VMD-L Mailing List

From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Fri May 12 2017 - 14:11:13 CDT

Hi David,

        Kindly include vmd-l_at_ks.uiuc.edu on the Cc: or To: line of your email replies -- i.e. use "Reply All" to this mail . This way, the rest of the list can see the discussion.
        
        Okay, to be clear: you are now able to use VMD in two ways to successfully open files which are on your mapped drive, correct? Opening files with VMD's GUI file browser works for you, and opening files with the VMD console works for you, yes?

        So do I have it right that the problem now is: you want the a _third_ method to open files on mapped drives with VMD? The third method you have in mind is: browse files with the Mac OS Finder -- that is, click around files with your mouse when the word "Finder" is on the upper left of the screen right next to the apple symbol -- and then load the file into VMD with the right-click contextual menu "Open With.." .This _sounds_ reasonable -- in Mac OS X it is the same way you might open a .txt file with TextEdit, for example. Unfortunately, VMD doesn't support this third method. Instead, as above, launch VMD then use VMD's own GUI file browser.

        However, there is a method which_ does_ work to start VMD and have it immediately load a script or file. This method uses the command line -- here, I mean the Unix command line via Terminal.app, not the VMD console. For example, on a Mac,
/Applications/VMD\ 1.9.3.app/Contents/Resources/VMD.app/Contents/MacOS/VMD my-coord.pdb
will launch VMD and load my-coord.pdb
and
/Applications/VMD\ 1.9.3.app/Contents/Resources/VMD.app/Contents/MacOS/VMD -e my-saved-state.vmd
will launch VMD and load the saved state, including all molecules, in my-saved-state.vmd .
and
/Applications/VMD\ 1.9.3.app/Contents/Resources/VMD.app/Contents/MacOS/VMD -e my-script.tcl
will launch VMD and execute the commands in my-script.tcl (Note that the saved state .vmd files are just scripts themselves).
More information in the VMD User guide,
"VMD Command-Line Options"
http://www.ks.uiuc.edu/Research/vmd/current/ug/node246.html

        Let me me know if I'm interpreting you correctly on the "third" file opening method I ask about above.

