Dear Monisha, If you get a Chimera daily build (version 1.6, whereas you probably have 1.5), there will be AddH options for all those residue types I mentioned. The options in AddH are for the side chains. The N-terminus of the backbone will already get a +1 charge, and the C-terminus -1. If the backbone N is not the N-terminus, it is in an amide group and will not be formally charged. However... There is a limit as to what total charge is reasonable for a given protein sequence. If you just arbitrarily increase positive charges everywhere to try to reach some value (why??), it will become less representative of reality. Another approach you might consider if you are trying to make your "system" more neutral is to add counterions (see Tools... Structure Editing... Add Ions). I hope this helps, Elaine ----- 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 11:47 AM, Monisha Hajra wrote:
Dear Elaine,
Thank you for your reply.
However I find in AddH option, its only Histidine specific, what should I do if I want to alter specific protonation state of Lys, Arg.
Also, read from the link that you had send is that "lysine positive or neutral • charges for the neutral LYN residue are assigned if the atom named NZ has atom type N3 and thus two attached hydrogens rather than three" Is that mean that I can't create +2 charge for Lys, by adding another H to N (which is attached to alpha C)?
I tried even by command line " addh #0: 34@N", its showing error, though chain #0: 34@N is showing the N atom.
Kindly provide some solution. Right now charge of my protein is -22, I have to bring it up to +10. Really appreciate on general comment of yours on how do do that?
Regards Monisha
On Fri, Apr 22, 2011 at 9:38 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: 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: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>
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 <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html#chargelabels> but we don't have that for whole residues.
I hope this helps, Elaine ----- 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