VMD-L Mailing List

From: Nada Afiva (nadaafiva_at_gmail.com)
Date: Mon Apr 20 2020 - 03:16:57 CDT

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
>