Re: [ccp4bb] Tyr pushed out during refinement
Hi All, there was a bug at some point that could potentially lead to this. This all should be fixed in current Phenix nightly builds: http://phenix-online.org/download/nightly_builds.cgi If not, get back to us (phenixbb or Phenix help lists or reply directly to me). Pavel On Mon, Oct 19, 2020 at 11:52 AM Boniecki, Michal wrote: > Hello, > I have a problem during refining with one of the Tyr residues. It is > constantly pushed out of the position during refinement in all 4 chains in > ASU. > I have tried to exclude it from refinement in phenix but it is refined > anyway out of the position with wrong geometry. Is there a possibility to > fix it during refinement? > The closest contact it has, is 2.4A between hydroxyl group and C=O of Pro, > but Tyr itself is inside hydrophobic cleft (Ile,Pro,Leu) > Thank You for all help. Stay safe, > Michal > > > 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/
Re: [ccp4bb] Tyr pushed out during refinement
I've seen a similar behavior when, for the Phenix.refine refinement strategy, I accidentally selected both XYZ (reciprocal-space) and XYZ (real-space) at the same time. As well as a Phe jumping out of density in one NCS copy, planarity was very poor for several sidechains (but no obvious pattern as to which ended up with poor geometry). Hope this helps, Andy Purkiss. Quoting "Philip D. Jeffrey" : As Paul observes, there's a bona fide email list for phenix, but in fact comparing REFMAC to phenix.refine might be useful to see if this really is a program bug or if it's a bug in the model. Sometimes one is better than the other. For phenix.refine: Put the Tyr in the "right" place and scour the .geo file created at the start of refinement for bad angles or bonds or bumps etc. This will tell you what the offending energy term is, if there is one. If not, try turning off the rotamer fixing aspect of phenix.refine. I've had aspects of the algorithm "anti-refine" a structure (geometry, Rwork, Rfree all got worse at once) so I tend to streamline the process and run it as: strategy=individual_sites+individual_adp+occupancies (+tls if you're using it) from the command line (since I'm a Luddite and mostly eschew the GUI). For example if it's enforcing rotamers during NCS refinement it could pull your s/chain out of density. But also try REFMAC if the problem persists. Cheers Phil Jeffrey Princeton From: CCP4 bulletin board on behalf of Paul Emsley Sent: Monday, October 19, 2020 2:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Tyr pushed out during refinement On 19/10/2020 19:52, Boniecki, Michal wrote: I have a problem during refining with one of the Tyr residues. It is constantly pushed out of the position during refinement in all 4 chains in ASU. I have tried to exclude it from refinement in phenix but it is refined anyway out of the position with wrong geometry. Is there a possibility to fix it during refinement? If this is a question about refinement in phenix, then this may not be the most useful mailing list. If this is a question about how to pin down atoms and tweak bonds and contacts in Coot or Refmac, then we can proceed. Regards, Paul. 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/ 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/
Re: [ccp4bb] Tyr pushed out during refinement
Dear Michael I would carefully check the backbone region around the tyrosine and make sure it’s correct as errors there might be the issue. Regards Christine Sent from my iPhone > On Oct 19, 2020, at 11:52 AM, Boniecki, Michal > wrote: > > > Hello, > I have a problem during refining with one of the Tyr residues. It is > constantly pushed out of the position during refinement in all 4 chains in > ASU. > I have tried to exclude it from refinement in phenix but it is refined anyway > out of the position with wrong geometry. Is there a possibility to fix it > during refinement? > The closest contact it has, is 2.4A between hydroxyl group and C=O of Pro, > but Tyr itself is inside hydrophobic cleft (Ile,Pro,Leu) > Thank You for all help. Stay safe, > Michal > > > > 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/
Re: [ccp4bb] Tyr pushed out during refinement
As Paul observes, there's a bona fide email list for phenix, but in fact comparing REFMAC to phenix.refine might be useful to see if this really is a program bug or if it's a bug in the model. Sometimes one is better than the other. For phenix.refine: Put the Tyr in the "right" place and scour the .geo file created at the start of refinement for bad angles or bonds or bumps etc. This will tell you what the offending energy term is, if there is one. If not, try turning off the rotamer fixing aspect of phenix.refine. I've had aspects of the algorithm "anti-refine" a structure (geometry, Rwork, Rfree all got worse at once) so I tend to streamline the process and run it as: strategy=individual_sites+individual_adp+occupancies (+tls if you're using it) from the command line (since I'm a Luddite and mostly eschew the GUI). For example if it's enforcing rotamers during NCS refinement it could pull your s/chain out of density. But also try REFMAC if the problem persists. Cheers Phil Jeffrey Princeton From: CCP4 bulletin board on behalf of Paul Emsley Sent: Monday, October 19, 2020 2:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Tyr pushed out during refinement On 19/10/2020 19:52, Boniecki, Michal wrote: I have a problem during refining with one of the Tyr residues. It is constantly pushed out of the position during refinement in all 4 chains in ASU. I have tried to exclude it from refinement in phenix but it is refined anyway out of the position with wrong geometry. Is there a possibility to fix it during refinement? If this is a question about refinement in phenix, then this may not be the most useful mailing list. If this is a question about how to pin down atoms and tweak bonds and contacts in Coot or Refmac, then we can proceed. Regards, Paul. 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/
Re: [ccp4bb] Tyr pushed out during refinement
You dont say what resolution your data goes to - certainly REFMAC and I guess PHENIX have restraints to prevent van der waal clashes. If there is high resolution data then these restraints can be overridden to some extent. Maybe set the occupancy of the PRO C=O to 0.0 and see where the TYR finishes up? Eleanor On Mon, 19 Oct 2020 at 19:58, Paul Emsley wrote: > > On 19/10/2020 19:52, Boniecki, Michal wrote: > > > I have a problem during refining with one of the Tyr residues. It is > constantly pushed out of the position during refinement in all 4 chains in > ASU. > I have tried to exclude it from refinement in phenix but it is refined > anyway out of the position with wrong geometry. Is there a possibility to > fix it during refinement? > > > If this is a question about refinement in phenix, then this may not be the > most useful mailing list. If this is a question about how to pin down atoms > and tweak bonds and contacts in Coot or Refmac, then we can proceed. > > > Regards, > > Paul. > > > > -- > > 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/
Re: [ccp4bb] Tyr pushed out during refinement
On 19/10/2020 19:52, Boniecki, Michal wrote: I have a problem during refining with one of the Tyr residues. It is constantly pushed out of the position during refinement in all 4 chains in ASU. I have tried to exclude it from refinement in phenix but it is refined anyway out of the position with wrong geometry. Is there a possibility to fix it during refinement? If this is a question about refinement in phenix, then this may not be the most useful mailing list. If this is a question about how to pin down atoms and tweak bonds and contacts in Coot or Refmac, then we can proceed. Regards, Paul. 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/
