VMD-L Mailing List

From: Chris Taylor (christay_at_usc.edu)
Date: Thu Oct 14 2021 - 14:21:39 CDT

I got this to work for now with the 5ire.pdb1 by adding:
 pdbalias residue NAG DUM

to the mergemultiframepdb.tcl script.

Chris

From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> On Behalf Of Chris Taylor
Sent: Tuesday, October 12, 2021 19:46
To: vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: Merge frames of PDB asymmetric unit to biological assembly

I’ve been working with this some more- I downloaded the 1k4r.pdb1 and 5ire.pdb1 biological assembly files from the RCSB.org protein databank and the mergemultiframepdb.tcl script. In VMD, I run

source mergemultiframepdb.tcl

..and then:
mol new 1k4r.pdb1 type pdb
merge_multi_frame_structure top /Users/cht/Downloads/temp 1k4r_merged

Sometimes this completes fine, and other times it dies with an error:
psfgen) reading coordinates from pdb file C:/Users/cht/Downloads/temp/merge0000.F.pdb for segment V6
psfgen) Warning: failed to set coordinate for atom CD1 ILE:36 V6
PDB: C:/Users/cht/Downloads/temp/merge0000.G.pdb V7
psfgen) building segment V7
psfgen) setting patch for first residue to NONE
psfgen) setting patch for last residue to NONE
psfgen) reading residues from pdb file C:/Users/cht/Downloads/temp/merge0000.G.pdb
psfgen) unknown residue type NAG
psfgen) unknown residue type NAG
psfgen) extracted 2 residues from pdb file
Info: generating structure...
psfgen) unknown residue type NAG