Re: [ccp4bb] Symmetry problem
I thought I saw this problem before. Though I wouldn't try it if you had solutions from different space groups. http://www.phenix-online.org/documentation/find_alt_orig_sym_mate.htm F On Feb 20, 2014, at 6:09 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Monika, > > would you mind summarising how you solved your problem? It might help > people with similar problems! > > Regards, > Tim > > On 02/20/2014 02:45 PM, Monika Coronado wrote: >> Dear users, >> >> thanks alot for the tips. The problem was solved! >> >> Warmest regard, >> >> >> >> Monika Coronado >> >> >> 2014-02-20 0:57 GMT-03:00 Jens Kaiser : >> >>> Monika, There are several possible causes for the problem you >>> are encountering, but your description is a little too vague to >>> discern them. Scenario 1) You ran phaser with the option "all >>> possible spacegroups", for several different components of your >>> crystal, setup individually, and the runs do not agree on the >>> "best spacegroup"? -- In that case, phaser had problems >>> determining the correct spacegroup, I'd suggest you search for >>> all components, but in separate runs for each possible >>> spacegroup. Scenario 2) You assumed your spacegroup assignment >>> was correct, and ran MR for each of your components individually, >>> and when you display the solutions, they overlap. In this case, >>> you might have your solutions on different origins. The best way >>> out is to use the first solution as a "fixed solution", which is >>> possible in most MR programs, and then search for the next >>> component. There might be other scenarios, if you describe your >>> situation in more detail (how many components in the crystal >>> setup, what program you used, how you used it, and what you mean >>> by "different symmetries"), we might be able to help you better, >>> >>> Cheers, >>> >>> Jens >>> >>> On Tue, 2014-02-18 at 14:59 -0300, 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 -- __o _`\<,_ (*)/ (*) -+-+-+-+-+-+- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ...E tudo muda... * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * >>> >>> >>> >> >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Icedove -http://www.enigmail.net/ > > iD8DBQFTBgyvUxlJ7aRr7hoRAo2BAJ0VPGwcH9FLrLI09sBwgJL9MPOVWQCgjIy1 > HoLKpUi/ZtXoP5fOOMP/Kso= > =44Yv > -END PGP SIGNATURE-
Re: [ccp4bb] Symmetry problem
Dear Tim, I have used coot. "merge molecules" (calculate -> merge molecules). Using coot I have moved the molecules to the same asymmetric unit. I have the same problem with two different proteins in one case it works. However, for the other I am still working :-( Greetings, Mônika 2014-02-20 11:09 GMT-03:00 Tim Gruene : > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Monika, > > would you mind summarising how you solved your problem? It might help > people with similar problems! > > Regards, > Tim > > On 02/20/2014 02:45 PM, Monika Coronado wrote: > > Dear users, > > > > thanks alot for the tips. The problem was solved! > > > > Warmest regard, > > > > > > > > Monika Coronado > > > > > > 2014-02-20 0:57 GMT-03:00 Jens Kaiser : > > > >> Monika, There are several possible causes for the problem you > >> are encountering, but your description is a little too vague to > >> discern them. Scenario 1) You ran phaser with the option "all > >> possible spacegroups", for several different components of your > >> crystal, setup individually, and the runs do not agree on the > >> "best spacegroup"? -- In that case, phaser had problems > >> determining the correct spacegroup, I'd suggest you search for > >> all components, but in separate runs for each possible > >> spacegroup. Scenario 2) You assumed your spacegroup assignment > >> was correct, and ran MR for each of your components individually, > >> and when you display the solutions, they overlap. In this case, > >> you might have your solutions on different origins. The best way > >> out is to use the first solution as a "fixed solution", which is > >> possible in most MR programs, and then search for the next > >> component. There might be other scenarios, if you describe your > >> situation in more detail (how many components in the crystal > >> setup, what program you used, how you used it, and what you mean > >> by "different symmetries"), we might be able to help you better, > >> > >> Cheers, > >> > >> Jens > >> > >> On Tue, 2014-02-18 at 14:59 -0300, 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 > >>> > >>> -- __o _`\<,_ (*)/ (*) -+-+-+-+-+-+- * * * * * * * * * * * * * > >>> * * * * * * * * * * * * * * * * * * * * * * * * * * ...E tudo > >>> muda... > >>> > >>> * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > >>> * * * * * * * > >>> > >> > >> > >> > > > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Icedove - http://www.enigmail.net/ > > iD8DBQFTBgyvUxlJ7aRr7hoRAo2BAJ0VPGwcH9FLrLI09sBwgJL9MPOVWQCgjIy1 > HoLKpUi/ZtXoP5fOOMP/Kso= > =44Yv > -END PGP SIGNATURE- > -- __o _`\<,_ (*)/ (*) -+-+-+-+-+-+- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ...E tudo muda... * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Re: [ccp4bb] Symmetry problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Monika, would you mind summarising how you solved your problem? It might help people with similar problems! Regards, Tim On 02/20/2014 02:45 PM, Monika Coronado wrote: > Dear users, > > thanks alot for the tips. The problem was solved! > > Warmest regard, > > > > Monika Coronado > > > 2014-02-20 0:57 GMT-03:00 Jens Kaiser : > >> Monika, There are several possible causes for the problem you >> are encountering, but your description is a little too vague to >> discern them. Scenario 1) You ran phaser with the option "all >> possible spacegroups", for several different components of your >> crystal, setup individually, and the runs do not agree on the >> "best spacegroup"? -- In that case, phaser had problems >> determining the correct spacegroup, I'd suggest you search for >> all components, but in separate runs for each possible >> spacegroup. Scenario 2) You assumed your spacegroup assignment >> was correct, and ran MR for each of your components individually, >> and when you display the