From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Apr 20 2020 - 17:16:33 CDT

Please read the line command explanation on the original link shared to
find out how to control width.

https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node128.html

When you render using Tachyon right below it is a box which holds the
render command. It already has a command in it. You are only supposed to
add

-red 2400 2400

within the already existing command. This means that do not remove any of
the old command and just add. It should work (I think).

On Tue, 21 Apr 2020, 5:38 AM Nada Afiva, <nadaafiva_at_gmail.com> wrote:

> Thanks so much, Sir,
> Using TARGA -res 2400 2400 -o, the picture is now rendered.
> However, I noticed in the cmd windows
>
> Info) ...
> 'TARGA' is not recognized as an internal or external command, operable
> program or batch file.
> Info) Rendering complete.
>
> Another question, is there a way to increase the line width of the box?
> Thank you.
>
> Best regards,
> Nadaafiva
>
> Pada tanggal Sen, 20 Apr 2020 pukul 20.54 Ashar Malik <asharjm_at_gmail.com>
> menulis:
>
>> No such thing as "best resolution". However, you can use tachyon and in
>> the Render Command
>>
>> between the word
>>
>> TARGA -o
>>
>> add
>>
>> -res 2400 2400
>>
>> so it looks like
>>
>> TARGA -res 2400 2400 -o
>>
>> click start rendering. After rendering, you will get a file with a .tga
>> extension. Use a graphic program for example GIMP/Photoshop to open the
>> file for editing/conversion. If you are using Linux, the default image
>> viewer should also be able to open it.
>>
>> On Mon, Apr 20, 2020 at 9:30 PM Nada Afiva <nadaafiva_at_gmail.com> wrote:
>>
>>> Dear Sir,
>>> Thank you again for helping me.
>>> Now it is time to get the best resolution picture.
>>> When using rendering, there several options such as snapshot (VMD),
>>> Tychon, POV-Ray 3.6, etc.
>>> I tried snapshot, but the picture not so good. Tychon is better.
>>> and POV-Ray, I did not have idea to open the file.
>>> Please if you have suggestions, please let me know.
>>> My aim is to have the best resolution picture.
>>> Thank you.
>>>
>>> Best regards,
>>> Nadaafiva
>>>
>>> Pada tanggal Sen, 20 Apr 2020 pukul 19.55 Ashar Malik <asharjm_at_gmail.com>
>>> menulis:
>>>
>>>> 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,
>>>>> Nadaafiva
>>>>>
>>>>> Pada tanggal Sen, 20 Apr 2020 pukul 16.35 Ashar Malik <
>>>>> asharjm_at_gmail.com> menulis:
>>>>>
>>>>>> 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
>>>>>>>>
>>>>>>>
>>>>
>>>> --
>>>> Best,
>>>> /A
>>>>
>>>
>>
>> --
>> Best,
>> /A
>>
>