Re: [ccp4bb] point group...321
Look at CCP4 v7.0 Program Documentation reindexing Yes PG 321 has two indexing options.. - *i.e.* reindex (h,k,l) to (k,h,-l) which is equivalent here to reindexing (h,k,l) to (-h,-k,l). On 29 March 2018 at 21:26, Gihan Ketawala wrote: > Hi, > Can the point group 321 show indexing ambiguities? if not since I'm > dealing with non-anomalous dataset can I use 3m1 instead? > > Thank you, > Best, > Gihan >
Re: [ccp4bb] point group...321
Yes, several, but it's only important when merging multiple data sets. And it's not really ambiguities but alternatives. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004 + The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gihan Ketawala Sent: Thursday, March 29, 2018 4:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] point group...321 Hi, Can the point group 321 show indexing ambiguities? if not since I'm dealing with non-anomalous dataset can I use 3m1 instead? Thank you, Best, Gihan
[ccp4bb] point group...321
Hi, Can the point group 321 show indexing ambiguities? if not since I'm dealing with non-anomalous dataset can I use 3m1 instead? Thank you, Best, Gihan
Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Point group
You do know even that if the pointgroup is P422 the the SPACEgroup can by P 4 2 2 or P 41 21 2 or P43 21 2 or P41 22 or .. Lots of possibilities! Eleanor Although you R factors look good.. On 22 May 2015 at 08:13, wrote: > So both space groups most likely describe the same crystal packing. In > this case I would choose the highest symmetry which still gives good > refinement results. > > > > Best, Herman > > > > > > > > *Von:* dhaval patel [mailto:pateldhaval...@gmail.com] > *Gesendet:* Freitag, 22. Mai 2015 09:09 > *An:* Schreuder, Herman R&D/DE > *Cc:* ccp4bb > *Betreff:* Re: [ccp4bb] AW: [ccp4bb] Point group > > > > Dear Herman > > > > Thanks for reply. My molecule is generally found to be tetramer. In > P212121 space group cell content analysis shows 4molecules in asymmetric > unit and in P4212 it shows two molecules in asymmetric unit. > > > Dhaval Patel > > PhD Student, > > Bioinformatics & > > Structural Biology > Indian Institute of > > Advanced Research > +91-9925450504 > > > > On Fri, May 22, 2015 at 12:31 PM, wrote: > > Dear Dhaval, > > > > In principle, it does not matter how you describe the packing of the > molecules in your crystal. E.g. you can refine a P212121 structure in space > group P212121 with one molecule in the asymmetric unit, or in P1 with 4 > molecules in the asymmetric unit. In the latter case, these 4 molecules are > related by non-crystallografic symmetry operators, which are identical to > the crystallographic symmetry operators in P212121 (provided of course, > that the same origin was choosen in both cases.). > > > > So if your molecule is a tetramer with an internal 4-fold axis, the > crystal packing could be described in P4212 with one molecule in the > asymmetric unit, or in P212121 with 2 molecules in the asymmetric unit. In > the latter description, the 4-fold axis is non-crystallographic. (I did not > check though, how this works out with 2-fold versus 21 axes). > > > > In general, if there is no reason to assume lower symmetry, e.g. too high > Rfactors during refinement, one generally chooses the highest symmetry, > since there is no reason to assume that the molecules are different. > However, if there are clear differences during refinement in the different > space groups, one chooses the space group which yields the lowest Rfactors. > Beware that in lower symmetry, Rfactors might be somewhat lower, just > because the refinement program has more parameters to fiddle with. This is, > in my eyes, not significant. > > > > Best, > > Herman > > > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *dhaval patel > *Gesendet:* Freitag, 22. Mai 2015 06:21 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* Re: [ccp4bb] Point group > > > > Even I have the same problem my crystals get processed in to P212121 as > well as P4212 and I am currently analysing the data but not able to > conclude the space group. Any idea? Both structure while refining is giving > around same R/Rfree. Any help will be appreciable. > > >Dhaval Patel > > PhD Student, > > Bioinformatics & > > Structural Biology > Indian Institute of > > Advanced Research > +91-9925450504 > > > > On Thu, May 21, 2015 at 10:57 PM, frazao wrote: > > On 05/21/2015 05:23 PM, Keller, Jacob wrote: > > I can process my 3.8 A dataset in either P4 or P422 point groups. > > Do the scaling statistics look similar for both? If so, go with P422. > Trying to enforce an incorrect symmetry operator would blow up your stats. > > ...But in the case of twinning, lower space groups can masquerade as > higher ones. I say try out P4 with twin refinement, see how your stats go. > > JPK > > Or eventually even to further lower symmetry... I had once an example of > true P21212 crystals that processed nicely as P4212, due to a twinning > two-fold axis parallel to the a,b diagonal > > Carlos > > -- > ** > Dr. Carlos Frazao > Structural Biology Laboratory - > Macromolecular Crystallography Unit > ITQB-UNL, Av Republica, Apartado 127 > 2781-901 Oeiras, Portugal > > Phone: (351)-214469666/609 > FAX:(351)-214433644 > e-mail: fra...@itqb.unl.pt > www.itqb.unl.pt > > > > >
