VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 08 2007 - 18:34:34 CST

Hi Matt,
  Many of the modeling related tasks involving changing coordinates,
adding/deleting atoms, and so on are covered in the various NAMD tutorials
even though the majority of those operations are done within VMD.
This may be why you didn't see what you were looking for when reading the
tutorials previously. You can find all of the more modeling oriented
tutorial materials here, but I have suggestions below that may be more
directly relevant to your problems:
  http://www.ks.uiuc.edu/Training/Tutorials/

There are a few key details that may be causing your confusion:
  1) Moving molecules in the VMD view doesn't necessarily
     alter their coordinates. (e.g. rotating/translating/toggling
     "fixed" etc only affects the display and not the underlying atoms)

  2) If you do want to change the atom coordinates, you need to use
     the Mouse -> Move menus to do that.

  3) After you have made changes to atom coordinates, you must re-write
     your structure file. This is normally done using the
     File -> Save Coordinates menu. This menu is activated for use
     once you have selected a molecule in the molecule browser of the main
     VMD window. (e.g. a molecule line is highlighted yellow)
     The Load State and Save State menus DO NOT make any changes
     to your structure files, they only save the molecular graphics scene.
    
If you built the structure non-graphically using the various atom selection
commands, you can either save the new structure using the GUI, or you can
save it using commands like "$sel writepdb foo.pdb", for example.

I find it's often much easier to answer very specific questions than
very general ones, so it might be easier to work through the problems
you're having one step at a time rather than all at once. I'm happy to
help you out as best I can.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 08, 2007 at 02:09:52PM -0800, wolfinbm_at_uci.edu wrote:
> Hello
> I am having extreme difficulty doing what are seemingly the most basic
> things in VMD. For example, I have two PET molecules that I have moved to
> start the membrane. It seems that I should just be able to save the state
> and save all the work I have done. But this is not how it works. When I
> go to re-load, the coordinates are not saved (yes I sent a message to this
> effect before, but the only responses I got seemed extremely cryptic, much
> like everything else I try to do in VMD). I am not trying to be rude or
> insult the programmers of VMD (it seems like a very powerful program if
> one can get it to work!), but I really do need some help. I have have
> spent dozens (or maybe hundreds) of hours trying to do what are
> intuitively very simple things (i.e., making a polymer from a monomer, and
> saving multiple molecules) and gotten absolutely nowhere. I would just
> give up and say it's my stupidity, but I've had no problem with many other
> challenging endeavors (I managed an 800 [highest score] on the GRE math,
> 680 on the verbal, and 740 on the physics, and I am a senior physics
> major). Could someone please give me some pointers, outside of "read the
> tutorials?"
>
> Any help is sincerely and greatly appreciated.
> Thanks,
> Matt Wolfinbarger
> 

-- 
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