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
------------------------------------------------------------------------------
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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