[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Point group
So both space groups most likely describe the same crystal packing. In this case I would choose the highest symmetry which still gives good refinement results. Best, Herman Von: dhaval patel [mailto:pateldhaval...@gmail.com] Gesendet: Freitag, 22. Mai 2015 09:09 An: Schreuder, Herman R&D/DE Cc: ccp4bb Betreff: Re: [ccp4bb] AW: [ccp4bb] Point group Dear Herman Thanks for reply. My molecule is generally found to be tetramer. In P212121 space group cell content analysis shows 4molecules in asymmetric unit and in P4212 it shows two molecules in asymmetric unit. Dhaval Patel PhD Student, Bioinformatics & Structural Biology Indian Institute of Advanced Research +91-9925450504 On Fri, May 22, 2015 at 12:31 PM, mailto:herman.schreu...@sanofi.com>> wrote: Dear Dhaval, In principle, it does not matter how you describe the packing of the molecules in your crystal. E.g. you can refine a P212121 structure in space group P212121 with one molecule in the asymmetric unit, or in P1 with 4 molecules in the asymmetric unit. In the latter case, these 4 molecules are related by non-crystallografic symmetry operators, which are identical to the crystallographic symmetry operators in P212121 (provided of course, that the same origin was choosen in both cases.). So if your molecule is a tetramer with an internal 4-fold axis, the crystal packing could be described in P4212 with one molecule in the asymmetric unit, or in P212121 with 2 molecules in the asymmetric unit. In the latter description, the 4-fold axis is non-crystallographic. (I did not check though, how this works out with 2-fold versus 21 axes). In general, if there is no reason to assume lower symmetry, e.g. too high Rfactors during refinement, one generally chooses the highest symmetry, since there is no reason to assume that the molecules are different. However, if there are clear differences during refinement in the different space groups, one chooses the space group which yields the lowest Rfactors. Beware that in lower symmetry, Rfactors might be somewhat lower, just because the refinement program has more parameters to fiddle with. This is, in my eyes, not significant. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von dhaval patel Gesendet: Freitag, 22. Mai 2015 06:21 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: Re: [ccp4bb] Point group Even I have the same problem my crystals get processed in to P212121 as well as P4212 and I am currently analysing the data but not able to conclude the space group. Any idea? Both structure while refining is giving around same R/Rfree. Any help will be appreciable. Dhaval Patel PhD Student, Bioinformatics & Structural Biology Indian Institute of Advanced Research +91-9925450504 On Thu, May 21, 2015 at 10:57 PM, frazao mailto:fra...@itqb.unl.pt>> wrote: On 05/21/2015 05:23 PM, Keller, Jacob wrote: I can process my 3.8 A dataset in either P4 or P422 point groups. Do the scaling statistics look similar for both? If so, go with P422. Trying to enforce an incorrect symmetry operator would blow up your stats. ...But in the case of twinning, lower space groups can masquerade as higher ones. I say try out P4 with twin refinement, see how your stats go. JPK Or eventually even to further lower symmetry... I had once an example of true P21212 crystals that processed nicely as P4212, due to a twinning two-fold axis parallel to the a,b diagonal Carlos -- ** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666/609 FAX:(351)-214433644 e-mail: fra...@itqb.unl.pt<mailto:fra...@itqb.unl.pt> www.itqb.unl.pt<http://www.itqb.unl.pt>
Re: [ccp4bb] AW: [ccp4bb] Point group
Dear Herman Thanks for reply. My molecule is generally found to be tetramer. In P212121 space group cell content analysis shows 4molecules in asymmetric unit and in P4212 it shows two molecules in asymmetric unit. Dhaval Patel PhD Student, Bioinformatics & Structural Biology Indian Institute of Advanced Research +91-9925450504 On Fri, May 22, 2015 at 12:31 PM, wrote: > Dear Dhaval, > > > > In principle, it does not matter how you describe the packing of the > molecules in your crystal. E.g. you can refine a P212121 structure in space > group P212121 with one molecule in the asymmetric unit, or in P1 with 4 > molecules in the asymmetric unit. In the latter case, these 4 molecules are > related by non-crystallografic symmetry operators, which are identical to > the crystallographic symmetry operators in P212121 (provided of course, > that the same origin was choosen in both cases.). > > > > So if your molecule is a tetramer with an internal 4-fold axis, the > crystal packing could be described in P4212 with one molecule in the > asymmetric unit, or in P212121 with 2 molecules in the asymmetric unit. In > the latter description, the 4-fold axis is non-crystallographic. (I