Hello, I truly appreciate the development and distribution of software such as Chimera to the scientific community, but alas I am not 'computer-savvy.' I would like to map highly conserved residues of a protein onto its crystal structure (PDB 3V0I). I can view the PDB file of the crystal structure using Chimera, but I am having a hard time figuring out how to highlight residues. Could you please give me some advice about how to identify and mark particular residues using this file? I apologize if this request seems trivial, and I appreciate any advice. Thanks, -Wil Ratzan Dept. of Cell Biology and Neuroscience Montana State University Bozeman, MT 59717
Hi Wil, Have you tried ConSurf server? http://consurf.tau.ac.il I haven't tried for a long time, but I think it can perform a sequence analysis using the sequence associated to the PDB ID (3V0I for you) and then it will map the residue conservation on to the structure. One the files in the results page will be a kind of Chimera session file. You need to download and open it in Chimera, then you’ll see the highlighted residues according to the conservation score. Regards, Aldo 2018-02-12 11:38 GMT+00:00 Wil Ratzan <wilratzan@gmail.com>:
Hello,
I truly appreciate the development and distribution of software such as Chimera to the scientific community, but alas I am not 'computer-savvy.'
I would like to map highly conserved residues of a protein onto its crystal structure (PDB 3V0I). I can view the PDB file of the crystal structure using Chimera, but I am having a hard time figuring out how to highlight residues. Could you please give me some advice about how to identify and mark particular residues using this file?
I apologize if this request seems trivial, and I appreciate any advice.
Thanks,
-Wil Ratzan
Dept. of Cell Biology and Neuroscience Montana State University Bozeman, MT 59717
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-- ========================================= Aldo Segura-Cabrera Chemogenomics Scientist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton, Cambridge, UK e-mail: asegura@ebi.ac.uk <asegurac@ipn.mx>; aldosegura@gmail.com website: http://aseguralab.org/ =========================================
Hello Wil, If you just mean that you don’t know how to specify or select individual residues, there are many ways…. some are outlined in this recent post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-February/014344.html> Command “color red :258.A” would color residue 258 in chain A red, for example. Also, if you are showing the sequence, another way to select a specific residue is by using the mouse to drag a box around it in the sequence. If you have a sequence alignment already, it is easy to show the conservation from that alignment on the structure. This tutorial is all about mapping sequence conservation: <https://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html> If you never showed sequence alignments in Chimera before, this tutorial helps get you started, and it also has a color-by-conservation example at the end: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html> 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 12, 2018, at 3:38 AM, Wil Ratzan <wilratzan@gmail.com> wrote:
Hello, I truly appreciate the development and distribution of software such as Chimera to the scientific community, but alas I am not 'computer-savvy.'
I would like to map highly conserved residues of a protein onto its crystal structure (PDB 3V0I). I can view the PDB file of the crystal structure using Chimera, but I am having a hard time figuring out how to highlight residues. Could you please give me some advice about how to identify and mark particular residues using this file?
I apologize if this request seems trivial, and I appreciate any advice. Thanks, -Wil Ratzan
Thanks for the great advice! -Wil On Mon, Feb 12, 2018 at 11:01 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Wil, If you just mean that you don’t know how to specify or select individual residues, there are many ways…. some are outlined in this recent post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018- February/014344.html>
Command “color red :258.A” would color residue 258 in chain A red, for example.
Also, if you are showing the sequence, another way to select a specific residue is by using the mouse to drag a box around it in the sequence.
If you have a sequence alignment already, it is easy to show the conservation from that alignment on the structure. This tutorial is all about mapping sequence conservation: <https://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html>
If you never showed sequence alignments in Chimera before, this tutorial helps get you started, and it also has a color-by-conservation example at the end: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>
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 12, 2018, at 3:38 AM, Wil Ratzan <wilratzan@gmail.com> wrote:
Hello, I truly appreciate the development and distribution of software such as Chimera to the scientific community, but alas I am not 'computer-savvy.'
I would like to map highly conserved residues of a protein onto its crystal structure (PDB 3V0I). I can view the PDB file of the crystal structure using Chimera, but I am having a hard time figuring out how to highlight residues. Could you please give me some advice about how to identify and mark particular residues using this file?
I apologize if this request seems trivial, and I appreciate any advice. Thanks, -Wil Ratzan
Elaine and Aldo, Your advice was spot-on and I was able to quickly map conserved residues onto our protein's crystal structure by saving an alignment that I made as an .aln file and then opening it concurrently with the crystal structure .pdb file in Chimera. Thanks for providing such great software and support! -Wil On Mon, Feb 12, 2018 at 11:01 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Wil, If you just mean that you don’t know how to specify or select individual residues, there are many ways…. some are outlined in this recent post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018- February/014344.html>
Command “color red :258.A” would color residue 258 in chain A red, for example.
Also, if you are showing the sequence, another way to select a specific residue is by using the mouse to drag a box around it in the sequence.
If you have a sequence alignment already, it is easy to show the conservation from that alignment on the structure. This tutorial is all about mapping sequence conservation: <https://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html>
If you never showed sequence alignments in Chimera before, this tutorial helps get you started, and it also has a color-by-conservation example at the end: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>
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 12, 2018, at 3:38 AM, Wil Ratzan <wilratzan@gmail.com> wrote:
Hello, I truly appreciate the development and distribution of software such as Chimera to the scientific community, but alas I am not 'computer-savvy.'
I would like to map highly conserved residues of a protein onto its crystal structure (PDB 3V0I). I can view the PDB file of the crystal structure using Chimera, but I am having a hard time figuring out how to highlight residues. Could you please give me some advice about how to identify and mark particular residues using this file?
I apologize if this request seems trivial, and I appreciate any advice. Thanks, -Wil Ratzan
participants (3)
-
Aldo Segura -
Elaine Meng -
Wil Ratzan