VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Dec 25 2006 - 11:38:07 CST

Hi Matt,
Molefacture (and, for that matter, all plugins) does not yet save its
state along with th rest of the VMD save state function. It's something
we are currently working on, but it is difficult to combine the
modularity (and variety of origins) of the plugins with the machinery
necessary for a true save state. In the meantime, though, you should be
able to just save your molecule as an XBGF (using the molefacture file
menu) and load it again to restore your place, since molefacture's
internal state is almost all calculated on the fly from the molecule
being worked on.
Peter

wolfinbm_at_uci.edu wrote:
> Hello
> The problem I had was fixed; however, I am having a problem saving my
> work. I can use the "save state" function in VMD, but when I re-load it,
> nothing displays (even though the "D" button is on). Any suggestions?
>
> Thanks & Best,
> Matt Wolfinbarger
>
>
>> Hello
>> Thank You--the new version seems to work. But I've still got a long way
>> to go on building the membrane...
>>
>
>
>> Thanks & Best,
>> Matt Wolfinbarger
>>
>
>
>> Ah yes, the infamous spaces-in-filenames issue; this had been causing
>>
> problems on windows. This bug should have been fixed in the 1.8.5 plugin
> update -- did you download a fresh copy of the 1.8.5 installer? If so,
> please try the 1.8.6 alpha instead
>
>> (http://www.ks.uiuc.edu/Research/vmd/alpha/). Please let me know if you
>>
> still have problems.
>
>> Peter
>>
>> wolfinbm_at_uci.edu wrote:
>>
>>> Hello
>>>
>>>
>>>
>>>> Hi Matt,
>>>> two notes:
>>>> -which version of vmd are you using? I'm somewhat puzzled by these error
>>>>
>>>>
>>> messages...
>>>
>>>
>>>
>>>> I'm using version 1.8.5. Maybe the program, or at least the
>>>> molefacture
>>>> plugin, did not install correctly. I will try uninstalling VMD,
>>>>
>>>>
>>> download >whatever that latest version is available, and re-install.
>>>
> If that >doesn't work I'll send another message to the list and give
> more
>
>>>> specifics on the error message.
>>>>
>>>>
>>> I tried re-installing and I am still getting the error message. When I go
>>> to the menu function "Build" in molefacture, I use the menu function "new
>>> molecule from fragment." Here is the details of the error message:
>>>
>>> (BEGIN)
>>> wrong # args: should be "::Molefacture::new_mol_from_fragment fragpath"
>>>
> wrong # args: should be "::Molefacture::new_mol_from_fragment fragpath"
> while executing
>
>>> "::Molefacture::new_mol_from_fragment C:/Program Files/University of
>>>
> Illinois/VMD/plugins/noarch/tcl/molefacture1.1/lib/basemol/benzene.mfrag"
>
>>> (menu invoke)
>>> (END)
>>>
>>> Note that this applies for any fragment--benzene is just the one I
>>>
> happened to pick this time.
>
>>> Thank You,
>>> Matt
>>>
>>>
>>>
>>>
>
>
>
>