VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Sun Jun 03 2018 - 14:40:31 CDT

Loading a new molecule also returns the molid, so you can just do something
like 'set mymol [mol new mymol.pdb]' and 'mymol' will be the molid.

On Sun, Jun 3, 2018, 3:34 PM Rune Thomas Kidmose <rtk_at_mbg.au.dk> wrote:

> Ahh yes this could be smart little trick I was looking for.
>
>
> I knew that the latest loaded molecule becomes the top molecule, but I did
> not think of extracting whatever mol ID it is assigned, and use is as a
> variable to call later on.
>
>
> I think this might do it, and of course it was relative easy. That being
> said if anyone else has other suggestions I will be glad to hear them.
>
>
> Thx Ashar!
>
>
> Ruki
> ------------------------------
> *Fra:* Ashar Malik <asharjm_at_gmail.com>
> *Sendt:* 3. juni 2018 21:29
> *Til:* Rune Thomas Kidmose
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Emne:* Re: vmd-l: problem with mol IDs when running script from same VMD
> session.
>
> Every time a new molecule is loaded it becomes the "top" molecule.
> You can use this.
>
> if you load a molecule, you can fetch its ID using
>
> molinfo top get id
>
> you can save this number to a variable and use that in the remainder of
> your script.
>
> Hope I understood your problem and this helps. Otherwise write back.
>
> On Mon, Jun 4, 2018 at 7:02 AM, Rune Thomas Kidmose <rtk_at_mbg.au.dk> wrote:
>
>> Basically, I cant figure out how to reinitialize VMD before running the
>> same script twice or more in the same session.
>>
>>
>> My current problem is that I have a script which loads 5
>> different molecules. During the loading each molecule is then automatic
>> given a mol ID number (0-4) as is standard.
>>
>> I then use those mol IDs to set various features for specfic molecules
>> (view matrices, modstyles, modmaterials etc. so e.g. mol modcolor 0 3
>> ColorID 8 etc.). However, if I then make some changes within the tcl
>> script and I want to reload the script to see the effects of the changes,
>> I am hit with the problem that the molecules I now load get new mol ID's
>> assigned (not 0-4 but e.g. 5-9). This means that the mol id specific
>> commands are not executed on the newly loaded molecules. This is of course
>> because I run the script in the same VMD 1.93 session that I just ran the
>> script from. But even if manual delete the molecules before running the
>> script again I still face the same problem.
>>
>>
>> My current solution is to just restart VDM and run the script, which
>> works, but I cant help to wonder if there is some smart way to mitigate
>> this?
>>
>>
>> I run the scripts using the play command from the tcl consol.
>>
>>
>> In PyMol I always start my scripts with the command "reinitialize" which
>> resets everything in PyMol, does something related exist for VMD 1.93 ?
>>
>>
>> Does what I describe make sense?
>>
>>
>> Cheers
>>
>>
>> Ruki
>>
>>
>>
>>
>
>
> --
> Best,
> /A
>