On Dec 8, 2004, at 10:13 AM, Elaine Meng wrote:

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)

Wanted to add one little addendum. In the current version of Chimera (1.2056), the first "addh" (before the Define Attribute) is actually necessary -- it is necessary to force Chimera to compute the atom types before overriding them with your own. This will be corrected in the upcoming production release in mid/late December. There are other ways to force the computation besides addh; finding h-bonds or going into ball-and-stick mode (the atom radius depends on the atom type) are a couple of other ways.

Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu

Hi David, There are several issues, so many that I must summarize up top so you don't get lost in the longer explanations below. Summary:

- file format is wrong - if you want carboxylate, the atom type is O2- not O2 - even changing atom type to O2- won't do what you want because those groups already have hydrogens. Just remove the hydrogens! Then you don't even have to change any atom types.

(A) How to assign attributes. The proximal answer to your question is that the format of your attribute assignment file is wrong. It is always better to look in the User's Guide (see the Help menu in Chimera, which includes a search option) than in the mail archives, because the archives can have outdated information, and because the mail list server can annoyingly mess up files with particular formats or @ symbols in them (bingo). Using the Help menu shows the documentation included with your download. The same documentation is also on our web site, and here's the page that describes the attribute assignment format: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ defineattrib/defineattrib.html#attrfile> There are also example files linked to that page.

Your file contains (mail list readers beware, the server will probably mess this up): # attribute: idatmType match mode: 1-to-1 :ADA 4 @ om O2 :ADA 5 @ om O2 :ADA 6 @ om O2 :ADA 7 @ om O2 :ADA 8 @ om O2 :ADA 9 @ om O2 :ADA 10 @ om O2

The atom specifications in the first tab column of the assignment lines are wrong; they should be the same syntax that would work in the command line, for example ":4@om". You can always test beforehand whether some specification gets what you want by using it in the command line, for example using the command:

select :4@om

Command-line specification is documented here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html>

Actually, to assign a single value nowadays, you would just use the setattr command, for example:

setattr a idatmType O2 :4-10@om

(making sure to type capital O and not zero 0 in the atom type)

(B) Making the groups negatively charged carboxylates. Your subject line is "add h" but your message talks about adding charge, and your assignment file attempts to assign idatmType ... confusing. I guess you are ultimately assigning charge with Add Charge but wanted to set atom types to get a certain protonation state. However, those atoms already all have the atom type O2. Type O2 is neutral carbonyl. Carboxylate oxygen is O2- as shown in this page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html

I can tell the atom types by selecting the atoms and labeling them by atom type, for example with the commands: select :4-10@om labelopt info idatmType label sel

(the same stuff could be done with the menu but it would take longer to explain)

If you mean you want all the groups at atoms named C6 to be negatively charged carboxylates, you only need to remove the hydrogens that are already on them. You don't even have to change any atom types. E.g. commands:

delete element.H addh addcharge all method gas

(again these could be done with menus/GUIS). My example commands use the Gasteiger charge method; I couldn't get the other method to work on this structure, and we may look into that further, but hopefully Gasteiger charges will suffice.

(D) If some other researchers have already figured out good partial charges for these residues, you could just put them in an attribute assignment file and assign the attribute named charge directly instead of using the Add Charge tool or command addcharge.

(E) residues 1-3 in the structure strangely include some extra hydrogens not connected to anything... yet another reason to just delete the original hydrogens, as in (C).

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

P.S. in general user questions are more appropriate for chimera- users@cgl.ucsf.edu than for chimera-dev (programmer issues), but I see the archive mail you were looking at was sent to chimera-dev for some reason

On Apr 30, 2009, at 11:18 PM, Davide Mercadante wrote:

Hi Elaine,

I am a PhD student studying interactions between carbohydrates and proteins and I am trying to add charges to a molecule that I have to use for a simulation. I have followed the guidelines that you give in:

http://www.cgl.ucsf.edu/pipermail/chimera-dev/2004/000312.html

But doesn't work as I want...

My molecule is not a protein in this case but an oligosaccharide of ten residues long. I have written the pdb file using the server sweet II and now I am trying to add charges on the carboxylate groups present in the structures. I attach the pdb file and the attribute file that I have created in this mail.

The atoms where I would like to add the charges are the OM atoms specified in the pdb file for each ADA residue. However, when I try to give the attribute to the atoms chimera replies:

"Data line 1 or file either not selector/value or not tab-delimited"

Please, can you help me to solve this problem and tell me what I wrong?

Thanks in advance for your help.

Cheers, Davide

Davide Mercadante Ph.D. Department of Chemistry The University of Auckland, Auckland New Zealand<10mer30%Me_B.pdb><attribute10mer30% Me_B>_______________________________________________