VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Jul 26 2017 - 00:39:09 CDT

Sorry -- minor error:
the script should be this:
-----------------------------------------------------------------------------------------
puts -nonewline "Enter PDB code: "
flush stdout
set name [gets stdin]
puts "Getting $name"
package require http
set handle [::http::geturl http://files.rcsb.org/view/$name.pdb]
set pdb_file [open $name.pdb a]
puts $pdb_file [::http::data $handle]
mol load pdb $name.pdb
-----------------------------------------------------------------------------------------

In the previous version the web link was not modified.

On Wed, Jul 26, 2017 at 5:35 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> 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
> 

-- 
Best,
/A