[Chimera-users] Changing charge of protein

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 22 09:08:50 PDT 2011

Dear Monisha,
The charge of the protein is the sum of the charges of its residues, but charges are not saved in PDB format.

Maybe you mean you want to control the protonation state and thus the formal charges of certain residues (for example, specifying which histidines should be positive and which should be neutral)?  That can be done when you are adding hydrogens.  In the AddH tool (under Tools... Structure Editing) there is "Protonation states for" setting for controlling protonation states of histidine, glutamic acid, aspartic acid, lysine, and cysteine residues.  You would have to decide yourself which residues should be in which states.  You could indicate that by editing the input PDB file to contain special residue names, or just choose "specified individually" for it to go through and ask you about each one.  Details:

Then, you could save the PDB file including the hydrogens using "File... Save PDB" in the Chimera menu.

Charges are a somewhat separate matter, and are not saved in PDB files.  There would not be any charge assignments until after you used Add Charge (under Tools... Structure Editing).  Then, you could see the atom and residue charges in histograms in Render by Attribute, or save them to a file using that tool.  If you really meant you wanted to assign specific charges to specific atoms yourself, you could do that with Define Attribute or the command setattr.  You can label atoms with their charges as described here
but we don't have that for whole residues.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 22, 2011, at 5:20 AM, Monisha Hajra wrote:

> Dear User,
> Is there any way to increase or decrease total charge of the protein in Chimera? Can I see the residue wise (not atom wise) charge and modify, and should be able to save the modified protein in pdb.  Trying to look to add charge / "render by attribute" section, but didn't get much help.
> Any help will really be appreciated.
> Regards
> Monisha 

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