VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Jul 26 2017 - 00:35:27 CDT

I guess its something thats changed on the backend.
I recently ran into this and wrote a small script to handle this.

here it is:
-------------------------------------------------------------------------------
puts -nonewline "Enter PDB code: "
flush stdout
set name [gets stdin]
puts "Getting $name"
package require http
set handle [::http::geturl http://files.rcsb.org/view/1HV4.pdb]
set pdb_file [open $name.pdb a]
puts $pdb_file [::http::data $handle]
mol load pdb $name.pdb

-------------------------------------------------------------------------------
you will have to save it into the working directory of vmd

start vmd
in the tkconsole or the shell at the VMD prompt type

source name_of_the_script_file

it will ask for a PDB code -- only enter the 4 letter ID

it will do some webpage parsing - download the file to your working
directory and also as the last line of the code read load it into VMD as
well.

This is not a thoroughly tested fix and probably a plugin update is needed.
But i guess untill then you can use this.

Hope this helps.

Best,
/A

On Wed, Jul 26, 2017 at 4:40 PM, Mike McCallum <mmccallum_at_pacific.edu>
wrote:

> Hi there,
> I’m not quite sure when this happened, but I am unable to get ‘mol
> pdbload’ to work. I tried this with 1.9.2, 1.9.3 and 1.9.4a versions on OS
> X, new and old versions of the OS. I’m running a class right now and I’m
> asking the students to do this, so help is much appreciated. Here is the
> startup info + error.
> —
> Info) VMD for MACOSXX86, version 1.9.3 (November 30, 2016)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 8 CPUs detected.
> Info) OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /Applications/VMD 1.9.3.app/Contents/vmd/plugins/MACOSXX86/molfile
> vmd > The PDB is supported by RCSB, the NSF, US PHS, NIH, NCRP, NIGMS,
> NLM,
> and US DoE, who are not liable for the data. PDB files shall not be
> sold. See ftp://ftp.rcsb.org/advisory.doc
> <https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.rcsb.org_advisory.doc&d=DwMGaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=f0N5v4NY00lzag1jzuVkui7_420G9K7DR41QSpC55bU&m=rWWR9Az2MVsLhO_SXXIc2q-87aWJLXgWKZh3iS4aSww&s=THZnqm0QkLreWUIzWfNNHup7T3ZCORN2OPOYRoy7n7U&e=>
> for full details.
> Info) Using plugin webpdb for structure file 1anv
> ERROR) BaseMolecule: init_atoms called with invalid number of atoms: 0
> ERROR) molecule_structure: Unable to read structure for molecule 0
> ERROR) molecule_structure: severe error indicated by plugin aborting
> loading of molecule 0
> Info) Using plugin webpdb for structure file 1sse
> ERROR) BaseMolecule: init_atoms called with invalid number of atoms: 0
> ERROR) molecule_structure: Unable to read structure for molecule 1
> ERROR) molecule_structure: severe error indicated by plugin aborting
> loading of molecule 1
> --
>
> Cheers
> Mike
>
> --
> C. Michael McCallum
> Professor
> Department of Chemistry, UOP
> mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209)
> 946-2607 fax
>
>
>
>
>
> 

-- 
Best,
/A