[Chimera-users] Using mol2 files

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 16 09:28:14 PDT 2007

Hi Pasquale,
You can definitely open multiple PDB files and move them  
independently.  By default everything will move together, which might  
even be what you want.  However, if you don't want them to move  
together, you can freeze any structure in place ("deactivate" it),  
move the other(s), and then "activate" the first structure again if  
you want it to be movable.

There are several ways to control activation/deactivation; probably  
the easiest is to open the Model Panel (Favorites... Model Panel).   
Then just uncheck/check the box in the Active column to freeze/ 
unfreeze a model.  We use the word model to mean the contents of a  
structure file (PDB, Mol2, etc.), so if you read in two separate PDB  
files, there would be two models listed in the Model Panel.   
Alternative ways of controlling activation/deactivation are with the  
little checkboxes under the Command Line and using the command "select".

You would still be able to minimize multiple models as a single  
system by choosing all of them in the "Minimize Structure" dialog.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 16, 2007, at 7:59 AM, Pasquale Iacono wrote:

> well in order to make the dimer i used two separate pdb files and  
> imported them both into the same gaussian gjf file. then i imported  
> that file as a mol2 file into chimera, so unless i can manipulate  
> separate pdb files in chimera then that would be great but i cannot  
> figure out how to move separate pieces of my dimer.
> On 7/15/07, Elaine Meng <meng at cgl.ucsf.edu> wrote: Hi Pasquale,
> I had one long-shot possibility for getting the correct atom and
> residue names - did you start with a PDB file before the guassian
> calculations?  If so, that file may have had the correct atom and
> residue names.  If that starting file had all the same atoms
> (including hydrogens) and the order of the atoms is exactly the same
> in that gaussian output, you could simply replace (probably with a
> script) the coordinates in each line of the starting PDB file with
> those from the gaussian output.  That would only work if the order is
> exactly the same, however.
> Otherwise it would be extremely tedious to figure out which
> coordinates go with which atom/res/number.
> Best,
> Elaine

More information about the Chimera-users mailing list