did not > check though, how this works out with 2-fold versus 21 axes). > > > > In general, if there is no reason to assume lower symmetry, e.g. too high > Rfactors during refinement, one generally chooses the highest symmetry, > since there is no reason to assume that the molecules are different. > However, if there are clear differences during refinement in the different > space groups, one chooses the space group which yields the lowest Rfactors. > Beware that in lower symmetry, Rfactors might be somewhat lower, just > because the refinement program has more parameters to fiddle with. This is, > in my eyes, not significant. > > > > Best, > > Herman > > > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *dhaval patel > *Gesendet:* Freitag, 22. Mai 2015 06:21 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* Re: [ccp4bb] Point group > > > > Even I have the same problem my crystals get processed in to P212121 as > well as P4212 and I am currently analysing the data but not able to > conclude the space group. Any idea? Both structure while refining is giving > around same R/Rfree. Any help will be appreciable. > > > Dhaval Patel > > PhD Student, > > Bioinformatics & > > Structural Biology > Indian Institute of > > Advanced Research > +91-9925450504 > > > > On Thu, May 21, 2015 at 10:57 PM, frazao wrote: > > On 05/21/2015 05:23 PM, Keller, Jacob wrote: > > I can process my 3.8 A dataset in either P4 or P422 point groups. > > Do the scaling statistics look similar for both? If so, go with P422. > Trying to enforce an incorrect symmetry operator would blow up your stats. > > ...But in the case of twinning, lower space groups can masquerade as > higher ones. I say try out P4 with twin refinement, see how your stats go. > > JPK > > Or eventually even to further lower symmetry... I had once an example of > true P21212 crystals that processed nicely as P4212, due to a twinning > two-fold axis parallel to the a,b diagonal > > Carlos > > -- > ** > Dr. Carlos Frazao > Structural Biology Laboratory - > Macromolecular Crystallography Unit > ITQB-UNL, Av Republica, Apartado 127 > 2781-901 Oeiras, Portugal > > Phone: (351)-214469666/609 > FAX:(351)-214433644 > e-mail: fra...@itqb.unl.pt > www.itqb.unl.pt > > >
[ccp4bb] AW: [ccp4bb] Point group
Dear Dhaval, In principle, it does not matter how you describe the packing of the molecules in your crystal. E.g. you can refine a P212121 structure in space group P212121 with one molecule in the asymmetric unit, or in P1 with 4 molecules in the asymmetric unit. In the latter case, these 4 molecules are related by non-crystallografic symmetry operators, which are identical to the crystallographic symmetry operators in P212121 (provided of course, that the same origin was choosen in both cases.). So if your molecule is a tetramer with an internal 4-fold axis, the crystal packing could be described in P4212 with one molecule in the asymmetric unit, or in P212121 with 2 molecules in the asymmetric unit. In the latter description, the 4-fold axis is non-crystallographic. (I did not check though, how this works out with 2-fold versus 21 axes). In general, if there is no reason to assume lower symmetry, e.g. too high Rfactors during refinement, one generally chooses the highest symmetry, since there is no reason to assume that the molecules are different. However, if there are clear differences during refinement in the different space groups, one chooses the space group which yields the lowest Rfactors. Beware that in lower symmetry, Rfactors might be somewhat lower, just because the refinement program has more parameters to fiddle with. This is, in my eyes, not significant. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von dhaval patel Gesendet: Freitag, 22. Mai 2015 06:21 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Point group Even I have the same problem my crystals get processed in to P212121 as well as P4212 and I am currently analysing the data but not able to conclude the space group. Any idea? Both structure while refining is giving around same R/Rfree. Any help will be appreciable. Dhaval Patel PhD Student, Bioinformatics & Structural Biology Indian Institute of Advanced Research +91-9925450504 On Thu, May 21, 2015 at 10:57 PM, frazao mailto:fra...@itqb.unl.pt>> wrote: On 05/21/2015 05:23 PM, Keller, Jacob wrote: I can process my 3.8 A dataset in either P4 or P422 point groups. Do the scaling statistics look similar for both? If so, go with P422. Trying to enforce an incorrect symmetry operator would blow up your stats. ...But in the case of twinning, lower space groups can masquerade as higher ones. I say try out P4 with twin refinement, see how your stats go. JPK Or eventually even to further lower symmetry... I had once an example of true P21212 crystals that processed nicely as P4212, due to a twinning two-fold axis parallel to the a,b diagonal Carlos -- ** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666/609 FAX:(351)-214433644 e-mail: fra...@itqb.unl.pt<mailto:fra...@itqb.unl.pt> www.itqb.unl.pt<http://www.itqb.unl.pt>
