VMD-L Mailing List

From: Janet Jacobsen (jsjacobsen_at_lbl.gov)
Date: Tue Sep 09 2008 - 12:07:24 CDT

Hi. Thank you for your reply. I did the compilation more than once, and it
seems that I have the files you mention in more than once place.

> pwd
    /usr/common/usg/vmd/1.8.6/lib/vmd/plugins
> ls
    LINUX LINUXAMD64 WIN32 include noarch
> ls noarch/tcl
    apbsrun1.2 dowser1.0 namdserver1.1 rmsdtt2.0
    ... <and all the others>
    dipwatch1.1 namdplot1.0 rmsd1.0

and

> pwd
    /usr/common/usg/vmd/1.8.6/vmd-1.8.6/plugins
> ls
    LINUX LINUXAMD64 WIN32 include noarch
> ls noarch/tcl
    apbsrun1.2 dowser1.0 namdserver1.1 rmsdtt2.0
    ... <and all the others>
    dipwatch1.1 namdplot1.0 rmsd1.0

Based on your email, it seems the former location is the preferred
location.

But given that I did the "make distrib" and do in fact have a plugins
directory tree, what else do I need to do to make the extensions show
up in the Extensions menu?

Thanks,
Janet

John Stone wrote:
> Hi,
> It sounds to me like your self-compiled VMD installation is missing
> the contents of its plugins directory tree. When you compiled your
> VMD plugin tree, did you also do a "make distrib" to copy the plugin
> tree to the directory used by your VMD compilation? You can check the
> contents of the plugin tree in your installed VMD, you should see something
> like this:
> % ls /Projects/vmd/pub/linux/lib/vmd187a30/plugins
> include LINUX noarch
>
> % ls /Projects/vmd/pub/linux/lib/vmd187a30/plugins/noarch/tcl
> apbsrun1.3 extendedpdb1.0 navfly1.0 runante0.1
> atomedit1.0 gofrgui1.0 navigate1.0 saltbr1.0
> autoimd1.6 hbonds1.0 optimization1.0 seqdata1.0
> autoionize1.2 idatm0.1 palettetool1.0 seqedit1.0
> bignum1.0 imdmenu1.0 paratool1.3 simpleedit1.0
> biocore1.1 inorganicbuilder0.1 pbctools2.2 solvate1.2
> blast1.0 membrane1.0 pdbtool1.0 ssrestraints1.0
> cgtools1.0 mergestructs1.0 phylotree1.0 stingtool1.0
> cliptool1.0 molefacture1.1 plotter1.2 textview1.1
> clonerep1.1 moltoptools0.1 qmtool1.1 timeline1.0
> colorbar1.0 multimolanim1.0 ramaplot1.1 utilities1.0
> colorscalebar1.2 multiplot1.1 readcharmmpar1.0 vdna1.2
> contactmap1.1 multiseq2.0 readcharmmtop1.0 viewmaster2.2
> dataimport1.0 multiseqdialog1.0 resptool1.1 vmdmovie1.6
> demomaster1.0 namdenergy1.2 rmsd1.0 vmdtkcon1.0
> dipwatch1.1 namdgui1.1 rmsdtt2.0 volmapgui1.0
> dowser1.0 namdplot1.0 rnaview1.0 zoomseq1.0
> exectool1.2 namdserver1.1 ruler1.0
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Sep 08, 2008 at 04:46:07PM -0700, Janet Jacobsen wrote:
>
>> Hi. I was asked to upgrade VMD from 1.8.3 to 1.8.6 on
>> a multi-user system for which I do not have root access.
>> It's a Linux x86_64 system (kernel 2.6.5).
>>
>> I'll skip the details, but I went down the path of building
>> fltk, netcdf, the VMD plugins, and VMD with a version of
>> gcc that is consistent with the version of GL on the machine.
>>
>> I cannot run vmd using the vmd script in ~bin (when I load
>> a molecule all windows disappear), but with the version I built,
>> I am able to run vmd by executing the binary in ~lib/vmd.
>>
>> I have run through the tutorial and tried loading a few proteins,
>> and most of that seems to work, but the Extensions menu is
>> blank.
>>
>> When I fire up VMD 1.8.3, I see a lot of entries in the Extensions
>> menu, so I assume that I should see the same extensions when
>> I start VMD 1.8.6. Any idea what step I may have missed in
>> building VMD? (As I mentioned above, I did compile the VMD
>> plugins, and I did define PLUGINDIR before compiling VMD.)
>>
>> In general, I am confused about the difference between extensions
>> and plugins. I tried experimenting with the .vmdrc file and with
>> "package require" at the command line, but based on my
>> understanding of the plugin documentation, I shouldn't need to
>> add plugins that come with the VMD distribution.
>>
>> I'd appreciate any pointers you can give me.
>>
>> Thanks,
>> Janet
>>