Re: [chimerax-users] chimeraX questions on representation
Hi Eddie, ChimeraX (and Chimera for that matter) connect atoms in standard residues using a connectivity template. Therefore the atoms have to have standard names. Some hydrogens in your file don’t have their PDB-standard names, and therefore wind up unconnected. I have committed a fix for this — if there are unconnected hydrogens after the template pass then Chimera(X) does an additional connect-by-distance pass. A second problem with the file is that it uses ATOM records for everything, including solvent, ions, and the lipid bilayer. ATOM records are for polymeric residues and imply connectivity between consecutive residues with the same chain ID. Therefore the non polymeric components of the file should have been using HETATM records. I have attached an edited version of your file with appropriate HETATM records. It should work much better in tomorrow’s fixed build.
—Eric
On Oct 16, 2018, at 11:31 AM, Dr. Eddie eackad@gmail.com wrote:
Thanks for the help! As for the pdb, I've attached it. It shows fine in vmd and pymol. Thanks, Eddie
On Tue, Oct 16, 2018 at 1:19 PM Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote:
On Oct 15, 2018, at 8:35 PM, Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> wrote:
I don’t know why your H’s are disconnected specifically, but it’s almost surely some issue with the input file.
If you provided the input file, we might be able to offer advice on how to get ChimeraX to handle it better. One thing you might try sight unseen is to remove the LINK/CONECT records in the file (assuming it’s a PDB file).
—Eric
Eric Pettersen UCSF Computer Graphics Lab
-- Eddie <popc.3a4.ionf.pdb>
Awesome, thanks!
On Tue, Oct 16, 2018 at 2:51 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Eddie, ChimeraX (and Chimera for that matter) connect atoms in standard residues using a connectivity template. Therefore the atoms have to have standard names. Some hydrogens in your file don’t have their PDB-standard names, and therefore wind up unconnected. I have committed a fix for this — if there are unconnected hydrogens after the template pass then Chimera(X) does an additional connect-by-distance pass. A second problem with the file is that it uses ATOM records for everything, including solvent, ions, and the lipid bilayer. ATOM records are for polymeric residues and imply connectivity between consecutive residues with the same chain ID. Therefore the non polymeric components of the file should have been using HETATM records. I have attached an edited version of your file with appropriate HETATM records. It should work much better in tomorrow’s fixed build.
—Eric
On Oct 16, 2018, at 11:31 AM, Dr. Eddie eackad@gmail.com wrote:
Thanks for the help! As for the pdb, I've attached it. It shows fine in vmd and pymol. Thanks, Eddie
On Tue, Oct 16, 2018 at 1:19 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
On Oct 15, 2018, at 8:35 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
I don’t know why your H’s are disconnected specifically, but it’s almost surely some issue with the input file.
If you provided the input file, we might be able to offer advice on how to get ChimeraX to handle it better. One thing you might try sight unseen is to remove the LINK/CONECT records in the file (assuming it’s a PDB file).
—Eric
Eric Pettersen UCSF Computer Graphics Lab
-- Eddie <popc.3a4.ionf.pdb>
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Dr. Eddie -
Eric Pettersen