VMD-L Mailing List

From: Jim Parker (jim.parker_at_prismsciences.com)
Date: Wed Sep 16 2009 - 23:29:11 CDT

John,
  Ok, more info:
I checked to see the value of $env(VMDDIR) in VMD

vmd > echo $env(VMDDIR)
/home/user/lib/vmd

bash> ls -l /home/user/lib/vmd/.vmdrc
-rw-r--r-- 1 user user 1813 2009-08-27 21:22 /home/user/lib/vmd/.vmdrc

(should these be executable?)

user_at_ubuntu1:~/tmp/vmd-1.8.7$ ls -la /home/user/lib/vmd/scripts/vmd/
total 152
drwxr-xr-x 3 user user 4096 2009-07-14 11:34 .
drwxr-xr-x 8 user user 4096 2009-08-27 21:22 ..
-rw-r--r-- 1 user user 4387 2007-01-12 14:11 atomselect.tcl
-rwxr-xr-x 1 user user 4267 2008-07-16 12:42 atomselmacros.dat
-rw-r--r-- 1 user user 3397 2009-06-23 15:53 biocore.tcl
-rwxr-xr-x 1 user user 4193 2000-07-03 12:30 chemical2vmd
-rwxr-xr-x 1 user user 3590 2006-09-12 03:02 colordefs.dat
drwxr-xr-x 2 user user 4096 2009-07-14 11:34 CVS
-rw-r--r-- 1 user user 1473 2007-01-12 14:11 draw.tcl
-rw-r--r-- 1 user user 4524 2007-01-12 14:11 graphlabels.tcl
-rw-r--r-- 1 user user 5205 2007-09-18 17:47 hotkeys.tcl
-rw-r--r-- 1 user user 10676 2009-07-14 11:34 loadplugins.tcl
-rw-r--r-- 1 user user 2547 2007-01-12 14:11 logfile.tcl
-rwxr-xr-x 1 user user 1203 2009-05-27 16:35 materials.dat
-rw-r--r-- 1 user user 5363 2007-01-12 14:11 openURL.tcl
-rw-r--r-- 1 user user 3637 2000-07-03 12:30 README.chemical2vmd
-rwxr-xr-x 1 user user 752 2005-07-27 19:27 restypes.dat
-rw-r--r-- 1 user user 17963 2009-05-15 23:58 save_state.tcl
-rw-r--r-- 1 user user 1213 2004-09-24 17:21 tclIndex
-rw-r--r-- 1 user user 10140 2008-05-12 11:17 vectors.tcl
-rw-r--r-- 1 user user 11485 2009-01-28 13:18 vmdinit.tcl
-rw-r--r-- 1 user user 2909 2007-01-12 14:11 www.tcl

re: ls -la and aliases....
I must have made a mistake in typing...puzzling because it was just a
cut and paste job, anyway here are the permissions of that directory

vmd > ls -la [file join $env(VMDDIR) plugins noarch tcl ]
total 308
drwxr-xr-x 77 user user 4096 2009-08-27 19:25 .
drwxr-xr-x 3 user user 4096 2009-08-27 19:25 ..
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 apbsrun1.3
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 atomedit1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 autoimd1.6
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 autoionize1.2
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 bignum1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 biocore1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 blast1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 cgtools1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 cliptool1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 clonerep1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 colorscalebar1.2
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 contactmap1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 dataimport1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 demomaster1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 dipwatch1.2
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 dowser1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 exectool1.2
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 extendedpdb1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 gofrgui1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 hbonds1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 idatm0.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 ilstools1.2
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 imdmenu1.0
drwxr-xr-x 3 user user 4096 2009-08-27 19:25 inorganicbuilder0.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 irspecgui1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 membrane1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 mergestructs1.0
drwxr-xr-x 3 user user 4096 2009-08-27 19:25 molefacture1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 moltoptools0.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 multimolanim1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 multiplot1.4
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 multiseq2.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 multiseqdialog1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 multitext1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 namdenergy1.2
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 namdgui1.2
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 namdplot1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 namdserver1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 nanotube1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 navfly1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 navigate1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 optimization1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 palettetool1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 paratool1.4
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 pbctools2.5
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 pdbtool1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 phylotree1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 psipred1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 qmtool1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 ramaplot1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 readcharmmpar1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 readcharmmtop1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 resptool1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 rmsd1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 rmsdtt2.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 rnaview1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 ruler1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 runante0.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 saltbr1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 seqdata1.1
drwxr-xr-x 3 user user 4096 2009-08-27 19:25 seqedit1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 solvate1.3
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 ssrestraints1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 stingtool1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 symmetrytool1.2
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 timeline2.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 topotools1.0
drwxr-xr-x 3 user user 4096 2009-08-27 19:25 trunctraj1.5
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 utilities1.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 vdna2.0
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 viewmaster2.2
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 vmdmovie1.7
drwxr-xr-x 3 user user 4096 2009-08-27 19:25 vmdtkcon1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 volmapgui1.1
drwxr-xr-x 2 user user 4096 2009-08-27 19:25 zoomseq1.1

