[Chimera-users] Chimera pH

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 3 17:01:57 PDT 2009

Hi Peter,
Chimera does not have any options to generate protonation states at  
different pHs.  It just aims for a state that is reasonable for  
physiological pH (i.e. near 7).

However, it sounds like you already have the desired protonation  
states in PQR format.  Unfortunately Chimera doesn't read PQR format  
(although we would like to have that capability in the future) -- the  
last two columns, charge and radius, are wider than the occupancy and  
bfactor columns of standard PDB format.

One possibility is to simply edit the PQR files to remove the last two  
columns, then read these now-acceptable PDB files into Chimera.  That  
retains the hydrogens as output from PDB2PQR.  I'm not sure what you  
mean by models... do you also need point charges?  A disadvantage of  
column removal is that the PDB2PQR charges will be lost.  However, you  
could use Add Charge in Chimera (or the addcharge command) to assign  
charges, and there are several AMBER options.  Because the hydrogens  
are already present, less common protonation states such as neutral  
Lys, Asp, Glu will be recognized correctly and assigned the  
appropriate charges.  Whether this approach is sufficient depends on  
whether you wanted to use the specific charge set from PDB2PQR as  
opposed to an AMBER charge set.

If you did want the exact charges from PDB2PQR, you could reformat  
those charges (next-to-last column in the original PQR file) into an  
attribute assignment file and reassign them with Define Attribute (or  
command defattr), after reading in the edited PDB files (PQR files  
with last 2 columns removed).
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 3, 2009, at 4:29 PM, Peter Baker wrote:

> I am trying to generate models of my protein at different pH. Any  
> suggestions as to run how to accomplish this? I do have PBD2PQR  
> files for the different pH but I am not sure how to apply them.
> Thanks
> -pjb

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