VMD-L Mailing List

From: Nada Afiva (nadaafiva_at_gmail.com)
Date: Mon Apr 20 2020 - 16:38:05 CDT

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
>