[Chimera-users] using modeller through chimera

[Taufiq Rahman]

Dear Elaine, Many thanks for your prompt reply. I think its my PC's problem 
since I can maximize the result window but can see it otherwise. Anyway, 
many thanks for your great help.

Regards,
taufiq

On Oct 3 2012, Elaine Meng wrote:

> Hi Taufiq, As you mentioned, the models will appear automatically in the 
> Chimera main window, and there will be an additional dialog, Modeller 
> results (a list of the homology models and other information). For 
> example, the two bottom figures in the Comparative Modeling tutorial show 
> this dialog: 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>
>
> I don't understand what you are clicking... it should not be necessary to 
> click anything.
>
>More details about the Modeller results dialog:
><http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html#modellist> 
>
>Best,
>Elaine
>
>On Oct 3, 2012, at 6:16 AM, Taufiq Rahman wrote:
>
>> Dear Elaine, Many thanks for the reply. It was very helpful and I can 
>> now do it. The only fresh problem is: whenever Modeller seems to 
>> complete the job (I assume), I can't click on 'modeller results' - its 
>> there but clicking on it doesn't open up anything, whilst in the 3d 
>> space, I can see the modelled structure as well as the templates. Any 
>> advice? Regards, taufiq
>> 
>> On Oct 3 2012, Elaine Meng wrote:
>> 
>>> Hi Taufiq, It is probably disabled because you are viewing a single 
>>> sequence rather than an alignment of 2 or more sequences. In Chimera, 
>>> there are several ways to get the needed inputs for Modeller, which 
>>> include the sequence alignment and a structure to use as the template. 
>>> Some ways are outlined here:
>>> 
>>>  
>>>  
>>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>
>>> 
>>> Once you have the inputs, you can run Modeller either via web service 
>>> or via your local installation. If you haven't already, you would also 
>>> need to obtain a Modeller license key before running (even if you are 
>>> going to use the web service).
>>> 
>>> I would also recommend that you get a newer version of Chimera (at 
>>> least 1.6.2). The Modeller interface is improved in that version 
>>> compared to older versions. The sequence window menu will then include 
>>> both "Structure... Modeller (homology)" and "... Modeller 
>>> (loops/refinement)" instead of a single "...Modeller Tools" entry.
>>> 
>>> This documentation is for 1.6.2: 
>>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
>>> 
>>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer 
>>> Graphics Lab (Chimera team) and Babbitt Lab Department of 
>>> Pharmaceutical Chemistry University of California, San Francisco
>>> 
>>> On Oct 2, 2012, at 7:49 AM, Taufiq Rahman wrote:
>>> 
>>>> Hello, I want to use modeller through Chimera's interface. I have 
>>>> seen the video and read about the way to do it. My problem is my 
>>>> 'modeller tool' option in the structure menu remains disabled. I have 
>>>> installed modeller locally but don't know how to integrate it into 
>>>> chimera. any suggestion? taufiq
>>> 
>>> 
>> 
>> -- 
>> Taufiq Rahman
>> MSc(Manchester), PhD (Cantab)
>> Royal Society University Research Fellow
>> University of Cambridge
>> Cambridge
>> CB2 1PD
>> UK
>> 
>
>

-- 
Taufiq Rahman
MSc(Manchester), PhD (Cantab)
Royal Society University Research Fellow
University of Cambridge
Cambridge
CB2 1PD
UK