From: Pawel Kedzierski (
Date: Wed Mar 25 2015 - 10:20:20 CDT

Dear Ajasja,

W dniu 25.03.2015 o 11:03, Ajasja Ljubetič pisze:
> Hi!
> One could argue that people using VMD should know at least the basics
> of using a computer.
I agree wholeheartedly that people nowaday should in general know the
basics of using a computer, but the notion of these "basics" among some
of my students seem to be limited to single or double clicking and it is
going to be "touching" in near future... Some don't even read the menu
entries past the first word and then complain that "Load visualization
state" does not load molecules.

While VMD is an advanced tool for advanced purposes, I believe that
frustration at the beginning of the learning process may prevent
discovering the full potential of the program.

> (But then perhaps by the same argument one could say that people using
> VMD should know how to use linux, which would have stopped many people
> (including me) from getting started with VMD).
I am myself primarily Linux user, but I understand that if someone has
only Windows experience, even the CLI interface is kind of problematic.
And not many Windows users know that Unix text files are not correctly
opened in Notepad. Therefore, while the vmd.rc file is documented in the
User Guide, many Windows users will not even get what a path like
"./vmd.rc" or "$HOME/vmd.rc" really means, and they may not be able to
get past the permission and text format issues.

> So I agree that it's advantageous for VMD to be accessible to the
> widest possible audience.
> In fact you would not need a separate version of .vmdrc (which could
> complicate the build process)
> just using:
> if {$tcl_platform(platform) == "windows"} {
> should do the trick.
It may be good idea indeed. I am not familiar how the build process is
implemented but it seemed to me that it would be simple to automate the
conversion. For example, in a Linux shell script:

cat vmd.rc -<<END|unix2dos > windows/vmd.rc

> Best regards,
> Ajasja Ljubetič

> On 25 March 2015 at 10:33, Pawel Kedzierski
> < <>> wrote:
> W dniu 25.03.2015 o 10:12, Ashar Malik pisze:
>> If the install path is changed during setup ... And the
>> installation done somewhere else, the rights issue does not come up.
> Yes, provided that the user knows a priori he or she needs to
> workaround a problem. Most do default install.
> And even then it shouldn't hurt to start in user folder by default
> - changing this is easy for those more experienced users and
> without the permission issue.
> The proposed change will benefit all beginners.
> Pawel
>> On Mar 25, 2015 10:06 PM, "Pawel Kedzierski"
>> <
>> <>> wrote:
>> Dear VMD developers and users,
>> I see on the vmd-l list and among my students that the
>> default settings of VMD on Windows OS are troublesome for
>> many users. The problem is that the working folder of VMD is
>> its install folder (within "Program Files" or "Program Files
>> (x86)") which is guarded by the OS. If one tries to save a
>> file there, it is saved in hidden user folder and while it
>> shows up in Explorer, the VMD plugins are not able to find it.
>> Many times a "solution" found on the web and on vmd-l list is
>> an advice to run VMD as administrator, which is a bad idea.
>> I have tested that appending a single line to the end of
>> vmd.rc in the VMD installation prevents such problems, and it
>> seems to me a general way:
>> However, for non-power users of Windows, editing the global
>> vmd.rc file is not trivial:
>> * the file is guarded by the OS too, due to location in
>> system folder.
>> * as the file has Unix format, Notepad will concatenate all
>> lines effectively destroying it;
>> For users, the simplest solution may be to run Wordpad as
>> administrator to make this change, but still this tend to be
>> confusing one must know how to "show all files" at opening
>> and then to save with original name and text format, but
>> neither with ".txt" appended, nor even worse, converted to
>> document format.
>> This is why I think that a better solution would be if the
>> vmd.rc on Windows would be installed with this fix included.
>> And possibly also converted to Windows text format.
>> Thanks,
>> Pawel