Hi Rajib & Yuktimmana,

If you're using PyMOL for education (that's what I guess since you want to 
learn about molecules), then you are eligible to download a self-sustaining 
package from http://pymol.org/edu/

However, PyMOL 1.5.0.1 on Debian 7.7 works fine for me to build molecules.

Cheers,
  Thomas

PS: I'm not a professor


On 20 Apr 2015, at 15:07, Rajib/Susmita Bandopadhyay <bkpsusmi...@gmail.com> 
wrote:

> Dear Prof. Holder,
> Surprisingly, I had tried the very step you stated but failed to run the
> program!
> Our discussion leads me to a conjecture that the Debian PyMol package is
> perhaps broken.
> I will do an extensive testing and be back with information.
> Is there a self-sustaining package in your website that can run on its
> own, just like Geogebra independent package?
> Regards,
> Rajib & Yuktimmana
> 
> On 04/20/2015 06:48 PM, Thomas Holder wrote:
>> Hi Rajib & Yuktimmana,
>> 
>> start like this:
>> 
>> 1) click "CH4"
>> 2) on the right side of the window click "Create As New Object"
>> 3) now you can start replacing elements or attaching more fragments.
>> 
>> Hope that works.
>> 
>> Cheers,
>>  Thomas
>> 
>> On 19 Apr 2015, at 14:12, Rajib/Susmita Bandopadhyay <bkpsusmi...@gmail.com> 
>> wrote:
>> 
>>> Dear Professor,
>>> 
>>> We had tried. When I clicked the carbon link, it says, "select the atoms to 
>>> replace with carbon"
>>> 
>>> When I clicked on CH4 it says, "Pick locations to attach methyl".
>>> 
>>> This goes on for others as well.
>>> 
>>> That is supposed to mean I can't build a molecule from scratch! I am using 
>>> the version 1.5.0.1, available from the Debian Repository.
>>> 
>>> My UI appears as the one immediately below, while the website has the one 
>>> at the bottom.
>>> 
>>> When I click on the drop-down menu Build the program shows: Fragment, 
>>> Residue, Sculpting, etc., but not single atom or single molecule.
>>> 
>>> <Mail Attachment.png>
>>> The one below is on the website.
>>> 
>>> <Mail Attachment.png>
>>> 
>>> The first step is always the toughest one, we know. Please get us moving. 
>>> Give me some concrete steps - click, then do this, then this, ... to build 
>>> one molecule from scratch.
>>> Regards,
>>> Rajib & Yuktimmana
>>> 
>>> On 04/19/2015 07:28 PM, Thomas Holder wrote:
>>>> Hi Rajib & Yuktimmana,
>>>> 
>>>> you can interactively build molecules using the builder:
>>>> 
>>>> http://pymolwiki.org/index.php/Builder
>>>> 
>>>> 
>>>> Enjoy!
>>>> 
>>>> Cheers,
>>>>  Thomas
>>>> 
>>>> On 19 Apr 2015, at 08:03, bkpsusmitaa 
>>>> <bkpsusmi...@gmail.com>
>>>> wrote:
>>>> 
>>>>> Dear Sir / Madam,
>>>>> My daughter and I are novices in PyMol. We have only just begun! :) I
>>>>> have seen the page
>>>>> 
>>>>> http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners
>>>>> .
>>>>> Begins with a protein molecule.
>>>>> We use the PyMol package from the Debian Repository in a Knoppix system.
>>>>> How can we begin by building a simple molecule, say, methane, or
>>>>> carbon tetrachloride, or butylene?
>>>>> Eagerly awaiting your reply,
>>>>> Rajib & Yuktimmana

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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