Re: [ccp4bb] Racemic crystallography and structure solving problem
Sorry, I meant to write "note that not all achiral space groups are centrosymmetric", since most are. However, even as written it's true, but less obvious... Harry -- Dr Harry Powell > On 7 Mar 2019, at 10:23, CCP4BB wrote: > > Hi all > > A genuine question; I'm wondering how well Phaser (or other MR programs) > deals with achiral space groups and the presence of both hands of a molecule > (just because you can have both hands of a chiral molecule related > crystallographically in a crystal, you don't need a centrosymmetric space > group - note that not all achiral space groups are not centrosymmetric...). > > Harry > -- > Dr Harry Powell > >> On 7 Mar 2019, at 10:11, Prasun Kumar wrote: >> >> Hi Tim: >> >> Thanx for your response and sorry for late acknowledgment . >> You are right, the peptide is forming an oligomer. I have used Xia2 and >> pipeline 3dii with small_molecule=true option as suggested earlier by >> Pierre. Now the space group is P-1. >> I will check for SHELXT. >> So far the molecular replacement is a problem for me. However, I am on it. >> >> Regards >> Prasun >> From: Tim Gruene >> Sent: 05 March 2019 10:02:53 >> To: Prasun Kumar >> Cc: CCP4BB@jiscmail.ac.uk >> Subject: Re: [ccp4bb] Racemic crystallography and structure solving problem >> >> Dear Prasun, >> >> in case you get atomic resolution (better than about 1.2A), you should be >> able >> to solve the structure with direct methods, e.g. SHELXT. You may want to >> check the processing if the cell is really this big. Unless you have several >> copies in the asymmetric unit, one might expect a smaller cell for only 30 >> residues. You can also try alternative programs, like XDS - start with >> XDSGUI >> in case you are not familiar with XDS from the command line. >> >> Best, >> Tim >> >> >> On Monday, March 4, 2019 4:33:20 PM CET Prasun Kumar wrote: >> > Hi All: >> > >> > I have performed racemic crystallography and got crystals that diffracted. >> > The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) >> > gives the space group as P1 and cell dimension >> > 42.78 52.16 54.49 114.11 92.16 92.31. >> > >> > Challanges start from here: >> > >> > 1) How much I should be assured of the space group as I expect my peptides >> > to get crystallized in the same group, but by default we get the same space >> > group. 2) Is there any seperate method for processing the raw images in my >> > case. >> > >> > I used the merged .mtz file for phasing. However, I always get the warning >> > that eLLG score is low and it is difficult to fit a single copy of the >> > ensemble. CC1/2 and I/SigI are in acceptable range. Completeness is also >> > more than 95%. >> > >> > My peptides, 30 residues long, form an oligomer. However, I do not have >> > reliable model of oligomers to start with. I have taken a single helix of >> > length 24, 12 and 6 residues to phase, but no luck so far. Any guidelines >> > will be really helpful. >> > >> > I am happy to provide any other relevant information, if one wants. >> > >> > Thanx in advance >> > Prasun >> > >> > >> > >> > To unsubscribe from the CCP4BB list, click the following link: >> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> >> -- >> -- >> Tim Gruene >> GPG Key ID = A46BEE1A >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Racemic crystallography and structure solving problem
Hi all A genuine question; I'm wondering how well Phaser (or other MR programs) deals with achiral space groups and the presence of both hands of a molecule (just because you can have both hands of a chiral molecule related crystallographically in a crystal, you don't need a centrosymmetric space group - note that not all achiral space groups are not centrosymmetric...). Harry -- Dr Harry Powell > On 7 Mar 2019, at 10:11, Prasun Kumar wrote: > > Hi Tim: > > Thanx for your response and sorry for late acknowledgment . > You are right, the peptide is forming an oligomer. I have used Xia2 and > pipeline 3dii with small_molecule=true option as suggested earlier by Pierre. > Now the space group is P-1. > I will check for SHELXT. > So far the molecular replacement is a problem for me. However, I am on it. > > Regards > Prasun > From: Tim Gruene > Sent: 05 March 2019 10:02:53 > To: Prasun Kumar > Cc: CCP4BB@jiscmail.ac.uk > Subject: Re: [ccp4bb] Racemic crystallography and structure solving problem > > Dear Prasun, > > in case you get atomic resolution (better than about 1.2A), you should be > able > to solve the structure with direct methods, e.g. SHELXT. You may want to > check the processing if the cell is really this big. Unless you have several > copies in the asymmetric unit, one might expect a smaller cell for only 30 > residues. You can also try alternative programs, like XDS - start with XDSGUI > in case you are not familiar with XDS from the command line. > > Best, > Tim > > > On Monday, March 4, 2019 4:33:20 PM CET Prasun Kumar wrote: > > Hi All: > > > > I have performed racemic crystallography and got crystals that diffracted. > > The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) > > gives the space group as P1 and cell dimension > > 42.78 52.16 54.49 114.11 92.16 92.31. > > > > Challanges start from here: > > > > 1) How much I should be assured of the space group as I expect my peptides > > to get crystallized in the same group, but by default we get the same space > > group. 2) Is there any seperate method for processing the raw images in my > > case. > > > > I used the merged .mtz file for phasing. However, I always get the warning > > that eLLG score is low and it is difficult to fit a single copy of the > > ensemble. CC1/2 and I/SigI are in acceptable range. Completeness is also > > more than 95%. > > > > My peptides, 30 residues long, form an oligomer. However, I do not have > > reliable model of oligomers to start with. I have taken a single helix of > > length 24, 12 and 6 residues to phase, but no luck so far. Any guidelines > > will be really helpful. > > > > I am happy to provide any other relevant information, if one wants. > > > > Thanx in advance > > Prasun > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > -- > -- > Tim Gruene > GPG Key ID = A46BEE1A > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Racemic crystallography and structure solving problem
Hi Tim: Thanx for your response and sorry for late acknowledgment . You are right, the peptide is forming an oligomer. I have used Xia2 and pipeline 3dii with small_molecule=true option as suggested earlier by Pierre. Now the space group is P-1. I will check for SHELXT. So far the molecular replacement is a problem for me. However, I am on it. Regards Prasun From: Tim Gruene Sent: 05 March 2019 10:02:53 To: Prasun Kumar Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Racemic crystallography and structure solving problem Dear Prasun, in case you get atomic resolution (better than about 1.2A), you should be able to solve the structure with direct methods, e.g. SHELXT. You may want to check the processing if the cell is really this big. Unless you have several copies in the asymmetric unit, one might expect a smaller cell for only 30 residues. You can also try alternative programs, like XDS - start with XDSGUI in case you are not familiar with XDS from the command line. Best, Tim On Monday, March 4, 2019 4:33:20 PM CET Prasun Kumar wrote: > Hi All: > > I have performed racemic crystallography and got crystals that diffracted. > The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) > gives the space group as P1 and cell dimension > 42.78 52.16 54.49 114.11 92.16 92.31. > > Challanges start from here: > > 1) How much I should be assured of the space group as I expect my peptides > to get crystallized in the same group, but by default we get the same space > group. 2) Is there any seperate method for processing the raw images in my > case. > > I used the merged .mtz file for phasing. However, I always get the warning > that eLLG score is low and it is difficult to fit a single copy of the > ensemble. CC1/2 and I/SigI are in acceptable range. Completeness is also > more than 95%. > > My peptides, 30 residues long, form an oligomer. However, I do not have > reliable model of oligomers to start with. I have taken a single helix of > length 24, 12 and 6 residues to phase, but no luck so far. Any guidelines > will be really helpful. > > I am happy to provide any other relevant information, if one wants. > > Thanx in advance > Prasun > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- -- Tim Gruene GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Racemic crystallography and structure solving problem
