VMD-L Mailing List

From: Nada Afiva (nadaafiva_at_gmail.com)
Date: Mon Apr 20 2020 - 17:36:38 CDT

Okay, Thank so much, Sir,
Your help is much appreciated.

best regards,
Nadaafiva

Pada tanggal Sel, 21 Apr 2020 pukul 05.16 Ashar Malik <asharjm_at_gmail.com>
menulis:

> 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
>>>
>>