From: Nick Palmer (tuf90798_at_temple.edu)
Date: Fri Jul 27 2018 - 10:05:31 CDT

Thank you for the replies, I have looked through your suggestions and I
think chimera is what I am looking for.

On Thu, Jul 26, 2018 at 8:33 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> VMD does have a very strong set of commands that can be used for
> structural transformations ... provided they are known before hand. If you
> want a more robust solution you will need something more than just
> "orient-ing", like some form of post-edit optimization.
>
>
>
> On Jul 27, 2018 05:50, "Dhiraj Srivastava" <dhirajks_at_gmail.com> wrote:
>
>> If you want control over the orientation of the two domains, you can try
>> using chimera or pymol. You can move one domain with respect to another
>> easily in those software. I don’t know if that functionality exists in vmd.
>>
>> Dhiraj
>>
>> Sent from my iPhone
>>
>> On Jul 26, 2018, at 4:01 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>>
>> In other words (if I understand this correctly), you have structures from
>> two domains connected by a linker protein??. I am not sure I am aware of a
>> package within vmd which does this, how ever since this sounds like a
>> typical model building problem, have you thought about considering the use
>> of modeller? E.g. here
>>
>> https://salilab.org/modeller/manual/node33.html
>>
>> The exercise will vary depending on your exact problem.
>>
>> Feel free to write back if you have further questions.
>>
>> On Jul 27, 2018 03:22, "Nick Palmer" <tuf90798_at_temple.edu> wrote:
>>
>>> Hello,
>>>
>>> I am attempting to fuse two proteins to the N and C terminus of a linker
>>> protein to run in further simulations. I know I can link them with a patch
>>> when creating a psf file, but I would like to know the best way to orient
>>> the proteins in a reasonable position before I link them.
>>>
>>> Thank you in advance!
>>>
>>> --
>>> Nicholas J. Palmer
>>>
>>

-- 
Nicholas J. Palmer