Thank You Pierre! I will have a look and let you know. Regards Prasun From: LEGRAND Pierre Sent: 04 March 2019 16:33:56 To: Prasun Kumar; CCP4BB@JISCMAIL.AC.UK Subject: RE:[ccp4bb] Racemic crystallography and structure solving problem Hi Prasum, In such case, with xia2 you could try to add the option: small_molecule=true. This will enable the consideration of centrosymmetric spacegourps. Or you can try in pointless the options: CHIRALITY NONCHIRAL or CENTROSYMMETRIC Your spacegroup could be P-1 (#2). Good luck, Pierre De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Prasun Kumar [prasun.ku...@bristol.ac.uk] Envoyé : lundi 4 mars 2019 16:33 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Racemic crystallography and structure solving problem Hi All: I have performed racemic crystallography and got crystals that diffracted. The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) gives the space group as P1 and cell dimension 42.78 52.16 54.49 114.11 92.16 92.31. Challanges start from here: 1) How much I should be assured of the space group as I expect my peptides to get crystallized in the same group, but by default we get the same space group. 2) Is there any seperate method for processing the raw images in my case. I used the merged .mtz file for phasing. However, I always get the warning that eLLG score is low and it is difficult to fit a single copy of the ensemble. CC1/2 and I/SigI are in acceptable range. Completeness is also more than 95%. My peptides, 30 residues long, form an oligomer. However, I do not have reliable model of oligomers to start with. I have taken a single helix of length 24, 12 and 6 residues to phase, but no luck so far. Any guidelines will be really helpful. I am happy to provide any other relevant information, if one wants. Thanx in advance Prasun To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Racemic crystallography and structure solving problem
Hi Prasum, In such case, with xia2 you could try to add the option: small_molecule=true. This will enable the consideration of centrosymmetric spacegourps. Or you can try in pointless the options: CHIRALITY NONCHIRAL or CENTROSYMMETRIC Your spacegroup could be P-1 (#2). Good luck, Pierre De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Prasun Kumar [prasun.ku...@bristol.ac.uk] Envoyé : lundi 4 mars 2019 16:33 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Racemic crystallography and structure solving problem Hi All: I have performed racemic crystallography and got crystals that diffracted. The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) gives the space group as P1 and cell dimension 42.78 52.16 54.49 114.11 92.16 92.31. Challanges start from here: 1) How much I should be assured of the space group as I expect my peptides to get crystallized in the same group, but by default we get the same space group. 2) Is there any seperate method for processing the raw images in my case. I used the merged .mtz file for phasing. However, I always get the warning that eLLG score is low and it is difficult to fit a single copy of the ensemble. CC1/2 and I/SigI are in acceptable range. Completeness is also more than 95%. My peptides, 30 residues long, form an oligomer. However, I do not have reliable model of oligomers to start with. I have taken a single helix of length 24, 12 and 6 residues to phase, but no luck so far. Any guidelines will be really helpful. I am happy to provide any other relevant information, if one wants. Thanx in advance Prasun To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Racemic crystallography and structure solving problem
Hi All: I have performed racemic crystallography and got crystals that diffracted. The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) gives the space group as P1 and cell dimension 42.78 52.16 54.49 114.11 92.16 92.31. Challanges start from here: 1) How much I should be assured of the space group as I expect my peptides to get crystallized in the same group, but by default we get the same space group. 2) Is there any seperate method for processing the raw images in my case. I used the merged .mtz file for phasing. However, I always get the warning that eLLG score is low and it is difficult to fit a single copy of the ensemble. CC1/2 and I/SigI are in acceptable range. Completeness is also more than 95%. My peptides, 30 residues long, form an oligomer. However, I do not have reliable model of oligomers to start with. I have taken a single helix of length 24, 12 and 6 residues to phase, but no luck so far. Any guidelines will be really helpful. I am happy to provide any other relevant information, if one wants. Thanx in advance Prasun To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
