(ps -- a better list to ask such questions on is Jmol-users, not
Jmol-developers)
On Mon, Oct 10, 2011 at 11:24 AM, Robert Hanson <[email protected]> wrote:
> First, let me assure you that there are definitely ways of handling all
> this. I recommend taking a look at the documentation at
> http://chemapps.stolaf.edu/jmol/docs and looking for discussions of "atom
> expressions" and "select," "wireframe," etc.
>
> A common visualization might look like this:
>
> frame *
> select 2.1; wireframe only
>
> and pershaps:
>
> display group within(5.0, true,1.1) # the "true" indicates to check within
> all models, not just model 1.1. For Jmol 12.0 you need within(group,
> within....))
>
> Bob
>
>
> On Mon, Oct 10, 2011 at 1:40 AM, Sam Paul D. <[email protected]>wrote:
>
>> When I clicked "view all frames" both the ligand and the protein are seen
>> in the viewer. I am not able to see where the ligand is as both the protein
>> and the ligand are in stick and balls.
>> *1. Is there any possibility of viewing one frame as 'sticks and balls'
>> and the other frame as 'wireframe'?
>> 2. Can change is colours be made for the ligand alone?*
>>
>> regards,
>> Sam
>>
>>
>>
>> On Mon, Oct 10, 2011 at 11:57 AM, Sam Paul D. <[email protected]>wrote:
>>
>>> Sir,
>>> Thank a lot for your suggestions.
>>> In the Script Console I typed - load files "ligand.mol2" "protein.mol2"
>>>
>>> Now my protein.mol2 is loaded in frame2.1 and ligand.mol2 in frame1.1. I
>>> am able to view them in seperate frames.
>>> *Is there any possibility of viewing both the protein and the ligand in
>>> the same frame, which will enable me to view the ligand's docking with
>>> the protein?*
>>> thanks and regards,
>>> Sam
>>>
>>>
>>>
>>>
>>> On Fri, Oct 7, 2011 at 5:06 PM, Robert Hanson <[email protected]>wrote:
>>>
>>>> oh, ---
>>>>
>>>> load files protein.mol2 ligand.mol2
>>>> frame *
>>>> select 1.1 # protein
>>>> select 2.1 # ligand
>>>>
>>>>
>>>> On Fri, Oct 7, 2011 at 6:35 AM, Robert Hanson <[email protected]>wrote:
>>>>
>>>>> sure. But you may want to keep them as separate "frames" and just
>>>>> display both frames. This is nice, because it allows you to more easily
>>>>> select one or the other independently.
>>>>>
>>>>> load files protein.mol2 ligand.mol2
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Oct 7, 2011 at 6:32 AM, Sam Paul D. <[email protected]>wrote:
>>>>>
>>>>>> hi,
>>>>>> I have a ligand(.mol2 format) and protein(.mol2 format) file
>>>>>> seperately.
>>>>>> In Jmol, is there any possibility of viewing both the protein and the
>>>>>> ligand in the same frame?
>>>>>> thanks and regards,
>>>>>> Sam
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> All of the data generated in your IT infrastructure is seriously
>>>>>> valuable.
>>>>>> Why? It contains a definitive record of application performance,
>>>>>> security
>>>>>> threats, fraudulent activity, and more. Splunk takes this data and
>>>>>> makes
>>>>>> sense of it. IT sense. And common sense.
>>>>>> http://p.sf.net/sfu/splunk-d2dcopy2
>>>>>> _______________________________________________
>>>>>> Jmol-developers mailing list
>>>>>> [email protected]
>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Robert M. Hanson
>>>>> Professor of Chemistry
>>>>> St. Olaf College
>>>>> 1520 St. Olaf Ave.
>>>>> Northfield, MN 55057
>>>>> http://www.stolaf.edu/people/hansonr
>>>>> phone: 507-786-3107
>>>>>
>>>>>
>>>>> If nature does not answer first what we want,
>>>>> it is better to take what answer we get.
>>>>>
>>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Robert M. Hanson
>>>> Professor of Chemistry
>>>> St. Olaf College
>>>> 1520 St. Olaf Ave.
>>>> Northfield, MN 55057
>>>> http://www.stolaf.edu/people/hansonr
>>>> phone: 507-786-3107
>>>>
>>>>
>>>> If nature does not answer first what we want,
>>>> it is better to take what answer we get.
>>>>
>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> All of the data generated in your IT infrastructure is seriously
>>>> valuable.
>>>> Why? It contains a definitive record of application performance,
>>>> security
>>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>>> sense of it. IT sense. And common sense.
>>>> http://p.sf.net/sfu/splunk-d2dcopy2
>>>> _______________________________________________
>>>> Jmol-developers mailing list
>>>> [email protected]
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>
>>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2dcopy1
>>
>> _______________________________________________
>> Jmol-developers mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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