renumbering missing residues
Dear sir or madam, I am working with structure 1p22 and want to renumber the residues of chain A so they match Uniprot Q9Y297, but when I tried to it does not work for the 2 missing structures on the pdb file, and it continues the numbering as if they were not there. Is there a way to number this part correctly? with kind regards Fiorella
Hi Fiorella, Use the Renumber Residues tool (in Tools->Structure Editing) but check the ‘selected residues’ button rather than the ‘chains’ button. Then select a stretch of residues you want to renumber and the desired starting number and click Apply’. Then select the next stretch and their starting number and click Apply and so on. It might be easiest to select the residue stretches using the Sequence tool (Favorites->Sequence). —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 8, 2016, at 4:35 AM, Charles, Fiorella <fiorella.charles.15@ucl.ac.uk> wrote:
Dear sir or madam,
I am working with structure 1p22 and want to renumber the residues of chain A so they match Uniprot Q9Y297, but when I tried to it does not work for the 2 missing structures on the pdb file, and it continues the numbering as if they were not there.
Is there a way to number this part correctly?
with kind regards
Fiorella _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
I should mention that the renumbering must not produce different residues in the same chain with the same number, even temporarily. So, depending on the renumbering you may have to renumber the last segment, then next-to-last, and so on. —Eric
On Jun 8, 2016, at 12:04 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Fiorella, Use the Renumber Residues tool (in Tools->Structure Editing) but check the ‘selected residues’ button rather than the ‘chains’ button. Then select a stretch of residues you want to renumber and the desired starting number and click Apply’. Then select the next stretch and their starting number and click Apply and so on. It might be easiest to select the residue stretches using the Sequence tool (Favorites->Sequence).
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 8, 2016, at 4:35 AM, Charles, Fiorella <fiorella.charles.15@ucl.ac.uk <mailto:fiorella.charles.15@ucl.ac.uk>> wrote:
Dear sir or madam,
I am working with structure 1p22 and want to renumber the residues of chain A so they match Uniprot Q9Y297, but when I tried to it does not work for the 2 missing structures on the pdb file, and it continues the numbering as if they were not there.
Is there a way to number this part correctly?
with kind regards
Fiorella _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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participants (2)
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Charles, Fiorella -
Eric Pettersen