[Chimera-users] changing HIS to HIP

Francesco Pietra chiendarret at gmail.com
Wed Dec 15 22:45:57 PST 2010

I need to change several histidine residues (both HIS and HIE,
although both called HIS) to HIP. I tried manually. In case of
monoprotonation at NE2:

modify structure
element N
bonds 3
geom trigonal
connect to preex atoms
color by element
change modified residue's name to HIP
set atom names to ND1
retain current atom names

In both cases the proton attached to ND1 takes the name "H1" instead
of the expected HD1.

Is that error in the above procedure or chimera bug? (chimera alpha
version 1.5 (build 30702) on GNU/LINUX 32bit)

Addendum: is there any other method of accomplishing the task with
chimera? It is rather troublesome to go through all monoprotonated
histidines of this large homomer (in different chains HIS of the same
number have been differently protonated by reduce). A problem with
reduce (if not my misuse of reduce) is that all histidines become
monoprotonated, while the experimental pH is such that all should be
diprotonated. I must add that I  am bound to reduce because the
program that I use subsequently goes through reduce.

thanks for help
francesco pietra

More information about the Chimera-users mailing list