VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Thu Apr 11 2024 - 12:56:15 CDT

Hi Dmitry,
since other representations behave normally that is something particular to
your computer :(
Do you mind giving us a few more details about your OS & hardware
(including graphics card)?

I don't think this is resolve the issue, but can you try forcing a display
update?
After launching VMD and computing the surface, from the terminal or
TkConsole type:
display update

(https://www.ks.uiuc.edu/Research/vmd/current/ug/node126.html#6897)

# Nanoshapper:
Although Nanoshapper is GPL v3, it is not redistributed with VMD.

You may download it from their GitHub.
https://urldefense.com/v3/__https://gitlab.iit.it/SDecherchi/nanoshaper__;!!DZ3fjg!_khHc71XyCRIssgEjCtAXMMjC1Iq0fkl3bt67bIoAkJBobky8NuPFo8pZGyJ3f14lEBw157sRDCcBSztHfJ2$

The precompiled binary is inside the compressed tarball named
"pkg_nanoshaper_0.7.8.tar.gz"

Friendly,
Diego.

On Thu, Apr 11, 2024 at 12:02 PM Dmitry Suplatov <genesup_at_gmail.com> wrote:

> 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
>>
> 

-- 
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