change aminoacid in sequence alignment
I have a "residue" KCX (PDB records are Hetatm). In the sequence alignment it comes as X. Is there a way to change it to K without making a PDB file and changing it to K there? Thank you,. Jackie Vitali Cleveland State University
Hi Jackie, If the PDB file has a MODRES record that specifies the "normal" form of the residue, then I believe it will show up as K when you display the sequence. For example, if I use these commands open 7k3m select :kcx ...and then show its sequence (menu: Favorites... Sequence) I can see that the selected residue is "K" in the sequence. The PDB file for 7k3m contains this MODRES line: MODRES 7K3M KCX A 71 LYS MODIFIED RESIDUE I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 23, 2022, at 11:39 PM, Jacqueline Vitali <jackie.vitali@gmail.com> wrote:
I have a "residue" KCX (PDB records are Hetatm). In the sequence alignment it comes as X. Is there a way to change it to K without making a PDB file and changing it to K there? Thank you,.
Jackie Vitali Cleveland State University
Thanks Elaine. At the end I selected the specific residue (X) and I went to Tools>structure editing>rotamers and selected Lys there. Then stored the session. On reopenong the residue was K. Jackie Vitali On Thu, Feb 24, 2022 at 11:50 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jackie, If the PDB file has a MODRES record that specifies the "normal" form of the residue, then I believe it will show up as K when you display the sequence.
For example, if I use these commands
open 7k3m select :kcx
...and then show its sequence (menu: Favorites... Sequence) I can see that the selected residue is "K" in the sequence.
The PDB file for 7k3m contains this MODRES line:
MODRES 7K3M KCX A 71 LYS MODIFIED RESIDUE
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 23, 2022, at 11:39 PM, Jacqueline Vitali <jackie.vitali@gmail.com> wrote:
I have a "residue" KCX (PDB records are Hetatm). In the sequence alignment it comes as X. Is there a way to change it to K without making a PDB file and changing it to K there? Thank you,.
Jackie Vitali Cleveland State University
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Elaine Meng -
Jacqueline Vitali