Cheers,
--Jim

John Stone wrote:
> Jim,
> Can you check the permissions on the files $env(VMDDIR)/.vmdrc
> and all the startup scripts in $env(VMDDIR)/scripts/vmd/
>
> I'm puzzled why the "ls -al" you did below did not list the
> file permissions? Do you have "ls" aliased in your shell?
> When I do it, I see the file permissions...
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Wed, Sep 16, 2009 at 10:53:24PM -0500, Jim Parker wrote:
>
>> John,
>> Thanks for the prompt reply. In answer to your questions
>> I cut and paste directly from the console to here...
>>
>>
>> vmd > package require solvate
>> 1.3
>>
>> vmd > ls -al [file join $env(VMDDIR) plugins noarch tcl ]
>> /home/user/lib/vmd/plugins/noarch/tcl:
>> ./ ../ apbsrun1.3/
>> atomedit1.0/ autoimd1.6/ autoionize1.2/
>> bignum1.0/ biocore1.1/ blast1.1/
>> cgtools1.0/ cliptool1.0/ clonerep1.1/
>> colorscalebar1.2/ contactmap1.1/ dataimport1.0/
>> demomaster1.0/ dipwatch1.2/ dowser1.0/
>> exectool1.2/ extendedpdb1.0/ gofrgui1.1/
>> hbonds1.1/ idatm0.1/ ilstools1.2/
>> imdmenu1.0/ inorganicbuilder0.1/ irspecgui1.1/
>> membrane1.0/ mergestructs1.0/ molefacture1.1/
>> moltoptools0.1/ multimolanim1.0/ multiplot1.4/
>> multiseq2.1/ multiseqdialog1.1/ multitext1.0/
>> namdenergy1.2/ namdgui1.2/ namdplot1.0/
>> namdserver1.1/ nanotube1.0/ navfly1.0/
>> navigate1.0/ optimization1.0/ palettetool1.0/
>> paratool1.4/ pbctools2.5/ pdbtool1.0/
>> phylotree1.1/ psipred1.1/ qmtool1.1/
>> ramaplot1.1/ readcharmmpar1.1/ readcharmmtop1.0/
>> resptool1.1/ rmsd1.0/ rmsdtt2.0/
>> rnaview1.0/ ruler1.0/ runante0.1/
>> saltbr1.0/ seqdata1.1/ seqedit1.1/
>> solvate1.3/ ssrestraints1.0/ stingtool1.0/
>> symmetrytool1.2/ timeline2.0/ topotools1.0/
>> trunctraj1.5/ utilities1.0/ vdna2.0/
>> viewmaster2.2/ vmdmovie1.7/ vmdtkcon1.1/
>> volmapgui1.1/ zoomseq1.1/
>> vmd >
>>
>>
>> Also, in order to begin work on the tutorials I was able to kludge
>> together the commands to force VMD to give me a TkConsole by manually
>> entering the script listed in plugins/tcl/vmdtkcon1.1/vmdtkcon.tcl. The
>> TkConsole appears to work normally once I got it to start.
>>
>> Cheers,
>> --Jim
>>
>> John Stone wrote:
>>
>>> Jim,
>>> What happens if you run this command from the VMD text console?:
>>> package require solvate
>>>
>>> And this:
>>> ls -al [file join $env(VMDDIR) plugins noarch tcl ]
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Wed, Sep 16, 2009 at 09:44:31PM -0500, Jim Parker wrote:
>>>
>>>
>>>> Hello,
>>>> I recently installed both VMD and NAMD on an Ubuntu 8.10 32-bit system
>>>>
>>> >from binaries. Both programs work fine separately. However, I would
>>>
>>>> like to use the VMD GUI extensions menu to interface between VMD and
>>>> NAMD, but when I select "Extensions" the menu is blank.
>>>>
>>>> I found a similar thread on the archives
>>>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12227.html
>>>>
>>>> but the solution provided was to ensure the plugin tree was available to
>>>> the user. My plugin tree does exist (as provided by the binary) under
>>>> directory <root-vmd-dir>/plugins and <root-vmd-dir>/plugins/noarch/tcl
>>>> lists the several directories (or upgrades from them) that are listed on
>>>> the archived message.
>>>>
>>>> I did modify the ./configure script to put my install_bin and
>>>> install_library_dir in appropriate positions, and my PATH variable lists
>>>> both directories (I wasn't sure if I needed both, but have tried with
>>>> and without the install_library_path to no avail)
>>>>
>>>> The namd2 executable directory is also in the PATH variable.
>>>>
>>>> Any help would be appreciated,
>>>>
>>>> --Jim Parker
>>>> UTSA Physics and Astronomy
>>>>
>>>>
>>>
>>>
>
>