VMD-L Mailing List

From: Luis Guillermo Cota Preciado (lgcota_at_gmail.com)
Date: Mon Jun 07 2010 - 00:17:58 CDT

John,

It does, thanks. However, I can't get it to appear during the startup if I
liberalize the permission strings even more. In order to rule out some
previous mistake of mine I deleted VMD and reinstalled it only to end up
with the same things:

1) When I follow the installation instructions from the README I can't
install on the default locations
(obviously so because it is in the realm of the superuser.)

2) When I toss in sudo or su I do get the installation, but no exec
permissions for the lowly user. Tweaking vmd_LINUX's to o+x is enough to get
VMD going, but not to display the main menu. Permissions for other files
seem to be correct:

-rw-r--r-- 1 root root 2020 2010-06-06 23:34 Announcement
drwxr-xr-x 2 root root 72 2010-06-04 01:24 doc
-rwxr-x--- 1 lgc lgc 246044 2009-05-11 12:54 libcudart.so.2
-rw-r--r-- 1 root root 7753 2010-06-06 23:34 LICENSE
drwxr-x--- 5 lgc lgc 120 2009-08-01 01:44 plugins
-rw-r--r-- 1 root root 14964 2010-06-06 23:34 README
drwxr-x--- 8 lgc lgc 216 2009-08-01 01:44 scripts
drwxr-x--- 3 lgc lgc 184 2009-08-01 01:41 shaders
-rwxr-xr-x 1 root root 1167079 2010-06-06 23:34 stride_LINUX
-rwxr-xr-x 1 root root 352948 2010-06-06 23:34 surf_LINUX
-rwxr-xr-x 1 root root 176272 2010-06-06 23:34 tachyon_LINUX
-rw-r--r-- 1 root root 3166 2010-06-06 23:34 vmd_completion.dat
-rwxr-x--x 1 root root 5921104 2010-06-06 23:34 vmd_LINUX,

(lgc is yours truly). My umask is 0027.

Apart from the possibility that I'm doing something wrong, in which case I
would like to know further, it seems to me that either the configure script
needs to be modified in order to take care of permissions issues and proper
mention be made to the use of "su" or "sudo" on the README, or the default
install should take place in the current directory without modifying the
configure script.

Thanks.

2010/6/4 John Stone <johns_at_ks.uiuc.edu>

> Luis,
> Does the main menu open when you type this command?:
> menu main on
>
> If so, then it must be more permissions issues caused by
> the behavior of sudo and the resulting file umask on your machine.
>
> If not, then tell me what this command says:
> vmdinfo options
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jun 04, 2010 at 10:19:01AM -0500, Luis Guillermo Cota Preciado
> wrote:
> > Hi John,
> > There seems to be no .vmdinit file anywhere. The .vmdrc file that
> sits in
> > /usr/local/lib/vmd is not empty, and there is no such file in my
> $HOME.
> > Here's the ls -al dump of /usr/local/lib/vmd:
> > drwxr-xr-x 6 root root 480 2010-06-04 01:24 .
> > drwxr-xr-x 10 root root 272 2010-06-04 01:24 ..
> > -rw-r--r-- 1 root root 2020 2010-06-04 01:24 Announcement
> > drwxr-xr-x 2 root root 72 2010-06-04 01:24 doc
> > -rwxr-xr-- 1 lgc lgc 246044 2009-05-11 12:54 libcudart.so.2
> > -rw-r--r-- 1 root root 7753 2010-06-04 01:24 LICENSE
> > drwxr-xr-- 5 lgc lgc 120 2009-08-01 01:44 plugins
> > -rw-r--r-- 1 root root 14964 2010-06-04 01:24 README
> > drwxr-xr-- 8 lgc lgc 216 2010-06-04 01:24 scripts
> > drwxr-xr-- 3 lgc lgc 184 2009-08-01 01:41 shaders
> > -rwxr-xr-x 1 root root 1167079 2010-06-04 01:24 stride_LINUX
> > -rwxr-xr-x 1 root root 352948 2010-06-04 01:24 surf_LINUX
> > -rwxr-xr-x 1 root root 176272 2010-06-04 01:24 tachyon_LINUX
> > -rw-r--r-- 1 root root 3166 2010-06-04 01:24 vmd_completion.dat
> > -rwxr-xr-x 1 root root 5921104 2010-06-04 01:24 vmd_LINUX
> > -rw-r----- 1 root root 1813 2010-06-04 01:24 .vmdrc
> > -rw-r----- 1 root root 1784 2010-06-04 01:24 .vmdsensors
> > Thank you for your help.
> > 2010/6/4 John Stone <johns_at_ks.uiuc.edu>
> >
> > Hi,
> > Did you verify that the .vmdinit file in the installation
> > directory is readable by a normal user? You might also check
> > that you don't have an empty .vmdrc sitting around in your
> > home directory. If neither of those is the problem, send me
> > the 'ls -al' output on your installation directory and I'll have
> > a quick look.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> > On Fri, Jun 04, 2010 at 02:32:23AM -0500, Luis Guillermo Cota
> Preciado
> > wrote:
> > > Hi,
> > > I followed the instructions within the README file, to no
> avail,
> > trying to
> > > do a default installation. I had to -but of course!- use sudo
> in
> > order to
> > > proceed without errors. However, I ended up with no permissions
> for
> > the
> > > normal user, which I had to tweak by hand in order to get VMD
> > running.
> > > However, somehow the otherwise usual "main" window (whatever
> its
> > name is),
> > > the one for loading and displaying and all that, is absent.
> Just
> > the
> > > terminal and the visualization area are present.
> > > What gives? Thanks.
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>