Re: [ccp4bb] A challenging MR problem
I would start with coot. As bostjan suggests - 1) choose whole chain as a fragment. 2) fit that over chain 2 and change its label to that of chain 2. (Remember to make this a a copy of your fragment..) 3) check is there any density for the missing bit? Then repeat till you have the whole thing. And then merge all the pieces. Of course your missing domain may be disordered. The twinning is suspicious. And are you sure you have the right spacegroup?. 16 copies makes me suspect there is more symmetry than you are using, fit whole chain over chain 2. On Wed, 9 Nov 2022 at 23:12, Bostjan Kobe wrote: > Superimposing that molecule on all the others? > > > > Bostjan > > > > -- > > Bostjan Kobe *FAA* > > Australian Laureate Fellow > Professor of Structural Biology > School of Chemistry and Molecular Biosciences > > and Institute for Molecular Bioscience (Division of Chemistry and > Structural Biology) and Australian Infectious Diseases Research Centre > > Cooper Road > University of Queensland > Brisbane, Queensland 4072 > Australia > Phone: +61 7 3365 2132 > Fax: +61 7 3365 4699 > E-mail: b.k...@uq.edu.au > URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe > Office: Building 76 Room 329 > Notice: If you receive this e-mail by mistake, please notify me, and do > not make any use of its contents. I do not waive any privilege, > confidentiality or copyright associated with it. Unless stated otherwise, > this e-mail represents only the views of the Sender and not the views of > The University of Queensland. > > > > > > > > *From: *CCP4 bulletin board on behalf of > Medhanjali DasGupta > *Reply to: *Medhanjali DasGupta > *Date: *Thursday, 10 November 2022 at 9:05 am > *To: *"CCP4BB@JISCMAIL.AC.UK" > *Subject: *Re: [ccp4bb] A challenging MR problem > > > > The data resolution is 2A. > > I have 16 chains in my model out of which only one of the chains has the > "missing" domain modeled. Is there a way to do MR to predict where the > missing domains will go in the rest of the chains, based on my > solved structure? > > > > Thanks for all the helpful suggestions!! > > > > M > > > > On Wed, Nov 9, 2022 at 3:11 PM Eleanor Dodson < > 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > Well you could just try the buccaneer pipeline. It would use the phases > from your solved domain and try to fit the missing sequence. What are your > twin fractions? And what is the resolution? > > Eleanor > > > > On Wed, 9 Nov 2022 at 21:06, Tim Gruene wrote: > > Dear Medhanjali DasGupta, > unless the resolution is really poor, the quickest try would be shelxe, > starting from what you already have. It might work at, say, 2.8A > resolution or better... > > Best, > Tim > > On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali > DasGupta wrote: > > > Hello! > > My protein structure has a missing domain and I am trying to figure > > out the best way to model this missing domain using the solved > > (modeled) fixed core domain? My data is also imperfectly twinned, > > with 4 twin fractions according to refmac5. > > > > Any help/ idea is appreciated! > > > > > > > > > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > -- > > Thanks, > > Medhanjali Dasgupta > > Postdoctoral Research Scientist > > Lawrence Berkeley National Laboratory > > [image: Image removed by sender.] > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] A challenging MR problem
Superimposing that molecule on all the others? Bostjan -- Bostjan Kobe FAA Australian Laureate Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Australian Infectious Diseases Research Centre Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. From: CCP4 bulletin board on behalf of Medhanjali DasGupta Reply to: Medhanjali DasGupta Date: Thursday, 10 November 2022 at 9:05 am To: "CCP4BB@JISCMAIL.AC.UK" Subject: Re: [ccp4bb] A challenging MR problem The data resolution is 2A. I have 16 chains in my model out of which only one of the chains has the "missing" domain modeled. Is there a way to do MR to predict where the missing domains will go in the rest of the chains, based on my solved structure? Thanks for all the helpful suggestions!! M On Wed, Nov 9, 2022 at 3:11 PM Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote: Well you could just try the buccaneer pipeline. It would use the phases from your solved domain and try to fit the missing sequence. What are your twin fractions? And what is the resolution? Eleanor On Wed, 9 Nov 2022 at 21:06, Tim Gruene mailto:tim.gru...