In this case calculating the rmsd is easy:
- get the coordinates of each structure as n x 3 numpy arrays. The Pymol
commands for this should look like:
xyz1 = cmd.get_coords('sele1', 1)
xyz2 = cmd.get_coords('sele2', 1)
Then,
rmsd = numpy.linalg.norm(numpy.sqrt((xyz1-xyz2)**2), axis=1)
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 28 Aug 2017, at 10:04, Johannes Sommerkamp
> <0000155b9e78396e-dmarc-requ...@jiscmail.ac.uk> 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
