• ## Outreach

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Apr 20 2020 - 07:55:37 CDT

draw color colour_name

for example

draw color red

you can run this once at the start and then all lines will be drawn in Red,
or if you want all lines in different colour -- you can keep
changing before you draw every line.

On Mon, Apr 20, 2020 at 8:31 PM Nada Afiva <nadaafiva_at_gmail.com> wrote:

> Thanks so much, Sir,
> It really helps me a lot.
> Using your guidance, the cubic box is now displayed.
> Another question, how to change the line colors.
> Thank you.
>
> Best regards,
>
> Pada tanggal Sen, 20 Apr 2020 pukul 16.35 Ashar Malik <asharjm_at_gmail.com>
>
>> 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 .
>>> 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,
>>>
>>>
>>> Pada tanggal Sen, 20 Apr 2020 pukul 08.31 Ashar Malik <asharjm_at_gmail.com>
>>>
>>>> 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.
>>>>>
>>>>>
>>>>>
>>>>> Pada tanggal Sen, 20 Apr 2020 pukul 06.00 Ashar Malik <
>>>>>
>>>>>> 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.
>>>>>>>
>>>>>>>
>>>>>>> Pada tanggal Sen, 20 Apr 2020 pukul 05.20 Ashar Malik <
>>>>>>>
>>>>>>>> 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.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Best,
>>>>>>>> /A
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Best,
>>>>>> /A
>>>>>>
>>>>>
>>>>
>>>> --
>>>> Best,
>>>> /A
>>>>
>>>

```--
Best,
/A
```