VMD-L Mailing List

From: Bokas George (bokas_at_wisc.edu)
Date: Thu May 15 2014 - 18:31:47 CDT

Thank you very much ones again Axel and Josh.

I thought about it also but I didn’t know how to bypass it.

In that manner your help was vital.

Best,
GBokas

Georgios Bokas
University of Wisconsin-Madison
gbokas_at_cae.wisc.edu
gbokas_at_cc.uoi.gr

On May 15, 2014, at 17:58, 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.
>
> 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.
>