VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 08 2009 - 14:44:06 CST

Hi,
  What happens if you do this:
package require psfgen

Do you get an error, or does that succeed?

Within your plugin builds, do you find the following compiled
shared object files?:
  vmd188a5/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so
  vmd188a5/plugins/LINUX/tcl/hesstrans1.0/hesstrans.so
  vmd188a5/plugins/LINUX/tcl/libbiokit1.1/tcl_libbiokit.so
  vmd188a5/plugins/LINUX/tcl/signalproc1.1/sgsmooth.so
  vmd188a5/plugins/LINUX/tcl/signalproc1.1/specden.so
  vmd188a5/plugins/LINUX/tcl/signalproc1.1/fftcmds.so
  vmd188a5/plugins/LINUX/tcl/autopsf1.2/psfcheck.so
  vmd188a5/plugins/LINUX/tcl/mutator1.2/libalchemify.so
  vmd188a5/plugins/LINUX/tcl/pmepot1.0/libpmepot.so
  vmd188a5/plugins/LINUX/tcl/psfgen1.4/libpsfgen.so

Also, for completeness, can you show me the top couple of
levels of the directory structure of your VMD installation?
I would expect to see something that looks almost exactly like this:

johns_at_casablanca.ks.uiuc.edu{335} ls vmd188a5
Announcement LICENSE scripts surf_LINUX vmd_LINUX
doc plugins shaders tachyon_LINUX
libcudart.so.2 README stride_LINUX vmd_completion.dat

johns_at_casablanca.ks.uiuc.edu{336} ls vmd188a5/plugins/
include LINUX noarch

johns_at_casablanca.ks.uiuc.edu{337} ls vmd188a5/plugins/noarch/tcl
apbsrun1.3 hbonds1.1 namdserver1.1 runante0.1
atomedit1.0 idatm0.1 nanotube1.0 saltbr1.0
autoimd1.6 ilstools1.2 navfly1.0 seqdata1.1
autoionize1.2 ilstools1.3 navigate1.0 seqedit1.1
bignum1.0 imdmenu1.0 optimization1.0 solvate1.3
biocore1.1 inorganicbuilder0.1 palettetool1.0 ssrestraints1.0
blast1.1 irspecgui1.1 paratool1.4 stingtool1.0
cgtools1.0 mdff0.2 pbctools2.5 symmetrytool1.2
cliptool1.0 membrane1.0 pdbtool1.0 symmetrytool1.3
clonerep1.1 mergestructs1.0 phylotree1.1 timeline2.0
colorscalebar1.2 molefacture1.1 psipred1.1 topotools1.0
colorscalebar1.3 moltoptools0.1 qmtool1.1 topotools1.1
contactmap1.1 multimolanim1.0 ramaplot1.1 trunctraj1.5
dataimport1.0 multiplot1.4 readcharmmpar1.1 utilities1.0
demomaster1.0 multiseq2.1 readcharmmtop1.0 vdna2.0
dipwatch1.2 multiseqdialog1.1 resptool1.1 viewmaster2.2
dowser1.0 multitext1.0 rmsd1.0 vmdmovie1.7
exectool1.2 namdenergy1.2 rmsdtt2.0 vmdtkcon1.1
extendedpdb1.0 namdgui1.2 rnaview1.0 volmapgui1.1
gofrgui1.1 namdplot1.0 ruler1.0 zoomseq1.1

On Tue, Dec 08, 2009 at 09:22:23PM +0100, Tru Huynh wrote:
> On Mon, Dec 07, 2009 at 02:43:51PM -0600, John Stone wrote:
> >
> > Hi,
> > Do you have the plugins correctly installed with the binary that
> > you compiled? Those errors make it look like they are not correctly
> > located in the installation directory.
>
> It's possible but I can't figure out what is missing compared to the
> binary distribution :(
>
> For instance:
> "> > The irspecgui package could not be loaded:"
>
> If I compare the irspecgui1.1 in my rebuild tree and yours:
>
> [tru_at_liberte 1.8.7]$ pwd
> /c5/shared/vmd/local/1.8.7
> [tru_at_liberte 1.8.7]$ du -sh ./plugins/noarch/tcl/irspecgui1.1 /c5/shared/vmd/vmd-1.8.7/plugins/noarch/tcl/irspecgui1.1
> 25K ./plugins/noarch/tcl/irspecgui1.1
> 25K /c5/shared/vmd/vmd-1.8.7/plugins/noarch/tcl/irspecgui1.1
>
> [tru_at_liberte 1.8.7]$ diff -uNr ./plugins/noarch/tcl/irspecgui1.1 /c5/shared/vmd/vmd-1.8.7/plugins/noarch/tcl/irspecgui1.1
> <- nothing returns
>
> Am I missing something obvious?
>
> Cheers,
>
> Tru
> --
> Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/
> mailto:tru_at_pasteur.fr | tel/fax +33 1 45 68 87 37/19
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France 

-- 
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