VMD-L Mailing List

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Thu Jun 25 2009 - 01:48:07 CDT

>
> hi,
> did you actually do this ?!
>
>
> in the ~/.vmdrc file you will need to include these lines
>
> lappend auto_path PATH/ (this line could be included in general if
> all your vmd related packages in this PATH)
> lappend auto_path PATH/la1.0
> lappend auto_path PATH/orient
>
> where, PATH must be the actual path where your unpacked orient and la1.0
> packages are located.
>
> A sample script :
> mol load psf old.psf pdb old.pdb
> wait forAll
>
> package require Orient
> namespace import Orient::orient
>
> set sel [atomselect top all]
> set P [draw principalaxes $sel]
> set A [orient $sel [lindex $P 2] {0 1 0}]
> $sel move $A
> set P [draw principalaxes $sel]
> $sel writepdb new_orient.pdb
>
> hope it helps.
> best
> Ramya
>

>> I got the files and put them in plugin/noarch/tcl..............I added the
>> path as directed....but its not working,can you please tell me why I am
>> getting errors
>> thanx alot
>> PRASUN (ASHOKA)
>>
>>
>>
>> On Thu, Jun 25, 2009 at 9:45 AM, prasun kumar <prasun30_at_gmail.com> wrote:
>>
>>> thanx alot for the help ........I will install and let you know with
>>> regards
>>> PRASUN (ASHOKA)
>>>
>>>
>>>
>>> On Thu, Jun 25, 2009 at 9:22 AM, Ramya Gamini <ramyabhargavi_at_gmail.com>wrote:
>>>
>>>> hi Prasun,
>>>> Orient plugin may be used for this purpose. You may want to look into
>>>> this:
>>>> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/
>>>>
>>>> Ramya
>>>>
>>>> On Wed, Jun 24, 2009 at 5:39 PM, prasun kumar <prasun30_at_gmail.com>wrote:
>>>>
>>>>> Dear all
>>>>> I have a problem regarding placement of the protein.
>>>>> I want to place my protein on a particular orientation.using VMD I can
>>>>> translate and get the new coordinate,but it doesnot work when we want to
>>>>> rotate the molecule and hence save the coordinates.
>>>>>
>>>>> Is there any software for doing so.waitting for positive response
>>>>> with regards and thanx in advance
>>>>> PRASUN (ASHOKA)
>>>>>
>>>>
>>>>
>>>
>>
>