                Cheers,

                Barry

> On May 12, 2017, at 12:33 PM, Perez,David H <dhperez_at_chem.ufl.edu> wrote:
>
> Hi Barry,
>
> The answer to all of your questions is yes and the version is 1.9.3, but the issue that I am having now is that: when I enter the mapped directory using my mouse through my normal GUI and right click on a .pdb file inside the directory, then select Open With and choose VMD as the program, the VMD program opens but the file is not loaded into the VMD GUI. In other words, it’s the equivalent of me opening a fresh VMD window with no files loaded. What should happen is that after pressing open the VMD GUI executes and the file is loaded, instead of just opening a fresh window of VMD.
>
> Thank you,
>
> David H. Perez
> Graduate Fellow
> University of Florida, Chemistry
> Dr. Rebecca Butcher Research Group
>
>
>> On May 12, 2017, at 1:01 PM, Barry Isralewitz <barryi_at_ks.uiuc.edu <mailto:barryi_at_ks.uiuc.edu>> wrote:
>>
>> Hi David,
>>
>> I'm copying the vmd-l discussion list on this mail thread; the earlier mails in the thread are quoted below.
>>
>> I'm a little unclear on how you are opening a file and viewing directory contents.
>> 1) Are you using the mouse to select File:New Molecule from the menu of the "VMD Main" window?
>> 2) Are you able to load a file from your mapped drive with a VMD text console command like
>> mol new /Volumes/your_mapped_drive/your_directory/your_coord_file.pdb
>> ? Does a similar command work with a file on your non-mapped drive?
>> 3) Can you see the file in a directory listing via the VMD text console with the "ls" command, or a command like "ls *.pdb" ? For example, in the VMD text console,
>> cd /Volumes/your_mapped_drive/your_directory
>> ls *.pdb
>> 4) Lastly, you mentioned you were using the "latest version" but just to be clear, what version of VMD are you running? At startup, there should be a line in the text console that starts "Info) VMD for MACOSXX86".
>>
>>
>> Cheers,
>>
>> Barry
>>
>>
>>> On May 12, 2017, at 9:08 AM, Perez,David H <dhperez_at_chem.ufl.edu <mailto:dhperez_at_chem.ufl.edu>> wrote:
>>>
>>> Greetings Barry,
>>>
>>> I can now see and access the mapped drive through \Volumes, but when using the command open with within the mapped directory the pdb structure is not loaded by VMD. The only action that takes place is the VMD GUI opening and that’s it. Please let me know of any suggestions to resolve this issue.
>>>
>>> Thank you,
>>>
>>> David H. Perez
>>> Graduate Fellow
>>> University of Florida, Chemistry
>>> Dr. Rebecca Butcher Research Group
>>>
>>>
>>
>>>
>>>> From: "Perez,David H" <dhperez_at_chem.ufl.edu <mailto:dhperez_at_chem.ufl.edu>>
>>>> Subject: Re: Accessing Mapped Drive Files on iMac
>>>> Date: May 12, 2017 at 7:08:01 AM CDT
>>>> To: Barry Isralewitz <barryi_at_ks.uiuc.edu <mailto:barryi_at_ks.uiuc.edu>>
>>>>
>>>> Good morning Barry,
>>>>
>>>> I am able to see it if I change the setting on my iMac to make connected drives on my desktop visible to the user which makes the directory appear on my desktop, but for some reason I cannot see it normally within my network folder nor can I see the many shared network drives within the VMD GUI. Even then once I click to enter the drive directory none of the files or sub folder within it are displayed. Also if I go to a .pdb file in my directory and choose the option open with VMD, the GUI of VMD will open, but the file is not loaded into VMD. It almost appears as if VMD is not able to see anything within the directory or access it, despite the fact that I don't have any settings prevent access to the directory as far as I know.
>>>>
>>>> - David Perez
>>>
>>>
>>>>> On May 12, 2017, at 5:13 AM, Barry Isralewitz <barryi_at_ks.uiuc.edu <mailto:barryi_at_ks.uiuc.edu>> wrote:
>>>>>
>>>>> Hello David,
>>>>>
>>>>> Are you able to see the desired mapped drive listed via
>>>>> ls /Volumes
>>>>> either in Terminal or the VMD console? If so:
>>>>>
>>>>> 1) For typing a path into the VMD console, for use in scripts, etc.:
>>>>> use the path name you need, starting with /Volumes, such as /Volumes/your_mapped_drive/your_directory/your_coord_file.pdb
>>>>> . The TkConsole will do tab completion to make typing faster.
>>>>> -- or instead,
>>>>> 2) For using the file browser GUI in Mac OS X VMD 1.9.3:
>>>>> Select "/" from the "Directory" popup to get to the root directory.
>>>>> Then navigate via /Volumes to your mapped disk and directory.
>>>>>
>>>>> Let me know if I understood your problem -- I wan't completely sure -- and if this solves it.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Barry Isralewitz
>>>>>
>>>>>> On May 11, 2017, at 7:41 PM, Perez,David H <dhperez_at_chem.ufl.edu <mailto:dhperez_at_chem.ufl.edu>> wrote:
>>>>>>
>>>>>> Greetings,
>>>>>>
>>>>>> I have recently installed the latest version of VMD for MacOS X OpenGL (32-bit Intel x86), but I am not able to see a mapped drive on my iMac 27 in Late 2015 model with OS Sierra. I would like to be able to access the files on my mapped drive directly within VMD without having to copy the files to my computer. Please let me know of any fixes.
>>>>>>
>>>>>> Thank you,
>>>>>>
>>>>>> David H. Perez
>>>>>> Graduate Fellow
>>>>>> University of Florida, Chemistry
>>>>>> Dr. Rebecca Butcher Research Group
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Barry Isralewitz
>>>>> Theoretical and Computational Biophysics Group
>>>>> 3043 Beckman, University of Illinois at Urbana-Champaign
>>>>> Office Phone: (217) 244-1612
>>>>> email: barryi_at_ks.uiuc.edu <mailto:barryi_at_ks.uiuc.edu> http://www.ks.uiuc.edu/~barryi <http://www.ks.uiuc.edu/~barryi>
>>>>
>>>
>> --
>> Barry Isralewitz
>> Theoretical and Computational Biophysics Group
>> 3043 Beckman, University of Illinois at Urbana-Champaign
>> Office Phone: (217) 244-1612
>> email: barryi_at_ks.uiuc.edu <mailto:barryi_at_ks.uiuc.edu> http://www.ks.uiuc.edu/~barryi <http://www.ks.uiuc.edu/~barryi> 

-- 
Barry Isralewitz
Theoretical and Computational Biophysics Group
3043 Beckman, University of Illinois at Urbana-Champaign
Office Phone: (217) 244-1612
email: barryi_at_ks.uiuc.edu   http://www.ks.uiuc.edu/~barryi