VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sun Apr 19 2020 - 20:31:17 CDT

A line isn't a box. :D

To make a cube -- you need 12 lines, which have to be drawn between 8
points.

This means that you have to run the graphics ... command 12 times.

Try to make a cube on a piece of paper and label all its vertices. It will
help with entering coordinates in the commands.

On Mon, Apr 20, 2020 at 7:54 AM Nada Afiva <nadaafiva_at_gmail.com> wrote:

> Thank so much Sir,
> It is solved, but I do not obtain the box I mean.
> When using graphic 0 line {110 118 127} {120 130 140}, i did not show the
> box.
> Please if you have further suggestion how to make box to assign active
> site.
> Thank you.
>
> Nadaafiva
>
>
> Pada tanggal Sen, 20 Apr 2020 pukul 06.00 Ashar Malik <asharjm_at_gmail.com>
> menulis:
>
>> when you load your system into vmd, the main window will list a number
>> against the newly loaded molecule. This number is the mol id. You have to
>> use this mol id so if it is 0 (i.e. the first molecule you loaded into VMD)
>> then the command should be:
>>
>> graphics 0 point {118 120 128}
>>
>>
>>
>>
>> On Mon, Apr 20, 2020 at 6:51 AM Nada Afiva <nadaafiva_at_gmail.com> wrote:
>>
>>> Dear Sir,
>>> Thanks.
>>> But when I use command below:
>>> graphics complex.pdb point {118 120 128}
>>> it comment: expected integer but got "complex.pdb"
>>> My system name is complex.pdb.
>>> What's wrong, Sir.
>>> Thank you.
>>>
>>> Nadaafiva
>>>
>>> Pada tanggal Sen, 20 Apr 2020 pukul 05.20 Ashar Malik <asharjm_at_gmail.com>
>>> menulis:
>>>
>>>> You can draw a line using information here.
>>>>
>>>> https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node128.html
>>>>
>>>> On Mon, Apr 20, 2020 at 6:15 AM Nada Afiva <nadaafiva_at_gmail.com> wrote:
>>>>
>>>>> Dear all,
>>>>> I would like to assign the active site of my protein with lines
>>>>> forming a cubic box using VMD.
>>>>> Does anyone have a suggestion?
>>>>> Thank you.
>>>>>
>>>>> Nadaafiva
>>>>>
>>>>
>>>>
>>>> --
>>>> Best,
>>>> /A
>>>>
>>>
>>
>> --
>> Best,
>> /A
>>
> 

-- 
Best,
/A