VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Thu Apr 11 2024 - 10:14:05 CDT

Hi Dmitry,
this is unusual for a molecule with only ~6800 atoms. I can help you debug
if you share the molecule.

The temporary file location is hardcoded in C++, you may change at will but
you will need to recompile VMD.

Friendly,
Diego.

On Thu, Apr 11, 2024 at 8:42 AM Dmitry Suplatov <genesup_at_gmail.com> wrote:

> Hello,
>
>
>
> I am having problems with ‘Surf’ as a “Drawing method” for proteins in VMD.
>
>
>
> So, I installed VMD 1.9.3 from this package -
> vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz. However,
> with VMD 1.9.4a I have the same problem.
>
>
> I used a default sequence of commands to deploy the package. However, it
> is important to note that I *installed it to my local folder*, not the
> global one.
>
>
>
> tar xzf vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz
> cd vmd-1.9.3/
> mcedit configure
> -> # Set these variables at the top of the script:
> -> #$install_bin_dir="$ENV{'HOME'}/vmd/bin";
> -> #$install_library_dir="$ENV{'HOME'}/vmd/lib/$install_name";
> ./configure
> cd src/
> make install
> export PATH=$HOME/vmd/bin/:$PATH
>
> Now I can run VMD using the ‘vmd’ command. When I load a pdb file and
> select ‘Surf’ as the ‘Drawing method’ the following happens - the
> 3D-viewer remains absolutely empty, I see this output in the bash command
> line of Linux, from which the vmd was launched:
>
>
>
> vmd > Reading 6882 atoms..done
>
> Probe radius = 1.400
>
> Constructing solvent-accessible surface ..
>
> Info) This surface is made with SURF from UNC-Chapel Hill. The reference
> is:
>
> Info) A. Varshney, F. P. Brooks, W. V. Wright, Linearly Scalable
> Computation
>
> Info) of Smooth Molecular Surfaces, IEEE Comp. Graphics and Applications,
>
> Info) v. 14 (1994) pp. 19-25.
>
> Info) Reading Surf geometry output file...
>
> Info) Read Surf output file, processing geometry...
>
> Info) Done.
>
>
>
> The next immediate action that I did was to investigate if the ‘surf’
> binary is correctly installed and set. So, while VMD was still running, I
> located the ‘surf_LINUXAMD64’ binary and renamed it:
>
>
>
> mv lib/vmd/surf_LINUXAMD64 lib/vmd/surf_LINUXAMD64_bak
>
>
>
> Then, I again selected ‘Surf’ as the ‘Drawing method’, and saw the
> following in the command line:
>
>
>
> vmd > sh: line 1: [my home folder]/vmd/lib/vmd/surf_LINUXAMD64: No such
> file or directory
>
> ERROR) Cannot read SURF output file: /tmp/vmdsurf.u1713953541.664.in.tri
>
> Info) Done.
>
>
>
> So, this tells me that the ‘surf’ binary exists and VMD is recognizing it
> (i.e. it throws an error when such binary is renamed, and no error when its
> in place). But for unknown reason the ‘Surf’ representation still does not
> work.
>
>
>
> *Questions:*
>
> 1. *Did anyone experience this and knows how to solve this?*
> 2. *Perhaps, the problem is with the temporary folder that is used to
> exchange data between VMD and Surf binary. Is there any way to set this
> folder from /tmp to a specific location?*
>
>
>
> Thanks and all have a great day
>
> Dmitry
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu