VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Apr 20 2020 - 04:35:30 CDT

to pass lines through 8 coordinates you need to work out what they are. For
that you will need the length or width or height (not just the centre).

For a cube - L = W = H

Your 8 coordinates can be calculated as

1) Cx - D/2 , Cy - D/2 , Cz - D/2
2) Cx - D/2 , Cy + D/2 , Cz - D/2
3) Cx + D/2 , Cy + D/2 , Cz - D/2
4) Cx + D/2 , Cy - D/2 , Cz - D/2

5) Cx - D/2 , Cy - D/2 , Cz + D/2
6) Cx - D/2 , Cy + D/2 , Cz + D/2
7) Cx + D/2 , Cy + D/2 , Cz + D/2
8) Cx + D/2 , Cy - D/2 , Cz + D/2

where Cx, Cy and Cz are the coordinates you mentioned and D = the length of
any of the cube's sides.

draw lines between 1-2, 2-3, 3-4, 4-1 --- this will give you the lower plane
draw lines between 5-6, 6-7, 7-8, 8-5 --- this will give you the upper plane
draw lines between 1-5, 2-6, 3-7, 4-8 --- and your cube is complete.

Disclaimer - I didn't test the above, so you may get weird results, just
try and play around.

On Mon, 20 Apr 2020, 4:17 PM Nada Afiva, <nadaafiva_at_gmail.com> wrote:

> Thanks so much Sir,
> I really appreciate it.
> Yes, you are right, Sir, a line is not a box .
> However, please help me with the steps to perform commands.
> What I need is to show the box, with the following center: center_x =
> 116.02, center_y = 118.37, center_z = 127.80.
> Thank you.
>
> Best regards,
> Nadaafiva
>
>
> Pada tanggal Sen, 20 Apr 2020 pukul 08.31 Ashar Malik <asharjm_at_gmail.com>
> menulis:
>
>> 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
>>
>