[Chimera-users] patching ACE NME

[Eric Pettersen]

Hi Francesco,
	Well, another possibility is to open open PDB files with just ACE/NME and use the "Join Models" tab of Build Structure to connect them to the N/C terminus of your chain.  Select the N/C of your chain and the C/N of the ACE/NME and use the "Form C-N peptide bond" option of the Join Models tab and click Apply.  If the ACE/NME didn't have the right residue number you might then need to use the Renumber Residues tool to get the numbering you want.
	Also, unless you use the build that come out tomorrow you may get an error message as you select the N in NME.  It's a harmless error that you can ignore.
	I've attached PDB files of isolated ACE and NME residues for your convenience.

--Eric

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



On May 2, 2014, at 10:06 AM, Francesco Pietra <chiendarret at gmail.com> wrote:

> Sorry, I had overlooked the option of changing residue name. So, what only remains is whether there is a tool for quicker capping.
> thanks
> francesco pietra
> 
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret at gmail.com>
> Date: Fri, May 2, 2014 at 6:51 PM
> Subject: patching ACE NME
> To: chimera <chimera-users at cgl.ucsf.edu>
> 
> 
> Hello;
> In parameterizing a new metal cluster, I would like to patch the various amino acids (which stand isolated from one another) with what are called by AMBER ACE and NME. I would like to do that within the whole block, not for each amino acid isolated from the block. Also, I would like to avoid tleap, which gets into troubles here.
> 
> I could do that by modifying structure, but a problem arises of residue names, i.e, the original residue takes the name ACE or NME, or viceversa the capping groups take the name of the amino acid being capped.
> 
> Is there a specific tool with chimera?
> 
> thanks
> 
> francesco pietra



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