA HYP"
atomselect macro large "protein and not (small or medium)"
atomselect macro neutral "resname VAL PHE GLN TYR HIS CYS MET TRP ASX GLX PCA HY
P"
atomselect macro polar "protein and not hydrophobic"
atomselect macro purine "resname ADE A GUA G"
atomselect macro pyrimidine "resname CYT C THY T URI U"
atomselect macro surface "protein and not buried"

### Rasmol sets which are not defined here:
#atomselect macro hydrogen "" ;# defined later
#atomselect macro ions "" ;# defined later
#atomselect macro ligand ""
#atomselect macro selected "" ;# cannot implemented (different philosophy)
#atomselect macro solvent "" ;# defined later

On Fri, Apr 11, 2003 at 10:37:51AM +0530, Y U Sasidhar wrote:
> 1. I already have vmd 1.72 on my RH Linux Intel PC. Now I want to
> install vmd 1.8. How do I un-install 1.72 ? Should I install 1.8 over
> existing version ?
>
> 2. I want to use rasmol syntax like:
>
> select sidechains and hydrophobic
> color red
>
> I understand I have to give a command like :
> Rasmol "color red"
> in graphics window. But vmd complains "no rasmol command "
> Pl let me know how I can issue rasmol commands.
>
> 3. I want to display labels using single letter code. There does not
> seem to be any menu option for this. How do I do this ?
>
> 4. Whenever I display sequence window and later pick an atom to display
> label, it also shows an "yellow cover". How do I disable this effect.
> best regards,
>
> --
> Sasidhar
>
>

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078