On Dec 7, 2004, at 4:17 PM, Virginie Lafont wrote:
I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks
Virginie
Hello Virginie, It is possible, with a few steps. As you already noticed, if you just use "addh" the aspartic and glutamic acid carboxylate groups will not get protonated. In the definitions of these residues, the carboxylate oxygen atoms are type O2-, which would not get protonated. You can use Define Attribute to change the types of these atoms. First you need to know the residue number of the aspartic acid you want to protonate and which of the oxygens (OD1 or OD2) you want to receive the proton. Next, create a define attribute input file in which you specify these two atoms and change type of the oxygen you want protonated to O3 and the one you don't want protonated to type O2 (example attached). There is a file description and more examples in the manual page for Define Attribute, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html In Chimera: open your PDB file of interest run addh (note the aspartic acid is not protonated in this step) Tools... Utilities... Define Attribute (open the previously prepared input file) now run addh again (note the aspartic acid will be protonated) The proton may not be pointing the direction you want, so you will probably then want to rotate the OH to the proper position, as described in http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/ structuremeas.html#adjust My define attribute example file (attached) works with the PDB file 1zik. The define attribute file tells Chimera to change the atom types of Asp residue number 7 in chain B so that the side chain will be neutralized when AddH is run. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco