VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Feb 11 2015 - 01:38:08 CST

Hi Christopher,

yes this .vmdrc has been created using VMDPrefs from an older version of
VMD. Thanks for the instructions, I didn't have so much individual settings
so it wasn't much effort to recreate my .vmdrc. Anyway as an addition, you
might want to add a version identifier to the .vmdrc, so that future
versions of VMD can detect that "old" file and do the required conversion
automatically.

Regards

Norman Geist

> -----Original Message-----
> From: Mayne, Christopher G [mailto:cmayne2_at_illinois.edu]
> Sent: Tuesday, February 10, 2015 10:38 PM
> To: Norman Geist
> Cc: John Stone
> Subject: Re: vmd-l: BUG: vmd-1.9.2 final Representations GUI
>
> Was your .vmdrc file created by VMDPrefs, by any chance?
>
> This may be an appropriate place to note that the addition of the
> Shininess attribute to materials change the syntax of many of the
> material commands. Once John told me this, I updated VMDPrefs to use
> the new syntax. Additionally, VMDPrefs should be able to read in old
> VMDPrefs "Theme" files and write them back out with the corrected
> syntax. If your old .vmdrc file came from VMDPrefs, you should be able
> to simply load the old .vmdrc file as a theme, and then use the "Write
> settings to VMDRC" button to write an updated file back out to a
> functioning .vmdrc file.
>
> Regards,
> Christopher Mayne
>
>
> On Feb 10, 2015, at 10:30 AM, Norman Geist wrote:
>
> > Hey,
> >
> > with your data I was able to dig the problem down to the ~/.vmdrc
> which was
> > created before that material RTChrome has been introduced.
> >
> > Thanks so far
> >
> > Norman Geist
> >
> >> -----Original Message-----
> >> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> >> Sent: Tuesday, February 10, 2015 5:10 PM
> >> To: Norman Geist
> >> Cc: VMD Mailing List
> >> Subject: Re: vmd-l: BUG: vmd-1.9.2 final Representations GUI
> >>
> >> Norman,
> >> So far I have not been able to reproduce the problem you describe
> by
> >> following the steps you listed.
> >>
> >> I have a key question about your instructions below.
> >> When I follow your steps, the first new material created
> >> by the "create new" step is "material23" not "material22".
> >> This is because there are already 23 materials (indices 0 to 22)
> >> in the material list. The last one shown is "RTChrome", which is
> >> index 22.
> >>
> >> What do you get from these commands if you run them from a fresh
> >> VMD session without loading anything?:
> >> llength [material list]
> >> material list
> >>
> >> If I run these from a fresh VMD I get:
> >> vmd > llength [material list]
> >> 23
> >> vmd > material list
> >> Opaque Transparent BrushedMetal Diffuse Ghost Glass1 Glass2 Glass3
> >> Glossy HardPlastic MetallicPastel Steel Translucent Edgy EdgyShiny
> >> EdgyGlass Goodsell AOShiny AOChalky AOEdgy BlownGlass GlassBubble
> >> RTChrome
> >>
> >> Cheers,
> >> John Stone
> >> vmd_at_ks.uiuc.edu
> >>
> >> On Tue, Feb 10, 2015 at 12:01:19PM +0100, Norman Geist wrote:
> >>> Hey,
> >>>
> >>> easy procedure to reproduce:
> >>>
> >>> 1. open vmd
> >>> 2. mol new 2WXC
> >>> 3. menu material on
> >>> 4. press 3x times on "create new"
> >>> 5. menu graphics on
> >>> 6. change material to "material22" <-- It will always show
> >> "material23"
> >>>
> >>> I'm using final VMD-1.9.2, OpenSuse 13.1
> >>>
> >>> Norman Geist.
> >>>
> >>>> -----Original Message-----
> >>>> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> >>>> Sent: Monday, February 09, 2015 10:38 PM
> >>>> To: Maxim Belkin
> >>>> Cc: Norman Geist; VMD Mailing List
> >>>> Subject: Re: vmd-l: BUG: vmd-1.9.2 final Representations GUI
> >>>>
> >>>> Hi,
> >>>> I'm just catching up after being out of town last week.
> >>>> Has anyone else run into the problem that Norman has described
> >>>> with changes to the material list? We haven't seen this problem
> >>>> locally (yet), but I want to keep and eye on this as it could be
> >>>> a symptom of some memory corruption of some kind. Norman,
> >>>> if you can provide any additional details about your machine/OS
> and
> >>>> or what files you typically work with that might be useful.
> >>>> Can you cause it to malfunction even if no molecule is loaded yet?
> >>>>
> >>>> Cheers,
> >>>> John
> >>>>
> >>>> On Mon, Feb 02, 2015 at 05:39:53AM -0600, Maxim Belkin wrote:
> >>>>> Hi Norman,
> >>>>> How many materials do you have defined? I have quite a few
> >> extra
> >>>> materials
> >>>>> defined myself and havenā**t encountered any issues (yet?).
> >>>>> Maxim
> >>>>>
> >>>>> On Feb 2, 2015, at 05:30, Norman Geist
> >>>>> <[1]norman.geist_at_uni-greifswald.de> wrote:
> >>>>> Seems the issue isnā**t related to the number of materials,
> >> but
> >>>> to
> >>>>> having added/removed something in the materials list. Anyway
> >> the
> >>>> shown
> >>>>> assignment of materials to representations in the GUI is
> >> messed
> >>>> up.
> >>>>>
> >>>>> Norman Geist.
> >>>>>
> >>>>> From: [2]owner-vmd-l_at_ks.uiuc.edu [[3]mailto:owner-vmd-
> >>>> l_at_ks.uiuc.edu] On
> >>>>> Behalf Of Norman Geist
> >>>>> Sent: Monday, February 02, 2015 10:53 AM
> >>>>> To: VMD Mailing List
> >>>>> Subject: vmd-l: BUG: vmd-1.9.2 final Representations GUI
> >>>>>
> >>>>> Hey there,
> >>>>>
> >>>>> seems I encountered a bug in the representations GUI. If
> >> there
> >>>> are too
> >>>>> many materials the assigning shown in the GUI gets wrong,
> >>>> although it
> >>>>> still uses the correct material in the background.
> >> Nevertheless
> >>>> its
> >>>>> quite confusing. Deleting some of the materials made it work
> >>>> again.
> >>>>>
> >>>>> Norman Geist
> >>>>>
> >>>>> References
> >>>>>
> >>>>> Visible links
> >>>>> 1. mailto:norman.geist_at_uni-greifswald.de
> >>>>> 2. mailto:owner-vmd-l_at_ks.uiuc.edu
> >>>>> 3. mailto:owner-vmd-l_at_ks.uiuc.edu
> >>>>
> >>>> --
> >>>> NIH Center for Macromolecular Modeling and Bioinformatics
> >>>> Beckman Institute for Advanced Science and Technology
> >>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> >>>> http://www.ks.uiuc.edu/Research/vmd/
> >>>
> >>
> >> --
> >> NIH Center for Macromolecular Modeling and Bioinformatics
> >> Beckman Institute for Advanced Science and Technology
> >> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> >> http://www.ks.uiuc.edu/Research/vmd/
> >