VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 15 2014 - 18:06:53 CDT

On Thu, May 15, 2014 at 6:58 PM, Bokas George <bokas_at_wisc.edu> wrote:

> Dear Axel,
>
> First of all I would like to thank you very much for your quick reply.
>
> I forgot to mention that I have used also the mol default command with no
> success.
>

​yes. i suspected as much. if you load files from the command line, VMD
initiates loading of those files way before it processes .vmdrc or vmd.rc.
this inconsistency is a legacy feature and ​made sense waaaay back when it
took a relatively long time to load VMD and large files. but with today's
hardware it is just irritating since it results in inconsistent behavior of
VMD and reduced utility of customization in .vmdrc.

axel.

>
> But the after idle method work like a charm.
>
> So thank you very much for your help.
>
> Best,
> GBokas
>
>
> On May 15, 2014, at 17:30, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>
>
>
> On Thu, May 15, 2014 at 5:48 PM, Bokas George <bokas_at_wisc.edu> wrote:
>
>> Hello all,
>>
>> I am attempting to create a script in order to open multiple molecules
>> together with predefined default representations.
>>
>> I think that I am close enough but I have a small problem.
>>
>> When I am calling vmd from terminal I am using this command:
>>
>> vmd -m traj*
>>
>> So I am achieving to have about 100 different molecules imported at the
>> vmd.
>> The problem is that only the first one has the predefined representation
>> I have set at the .vmdrc file.
>>
>> In particular I have added these three lines at the .vmdrc file:
>>
>> color Display Background white
>> display projection Orthographic
>> mol modstyle 0 0 CPK 1.000000 0.300000 10.000000 10.000000
>>
>> but only the first imported molecule appear with CPK representation.
>>
>
> ​yes, because you only apply the modification to the first molecule.​
>
>
>>
>> I tried also:
>> mol all modstyle 0 0 CPK 1.0000000 0.300000000 10.000000 10.000000
>>
>
> ​no. that is not a valid syntax. please look it up in the VMD user's guide.
>
> you should be using the "mol default" sub​command to change your default
> settings, or put a little piece of script code into a "after idle" section
> that loops over all molecules and changes/adds/deletes representations as
> you want/need it.
>
> axel.
>
>
>
>>
>> If anyone can help me I would appreciate it a much.
>>
>> Thank you very much in advance,
>> GBokas
>>
>>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.