Hi Boaz
Thank you. That works in Chimera (first superpose, then symmetry expand) but not in CCP4MG (independently of the order of the operations). It would be nice to have an equivalent option implemented in CCP4MG. Best regards Stefano Trapani Le 2021-06-02 16:20, Boaz Shaanan a écrit : > Hi Stefano, > Did you try first to expand a unit cell in each lattice (using its symmops) > and then superimpose two molecules from each lattice? Perhaps the expanded > lattice wil move with the moving molecule? > I don't know how to do this in ccp4mg but I think it's possible in Chimera. > > My 2p. > Cheers, > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On Jun 2, 2021 16:59, Stefano Trapani <trap...@cbs.cnrs.fr> wrote: > > Dear Stuart > > That does not work. > > "Transform coordinates" seems to move molecules, but not the crystal symmetry > elements (no update of the crystal symmetry operation matrices), so that > crystal symmetry expansion after "Transform coordinates" does not generate a > rotated/translated version of the "whole" crystal, but a new (different) > crystal packing. > > Stefano > > Le 2021-06-02 15:14, Stuart McNicholas a écrit : > > Dear Stefano, > It might be possible to do what you want in a roundabout way: > > i) Apply matrix to molecule: Molecule Icon -> Transform coordinates -> > Enter transformation > ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file. > iii) Load in the saved molecule > iv) For the new file: Molecule Icon -> Create crystal object. > > (Maybe ii) and iii) are not necessary.) > > Best wishes, > Stuart > > On Wed, 2 Jun 2021 at 13:50, Stefano Trapani <trap...@cbs.cnrs.fr> wrote: > Dear all I would like to visually compare (using some molecular graphics > software) the crystal packing of two different crystal forms of the same > protein. In order to identify the similarities/differences between the > crystal packings, I need to change the default unit cell origin and > orientation of one of the crystal forms. Is there a way, in CCP4MG or other > molecular graphics software, to apply a given rotation/translation matrix to > a "crystal object" (not to a single molecular object), so that further > expansions of the object by crystal symmetry will be consistent with the new > origin/orientation ? If yes: can the transformation be defined by a > least-squares superposition between molecules from the two crystal objects ? > Best regards -- Stefano Trapani Maître de Conférences > http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1] > ------------------------------------- Centre de Biologie Structurale (CBS) 29 > rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 ------------------------------------- Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 ------------------------------------- -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [2] -- This message has been scanned for viruses and dangerous content by MAILSCANNER [3], and is believed to be clean. ------------------------- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [2] On Jun 2, 2021 16:59, Stefano Trapani <trap...@cbs.cnrs.fr> wrote: > Dear Stuart > > That does not work. > > "Transform coordinates" seems to move molecules, but not the crystal symmetry > elements (no update of the crystal symmetry operation matrices), so that > crystal symmetry expansion after "Transform coordinates" does not generate a > rotated/translated version of the "whole" crystal, but a new (different) > crystal packing. > > Stefano > > Le 2021-06-02 15:14, Stuart McNicholas a écrit : > > Dear Stefano, > It might be possible to do what you want in a roundabout way: > > i) Apply matrix to molecule: Molecule Icon -> Transform coordinates -> > Enter transformation > ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file. > iii) Load in the saved molecule > iv) For the new file: Molecule Icon -> Create crystal object. > > (Maybe ii) and iii) are not necessary.) > > Best wishes, > Stuart > > On Wed, 2 Jun 2021 at 13:50, Stefano Trapani <trap...@cbs.cnrs.fr> wrote: > Dear all I would like to visually compare (using some molecular graphics > software) the crystal packing of two different crystal forms of the same > protein. In order to identify the similarities/differences between the > crystal packings, I need to change the default unit cell origin and > orientation of one of the crystal forms. Is there a way, in CCP4MG or other > molecular graphics software, to apply a given rotation/translation matrix to > a "crystal object" (not to a single molecular object), so that further > expansions of the object by crystal symmetry will be consistent with the new > origin/orientation ? If yes: can the transformation be defined by a > least-squares superposition between molecules from the two crystal objects ? > Best regards -- Stefano Trapani Maître de Conférences > http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1] > ------------------------------------- Centre de Biologie Structurale (CBS) 29 > rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 ------------------------------------- Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 ------------------------------------- -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [2] -- This message has been scanned for viruses and dangerous content by MAILSCANNER [3], and is believed to be clean. ------------------------- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [2] -- This message has been scanned for viruses and dangerous content by MAILSCANNER [3], and is believed to be clean. 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