@univie.ac.at>> wrote: Dear Medhanjali DasGupta, unless the resolution is really poor, the quickest try would be shelxe, starting from what you already have. It might work at, say, 2.8A resolution or better... Best, Tim On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali DasGupta mailto:medhanjalidasgu...@gmail.com>> wrote: > Hello! > My protein structure has a missing domain and I am trying to figure > out the best way to model this missing domain using the solved > (modeled) fixed core domain? My data is also imperfectly twinned, > with 4 twin fractions according to refmac5. > > Any help/ idea is appreciated! > > > -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- Thanks, Medhanjali Dasgupta Postdoctoral Research Scientist Lawrence Berkeley National Laboratory [Image removed by sender.] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] A challenging MR problem
The data resolution is 2A. I have 16 chains in my model out of which only one of the chains has the "missing" domain modeled. Is there a way to do MR to predict where the missing domains will go in the rest of the chains, based on my solved structure? Thanks for all the helpful suggestions!! M On Wed, Nov 9, 2022 at 3:11 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > Well you could just try the buccaneer pipeline. It would use the phases > from your solved domain and try to fit the missing sequence. What are your > twin fractions? And what is the resolution? > Eleanor > > On Wed, 9 Nov 2022 at 21:06, Tim Gruene wrote: > >> Dear Medhanjali DasGupta, >> unless the resolution is really poor, the quickest try would be shelxe, >> starting from what you already have. It might work at, say, 2.8A >> resolution or better... >> >> Best, >> Tim >> >> On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali >> DasGupta wrote: >> >> > Hello! >> > My protein structure has a missing domain and I am trying to figure >> > out the best way to model this missing domain using the solved >> > (modeled) fixed core domain? My data is also imperfectly twinned, >> > with 4 twin fractions according to refmac5. >> > >> > Any help/ idea is appreciated! >> > >> > >> > >> >> >> >> -- >> -- >> Tim Gruene >> Head of the Centre for X-ray Structure Analysis >> Faculty of Chemistry >> University of Vienna >> >> Phone: +43-1-4277-70202 >> >> GPG Key ID = A46BEE1A >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Thanks, Medhanjali Dasgupta Postdoctoral Research Scientist Lawrence Berkeley National Laboratory To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] A challenging MR problem
Well you could just try the buccaneer pipeline. It would use the phases from your solved domain and try to fit the missing sequence. What are your twin fractions? And what is the resolution? Eleanor On Wed, 9 Nov 2022 at 21:06, Tim Gruene wrote: > Dear Medhanjali DasGupta, > unless the resolution is really poor, the quickest try would be shelxe, > starting from what you already have. It might work at, say, 2.8A > resolution or better... > > Best, > Tim > > On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali > DasGupta wrote: > > > Hello! > > My protein structure has a missing domain and I am trying to figure > > out the best way to model this missing domain using the solved > > (modeled) fixed core domain? My data is also imperfectly twinned, > > with 4 twin fractions according to refmac5. > > > > Any help/ idea is appreciated! > > > > > > > > > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] A challenging MR problem
Dear Medhanjali DasGupta, unless the resolution is really poor, the quickest try would be shelxe, starting from what you already have. It might work at, say, 2.8A resolution or better... Best, Tim On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali DasGupta wrote: > Hello! > My protein structure has a missing domain and I am trying to figure > out the best way to model this missing domain using the solved > (modeled) fixed core domain? My data is also imperfectly twinned, > with 4 twin fractions according to refmac5. > > Any help/ idea is appreciated! > > > -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ pgpYL0tqPBypu.pgp Description: OpenPGP digital signature
