VMD-L Mailing List

From: Dmitry Suplatov (genesup_at_gmail.com)
Date: Thu Apr 11 2024 - 12:02:22 CDT

Thanks again for your response

>Can you:
>* check if QuickSurf works?

Yes, it works, no problem here

>* manually write to the /tmp folder? If for not,
>you may change the environment variable
>VMDTMPDIR

Did that, no effect, but I can see the new path in the error message for
Nanoshaper (see below)

>No matter the result, consider trying NanoShapper

Does not work.
Says, “Nanoshaper command not found, cannot read facet file”

>and/or MSMS, they're faster than Surf.

Cannot use it for licensing reasons

On Thu 11. Apr 2024 at 18:38, Diego Gomes <diego.enry_at_gmail.com> wrote:

> Never had this problem before.
>
> The message you've sent indicates VMD is reading Surf output ( .tri file
> in /tmp).
> For some weird reason it is just not displaying the 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.
>
> Can you:
> * check if QuickSurf works?
> * manually write to the /tmp folder? If for not, you may change the
> environment variable VMDTMPDIR
>
>
> No matter the result, consider trying NanoShapper and/or MSMS, they're
> faster than Surf.
>
> On Thu, Apr 11, 2024 at 10:31 AM Dmitry Suplatov <genesup_at_gmail.com>
> wrote:
>
>> Hi Diego,
>>
>> Thanks for the feedback.
>>
>> This problem persists for any proteins of any size. So the particular
>> protein is not the issue. Perhaps, the problem is with my access to the tmp
>> folder, I don’t know.
>>
>> So, did you experience anything similar when installing vmd to a
>> non-default location?
>>
>> Thanks again,
>> Dmitry
>>
>>
>> On Thu 11. Apr 2024 at 17:14, Diego Gomes <diego.enry_at_gmail.com> wrote:
>>
>>> 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
>>>
>>
>
> --
> 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
>