Just use the "rms_cur" command instead of "align".
https://pymolwiki.org/index.php/rms_cur
Cheers,
Thomas
> On Aug 28, 2017, at 10:04 AM, Johannes Sommerkamp <[log in to unmask]> wrote:
>
> Thanks a lot for your answers and the PyMOL mailing list hint. I didnt had in mind this list.
>
> I read the Pymol Wiki. The commands
> align moving, target, cycles=0, transform=0
>
> align moving, target, cycles=0
>
> give identical values for RMSD. So, the only difference is, that the moving structure is not moved in the graphical output. Additionally the RMSD with the argument cycles=0 can't be the RMSD before any movement because the values differ for the super and the align command. I think its just without refinement.
> Since the two structure I want to compare are already aligned based on the central beta sheet CA atoms, I want to calculate the RMSD without any movement.
>
>
> Regards
> Johannes
>
>
>
> On 27/08/17 19:18, Folmer Fredslund wrote:
>> Hi Johannes,
>>
>> Did you read the PymoWIKI entry on the align command?
>>
>> https://pymolwiki.org/index.php/Align#RMSD
>>
>> I think this should give you what you want within PyMOL.
>>
>> Btw, there is a nice dedicated PyMOL mailing list
>> https://pymolwiki.org/index.php/PyMOL_mailing_list
>> It is rather low traffic, but the replies are generally from the developers or very knowledgeable users.
>>
>> Hope this helps,
>> Folmer Fredslund
>>
>> On 2017-08-27 13:09, Johannes Sommerkamp wrote:
>>> Hello everybody,
>>> I have superposed two structures based on the central beta-sheet CA atoms with the "super" command in Pymol.
>>> Now, I want to calculate the RMSD between ALL atoms or ALL CA atoms without moving the structures again. The rms_cur command in Pymol would do that, but only works if all atom identifiers match. Adding "transform=0" to the super, oder align command still does the alignment and moves the structure but does not show the movement.
>>>
>>> Is there an easy way to just calculate the all atom RMSD between two already superposed structures in pymol or any other programm?
>>>
>>> Thanks in advance!
>>> Johannes
>>>
>
> --
> Johannes Sommerkamp
> Ruhr-Universität Bochum
> AG Röntgenstrukturanalyse an Proteinen, LS Biophysik, ND04/396
> Universitätsstraße 150
> 44801 Bochum
> Tel: +49-(0)234/32-25754
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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