Re: [ccp4bb] Point group
Dear Mohamed You can get the equivalent of frame.CBF by using the duals image viewer with datablock or experiments.json and integrated.pickle. this will allow you to step through the frames looking at the actual integration boxes. Best wishes Graeme On 21 May 2015 17:02, "Mohamed Noor" wrote: > Dear all > > I can process my 3.8 A dataset in either P4 or P422 point groups. MR > searches and refinement in SG P41 and P41212 results in R/Rfree of around > 30/35 % with 8 and 4 NCS copies, respectively. Pointless doesn't seem to > complain but Xtriage suggests 25 % twinning in the former (refinement was > done without twin law) and that the true point group could be P422. So do I > go with P422? > > Secondly, where can I find the DIALS equivalent to XDS FRAME.cbf? The > statistics are slightly better but I prefer to confirm it visually. I > recently had a case of pseudosymmetry which makes me suspicious of > automated processing suggestions. > > Thanks. >
Re: [ccp4bb] Point group
Even I have the same problem my crystals get processed in to P212121 as well as P4212 and I am currently analysing the data but not able to conclude the space group. Any idea? Both structure while refining is giving around same R/Rfree. Any help will be appreciable. Dhaval Patel PhD Student, Bioinformatics & Structural Biology Indian Institute of Advanced Research +91-9925450504 On Thu, May 21, 2015 at 10:57 PM, frazao wrote: > On 05/21/2015 05:23 PM, Keller, Jacob wrote: > >> I can process my 3.8 A dataset in either P4 or P422 point groups. >>> Do the scaling statistics look similar for both? If so, go with P422. >>> Trying to enforce an incorrect symmetry operator would blow up your >>> stats. >>> >> ...But in the case of twinning, lower space groups can masquerade as >> higher ones. I say try out P4 with twin refinement, see how your stats go. >> >> JPK >> > Or eventually even to further lower symmetry... I had once an example of > true P21212 crystals that processed nicely as P4212, due to a twinning > two-fold axis parallel to the a,b diagonal > > Carlos > > -- > ** > Dr. Carlos Frazao > Structural Biology Laboratory - > Macromolecular Crystallography Unit > ITQB-UNL, Av Republica, Apartado 127 > 2781-901 Oeiras, Portugal > > Phone: (351)-214469666/609 > FAX:(351)-214433644 > e-mail: fra...@itqb.unl.pt > www.itqb.unl.pt >
Re: [ccp4bb] Point group
On 05/21/2015 05:23 PM, Keller, Jacob wrote: I can process my 3.8 A dataset in either P4 or P422 point groups. Do the scaling statistics look similar for both? If so, go with P422. Trying to enforce an incorrect symmetry operator would blow up your stats. ...But in the case of twinning, lower space groups can masquerade as higher ones. I say try out P4 with twin refinement, see how your stats go. JPK Or eventually even to further lower symmetry... I had once an example of true P21212 crystals that processed nicely as P4212, due to a twinning two-fold axis parallel to the a,b diagonal Carlos -- ** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666/609 FAX:(351)-214433644 e-mail: fra...@itqb.unl.pt www.itqb.unl.pt
Re: [ccp4bb] Point group
>> I can process my 3.8 A dataset in either P4 or P422 point groups. >Do the scaling statistics look similar for both? If so, go with P422. >Trying to enforce an incorrect symmetry operator would blow up your stats. ...But in the case of twinning, lower space groups can masquerade as higher ones. I say try out P4 with twin refinement, see how your stats go. JPK -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Point group
On 05/21/15 11:56, Mohamed Noor wrote: Dear all I can process my 3.8 A dataset in either P4 or P422 point groups. Do the scaling statistics look similar for both? If so, go with P422. Trying to enforce an incorrect symmetry operator would blow up your stats. MR searches and refinement in SG P41 and P41212 results in R/Rfree of around 30/35 % with 8 and 4 NCS copies, respectively. Pointless doesn't seem to complain but Xtriage suggests 25 % twinning in the former (refinement was done without twin law) and that the true point group could be P422. So do I go with P422? Secondly, where can I find the DIALS equivalent to XDS FRAME.cbf? The statistics are slightly better but I prefer to confirm it visually. I recently had a case of pseudosymmetry which makes me suspicious of automated processing suggestions. Thanks. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] Point group
Dear all I can process my 3.8 A dataset in either P4 or P422 point groups. MR searches and refinement in SG P41 and P41212 results in R/Rfree of around 30/35 % with 8 and 4 NCS copies, respectively. Pointless doesn't seem to complain but Xtriage suggests 25 % twinning in the former (refinement was done without twin law) and that the true point group could be P422. So do I go with P422? Secondly, where can I find the DIALS equivalent to XDS FRAME.cbf? The statistics are slightly better but I prefer to confirm it visually. I recently had a case of pseudosymmetry which makes me suspicious of automated processing suggestions. Thanks.
