VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Apr 20 2020 - 08:54:41 CDT

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