Hi, Monika,
It sounds like you got the two domains separately in the asymmetric unit.
You could do the symmetric operation for one of the domains in pymol by generating the symmetric mates (say 10 Å).
Then you should see several same ones there. Select the one you need, and save the coordinates, then you can combine this to the other domain.
Cheers,
Shu
-------------------------------------------
Shu Xu, Ph.D.
Research Fellow
Department of Biochemistry
Vanderbilt University School of Medicine
Tel: (615)-343-7327
E-mail: [log in to unmask]
On Feb 19, 2014, at 4:40 AM, [log in to unmask] wrote:
> Another option would be the "merge molecules" option in coot (calculate -> merge molecules). In coot you would also be able to move the molecules to the same asymmetric unit if that would be necessary. However, depending on the space group the MR solutions could have different origins and with polar space groups one (or three in P1!) coordinates may be arbitrary, prohibiting any merging efforts.
>
> The best way to go is to search for both molecules in one go. E.g. Phaser has the possibility to give two or more search models and then first search with the first model, and then with the second in the context of the solution for the first solution. I am sure other MR programs have similar options. If you wish, I could provide you with a sample command file.
>
> Best regards,
> Herman
>
> -----Ursprüngliche Nachricht-----
> Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Tim Gruene
> Gesendet: Mittwoch, 19. Februar 2014 10:25
> An: [log in to unmask]
> Betreff: Re: [ccp4bb] Symmetry problem
>
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> Dear Monika,
>
> What program did you use for MR? I would expect the output PDB file has the correct cell and symmetry from the mtz-file you replaced against.
>
> To answer your question: you can simply concatenate the two files (e.g. with a text editor), remove the CRYST1 card and set it with pdbset:
>
> pdbset xyzin your.pdb xyzout yourpdb_with_new_sg.pdb << eof CELL yourA yourB yourC yourAlpha yourBeta yourGamma SPAC yourSpacegroup end eof
>
> Best,
> Tim
>
> On 02/18/2014 06:59 PM, Monika Coronado wrote:
>> Dear,
>>
>> Does anyone know how to merge two molecules with different symmetry?
>>
>> I will explain:
>>
>> I have done the molecular replacement using the domains of the
>> molecules separately, now I have to put all together, however they
>> have a different symmetry.
>>
>> I will appreciate any kind of help.
>>
>>
>> Regards,
>>
>>
>>
>> Mnika
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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