VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 18 2021 - 11:55:03 CDT

Hi,
  Thanks for the followup on this.
I've made updates to the script based on Axel's comments and yours, please
let me know if the new version I've attached to this email works for you
"as-is" or if further edits are still needed in your case.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 14, 2021 at 07:21:39PM +0000, Chris Taylor wrote:
> 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
>
>
>
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/