I am thinking this could be done using pdbset to apply symops and origin shifts, etc, with a bit of checking in Coot, creative chain-ID's and some trial and error? Or using Coot to apply symops and save the resulting pdb's with different chain ID's and then concatenate them into a mini-lattice? Cheers, Jon.C.
Sent from ProtonMail mobile -------- Original Message -------- On 2 Jun 2021, 15:42, Stefano Trapani wrote: > 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 >>>>> ------------------------------------- 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 >>> >>> -- >>> This message has been scanned for viruses and >>> dangerous content by [MailScanner](http://www.mailscanner.info/), 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 >> >> 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 >>>>> ------------------------------------- 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 >>> >>> -- >>> This message has been scanned for viruses and >>> dangerous content by [MailScanner](http://www.mailscanner.info/), 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 >> >> -- >> This message has been scanned for viruses and >> dangerous content by [MailScanner](http://www.mailscanner.info/), and is >> believed to be clean. > > -- > This message has been scanned for viruses and > dangerous content by [MailScanner](http://www.mailscanner.info/), 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
