Extracting secondary structure residue info
Hi Elaine, I have a PDB file which only has rows starting with ATOM. When I open it in UCSF chimera, it displays all the secondary structures which the residues form. Is it possible to extract the starting & ending residues of each alpha helix (or any other secondary structure for that matter)? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Hi Prathvi, When you open a protein structure file that doesn't already have HELIX and STRAND information, Chimera (and ChimeraX) automatically run a calculation to assign secondary structure. The algorithm is the same, but in Chimera it is the "ksdssp" command and ChimeraX it is the "dssp" command. Chimera "ksdssp" does NOT have the option, but if you open the structure in ChimeraX you can rerun the "dssp" command except with "report true" to give that information in the Log: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/dssp.html> This ChimeraX dssp report shown in the Log starts like this and has more details after the summaries: ---------------- Helix Summary LEU /A:105 -> ASP /A:107 ASN /A:198 -> GLN /A:200 Ladder Summary ASP /A:12 -> TYR /A:14 antiparallel GLY /A:44 -> LYS /A:46 GLY /A:15 -> SER /A:24 antiparallel ILE /A:331 -> PHE /A:340 [...etc.] In Chimera, there is a way to get the information, but it is much less convenient. You would have to save the residue attribute named isHelix to a text file, and then save the residue attribute named isStrand to another text file. Then you would have to look in the files to identify the ranges or residue numbers. How to save an attribute to a file is described in the bottom section of this page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 1, 2022, at 12:18 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I have a PDB file which only has rows starting with ATOM. When I open it in UCSF chimera, it displays all the secondary structures which the residues form. Is it possible to extract the starting & ending residues of each alpha helix (or any other secondary structure for that matter)?
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Thanks a lot Elaine. It helped enormously. I just have 2 more questions: 1. After running the dssp command in chimeraX, is there a command to save the reply log to file using a command? I searched for it & landed up at: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003739.html but chimeraX throws the "Unknown command" error. 2. Is there a way to extract polypeptide sequence from a PDB file & save as a FASTA file or even a simple text file which simply contains a string representing the amino acids as single letters alphabets? On Fri, Apr 1, 2022 at 9:15 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Prathvi, When you open a protein structure file that doesn't already have HELIX and STRAND information, Chimera (and ChimeraX) automatically run a calculation to assign secondary structure. The algorithm is the same, but in Chimera it is the "ksdssp" command and ChimeraX it is the "dssp" command.
Chimera "ksdssp" does NOT have the option, but if you open the structure in ChimeraX you can rerun the "dssp" command except with "report true" to give that information in the Log: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/dssp.html>
This ChimeraX dssp report shown in the Log starts like this and has more details after the summaries: ---------------- Helix Summary LEU /A:105 -> ASP /A:107 ASN /A:198 -> GLN /A:200
Ladder Summary ASP /A:12 -> TYR /A:14 antiparallel GLY /A:44 -> LYS /A:46 GLY /A:15 -> SER /A:24 antiparallel ILE /A:331 -> PHE /A:340 [...etc.]
In Chimera, there is a way to get the information, but it is much less convenient. You would have to save the residue attribute named isHelix to a text file, and then save the residue attribute named isStrand to another text file. Then you would have to look in the files to identify the ranges or residue numbers. How to save an attribute to a file is described in the bottom section of this page: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 1, 2022, at 12:18 AM, Prathvi Singh via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I have a PDB file which only has rows starting with ATOM. When I open it in UCSF chimera, it displays all the secondary structures which the residues form. Is it possible to extract the starting & ending residues of each alpha helix (or any other secondary structure for that matter)?
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Hi Prathvi, These answers are both for ChimeraX so I CC'd the chimerax-users list. (1) ChimeraX command "log save" saves it as HTML <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html> (2) in ChimeraX, open the structure, show the sequence of the chain of interest (menu: Tools... Sequence... Show Sequence Viewer, choose chain if there is more than one chain preset). Showing the sequence can also be done with the ChimeraX "sequence chain" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#chain> Then in the sequence viewer window, the context menu has a choice to save the contents (File... Save As...). <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context> You show a context menu in ChimeraX with Ctrl-click or right-click (depending on your system) in the tool window. <https://rbvi.ucsf.edu/chimerax/docs/user/window.html#context-menu> In Chimera, #2 is similar, use main tools menu to show sequence, use sequence-viewer tool's menu to save it to file. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.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 Apr 2, 2022, at 9:51 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thanks a lot Elaine. It helped enormously. I just have 2 more questions:
1. After running the dssp command in chimeraX, is there a command to save the reply log to file using a command? I searched for it & landed up at: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003739.html but chimeraX throws the "Unknown command" error.
2. Is there a way to extract polypeptide sequence from a PDB file & save as a FASTA file or even a simple text file which simply contains a string representing the amino acids as single letters alphabets?
participants (2)
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Elaine Meng -
Prathvi Singh