Re: cartoon not displaying in ChimeraX despite complete backbone
Dear ChimeraX users, I'm unable to display the cartoon representation for pdb file in ChimeraX, even though the residues and atoms appear complete. The structure contains standard RNA residues (A, G, U) , Each residue includes all expected backbone atoms (P, O5', C5', C4', C3', O3', C1', O4', etc.) as well as complete base atoms and hydrogens. The file was written out from MOE software and I am not sure if this is an issue. Some tips on how to edit the pdb file would be helpful Thanks, amith
Hi Amith, We cannot figure it out unless you send an example file for us to look at. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 22, 2025, at 10:55 AM, amith ranga via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users, I'm unable to display the cartoon representation for pdb file in ChimeraX, even though the residues and atoms appear complete. The structure contains standard RNA residues (A, G, U) , Each residue includes all expected backbone atoms (P, O5', C5', C4', C3', O3', C1', O4', etc.) as well as complete base atoms and hydrogens. The file was written out from MOE software and I am not sure if this is an issue. Some tips on how to edit the pdb file would be helpful Thanks, amith
Maybe your structure file is missing the secondary structure information. Run the dssp command and then try displaying the cartoon representation. -- Greg On 4/22/2025 1:17 PM, Elaine Meng via ChimeraX-users wrote:
Hi Amith, We cannot figure it out unless you send an example file for us to look at. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 22, 2025, at 10:55 AM, amith ranga via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users, I'm unable to display the cartoon representation for pdb file in ChimeraX, even though the residues and atoms appear complete. The structure contains standard RNA residues (A, G, U) , Each residue includes all expected backbone atoms (P, O5', C5', C4', C3', O3', C1', O4', etc.) as well as complete base atoms and hydrogens. The file was written out from MOE software and I am not sure if this is an issue. Some tips on how to edit the pdb file would be helpful Thanks, amith
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hi Greg/Elaine, thanks for the suggestions. this was an issue with the pdb file. the entire RNA was written as a HETATM record and i converted it all into ATOM and then i was able to resolve the cartoon issue. thanks again for your support, best amith
participants (4)
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amith ranga -
arangarajan＠initialtx.com -
Elaine Meng -
Greg Couch