solutions, they overlap. In this case, >> you might have your solutions on different origins. The best way >> out is to use the first solution as a "fixed solution", which is >> possible in most MR programs, and then search for the next >> component. There might be other scenarios, if you describe your >> situation in more detail (how many components in the crystal >> setup, what program you used, how you used it, and what you mean >> by "different symmetries"), we might be able to help you better, >> >> Cheers, >> >> Jens >> >> On Tue, 2014-02-18 at 14:59 -0300, 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 >>> >>> -- __o _`\<,_ (*)/ (*) -+-+-+-+-+-+- * * * * * * * * * * * * * >>> * * * * * * * * * * * * * * * * * * * * * * * * * * ...E tudo >>> muda... >>> >>> * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * >>> * * * * * * * >>> >> >> >> > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTBgyvUxlJ7aRr7hoRAo2BAJ0VPGwcH9FLrLI09sBwgJL9MPOVWQCgjIy1 HoLKpUi/ZtXoP5fOOMP/Kso= =44Yv -END PGP SIGNATURE-
Re: [ccp4bb] Symmetry problem
Dear users, thanks alot for the tips. The problem was solved! Warmest regard, Monika Coronado 2014-02-20 0:57 GMT-03:00 Jens Kaiser : > Monika, > There are several possible causes for the problem you are > encountering, but your description is a little too vague to discern > them. > Scenario 1) You ran phaser with the option "all possible spacegroups", > for several different components of your crystal, setup individually, > and the runs do not agree on the "best spacegroup"? -- In that case, > phaser had problems determining the correct spacegroup, I'd suggest you > search for all components, but in separate runs for each possible > spacegroup. > Scenario 2) You assumed your spacegroup assignment was correct, and > ran MR for each of your components individually, and when you display > the solutions, they overlap. In this case, you might have your solutions > on different origins. The best way out is to use the first solution as a > "fixed solution", which is possible in most MR programs, and then search > for the next component. > There might be other scenarios, if you describe your situation in more > detail (how many components in the crystal setup, what program you used, > how you used it, and what you mean by "different symmetries"), we might > be able to help you better, > > Cheers, > > Jens > > On Tue, 2014-02-18 at 14:59 -0300, 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, > > > > > > > > > > Mônika > > > > -- > > __o > > _`\<,_ > > (*)/ (*) > > -+-+-+-+-+-+- > > * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > > * * * * > > ...E tudo muda... > > > > * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > > * * * * > > > > > -- __o _`\<,_ (*)/ (*) -+-+-+-+-+-+- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ...E tudo muda... * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Re: [ccp4bb] Symmetry problem
Monika, There are several possible causes for the problem you are encountering, but your description is a little too vague to discern them. Scenario 1) You ran phaser with the option "all possible spacegroups", for several different components of your crystal, setup individually, and the runs do not agree on the "best spacegroup"? -- In that case, phaser had problems determining the correct spacegroup, I'd suggest you search for all components, but in separate runs for each possible spacegroup. Scenario 2) You assumed your spacegroup assignment was correct, and ran MR for each of your components individually, and when you display the solutions, they overlap. In this case, you might have your solutions on different origins. The best way out is to use the first solution as a "fixed solution", which is possible in most MR programs, and then search for the next component. There might be other scenarios, if you describe your situation in more detail (how many components in the crystal setup, what program you used, how you used it, and what you mean by "different symmetries"), we might be able to help you better, Cheers, Jens On Tue, 2014-02-18 at 14:59 -0300, 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, > > > > > Mônika > > -- > __o > _`\<,_ > (*)/ (*) > -+-+-+-+-+-+- > * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > * * * * > ...E tudo muda... > > * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > * * * * >
Re: [ccp4bb] [ccp4bb] Symmetry problem
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: xushuh...@gmail.com On Feb 19, 2014, at 4:40 AM, herman.schreu...@sanofi.com 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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tim > Gruene > Gesendet: Mittwoch, 19. Februar 2014 10:25 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: Re: [ccp4bb] Symmetry problem > > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > 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 > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Icedove - http://www.enigmail.net/ > > iD8DBQFTBHhtUxlJ7aRr7hoRApb1AJ9FwxpTIbtcIlJyuU0Rn7u1UxLHrACglchR > weQEKA+/lnmIkQKtHd+nhj4= > =LgoX > -END PGP SIGNATURE-
[ccp4bb] AW: [ccp4bb] Symmetry problem
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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tim Gruene Gesendet: Mittwoch, 19. Februar 2014 10:25 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Symmetry problem -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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 GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTBHhtUxlJ7aRr7hoRApb1AJ9FwxpTIbtcIlJyuU0Rn7u1UxLHrACglchR weQEKA+/lnmIkQKtHd+nhj4= =LgoX -END PGP SIGNATURE-
Re: [ccp4bb] Symmetry problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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 GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTBHhtUxlJ7aRr7hoRApb1AJ9FwxpTIbtcIlJyuU0Rn7u1UxLHrACglchR weQEKA+/lnmIkQKtHd+nhj4= =LgoX -END PGP SIGNATURE-
[ccp4bb] Symmetry problem
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, Mônika -- __o _`\<,_ (*)/ (*) -+-+-+-+-+-+- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ...E tudo muda... * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
