Disulfide bond for minimization?
Dear all, I am trying to minimize a structure with a disulfide bond. My initial pdb has a CYM residue for amino acids involved in the bridge. Chimera correctly recognize the binding. But when entering the minimization run, chimera complains about the atoms of the cysteinate residues. Before sending you files I was just wondering if this is something that is not implemented in chimera or a problem on how I prepare my structure. Best regards, JD
Hi JD, Chimera 1.9 certainly minimizes disulfides okay if they're named CYS. Chimera 1.10 seems to have a bug in this regard. So try 1.9. If that doesn't work, rename your residues to 1.9 and try again (setattr r type CYS :CYM). --Eric On Nov 7, 2014, at 8:36 AM, Jean Didier Pie Marechal <JeanDidier.Marechal@uab.cat> wrote:
Dear all,
I am trying to minimize a structure with a disulfide bond. My initial pdb has a CYM residue for amino acids involved in the bridge. Chimera correctly recognize the binding. But when entering the minimization run, chimera complains about the atoms of the cysteinate residues. Before sending you files I was just wondering if this is something that is not implemented in chimera or a problem on how I prepare my structure.
Best regards, JD
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
…rename your residues to CYS… (doh!) On Nov 10, 2014, at 10:18 AM, Eric Pettersen <pett@cgl.ucsf.EDU> wrote:
Hi JD, Chimera 1.9 certainly minimizes disulfides okay if they're named CYS. Chimera 1.10 seems to have a bug in this regard. So try 1.9. If that doesn't work, rename your residues to 1.9 and try again (setattr r type CYS :CYM).
--Eric
On Nov 7, 2014, at 8:36 AM, Jean Didier Pie Marechal <JeanDidier.Marechal@uab.cat> wrote:
Dear all,
I am trying to minimize a structure with a disulfide bond. My initial pdb has a CYM residue for amino acids involved in the bridge. Chimera correctly recognize the binding. But when entering the minimization run, chimera complains about the atoms of the cysteinate residues. Before sending you files I was just wondering if this is something that is not implemented in chimera or a problem on how I prepare my structure.
Best regards, JD
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Okay, I have found the problem and committed a fix. The fix will be in tonight's daily build and will be in the 1.10.1 release (if we make one). The problem affects all structures with "unusual" bonds involving standard residues (disulfides, glycosylations, etc.). --Eric On Nov 7, 2014, at 8:36 AM, Jean Didier Pie Marechal <JeanDidier.Marechal@uab.cat> wrote:
Dear all,
I am trying to minimize a structure with a disulfide bond. My initial pdb has a CYM residue for amino acids involved in the bridge. Chimera correctly recognize the binding. But when entering the minimization run, chimera complains about the atoms of the cysteinate residues. Before sending you files I was just wondering if this is something that is not implemented in chimera or a problem on how I prepare my structure.
Best regards, JD
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Eric Pettersen -
Jean Didier Pie Marechal