Re: [ccp4bb] [phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density
Thanks for the advice Pavel! I don't want to celebrate prematurely, but I just re-ran the same refinement in both the stable and in nightly 4070, and it _seems_ to be corrected in the nightly. Will let you know if it pops up again. - Igor Petrik, PhD On Thu, Dec 3, 2020 at 9:16 AM Pavel Afonine wrote: > Hi Igor, > > please make sure to try the same refinement using the latest Phenix > version from nightly builds first: > > http://phenix-online.org/download/nightly_builds.cgi > > The latest I see here is 1.19rc7-4070. > > Chances are the version you used had a bug that we fixed by now. > > If the problem persists please go ahead and send me inputs and indicate > residues that are bad and I will investigate right away! > > Pavel > > On 12/3/20 08:42, Igor Petrik wrote: > > Thanks Nigel, > > I will put together the input and output file from my latest refinement > and send them to you and Pavel later today. > > - Igor Petrik, PhD > > > On Wed, Dec 2, 2020 at 9:46 PM Folmer Fredslund wrote: > >> Dear Igor >> >> There's a phenix bulletin board for question like this, which is where >> you should post the question. ( I crosspost here) >> >> >> I would choose to not do the real space refinement in phenix.refine >> during the last rounds of refinement of a model, when sidechain positions >> are essentially correct. >> >> >> I hope this helps >> >> Folmer >> >> >> >> tor. 3. dec. 2020 05.48 skrev Igor Petrik : >> >>> I am refining a 1.71A X-ray structure with phenix refine. I have >>> everything modelled in - ~150 residues in the ASU and a heme - and my >>> R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out >>> that two of my sidechains have distorted geometries. One is a His, and >>> looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct >>> geometry, but the actual coordinates that phenix refine produce don't lie >>> in that density; there are significant difference map peaks showing that >>> the coordinates are in the wrong place. If I use real space refine in Coot >>> to put the coordinates back into the correct density and refine it again in >>> phenix, they get distorted again. >>> >>> What settings in phenix should I check to try to get it to properly >>> refine the coordinates? >>> >>> Thanks, >>> - Igor Petrik, PhD >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >>> >> > ___ > phenixbb mailing > listphenixbb@phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-le...@phenix-online.org > > > 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] Phenix refine distorting a sidechain despite correct density
Thanks Nigel, I will put together the input and output file from my latest refinement and send them to you and Pavel later today. - Igor Petrik, PhD On Wed, Dec 2, 2020 at 9:46 PM Folmer Fredslund wrote: > Dear Igor > > There's a phenix bulletin board for question like this, which is where you > should post the question. ( I crosspost here) > > > I would choose to not do the real space refinement in phenix.refine during > the last rounds of refinement of a model, when sidechain positions are > essentially correct. > > > I hope this helps > > Folmer > > > > tor. 3. dec. 2020 05.48 skrev Igor Petrik : > >> I am refining a 1.71A X-ray structure with phenix refine. I have >> everything modelled in - ~150 residues in the ASU and a heme - and my >> R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out >> that two of my sidechains have distorted geometries. One is a His, and >> looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct >> geometry, but the actual coordinates that phenix refine produce don't lie >> in that density; there are significant difference map peaks showing that >> the coordinates are in the wrong place. If I use real space refine in Coot >> to put the coordinates back into the correct density and refine it again in >> phenix, they get distorted again. >> >> What settings in phenix should I check to try to get it to properly >> refine the coordinates? >> >> Thanks, >> - Igor Petrik, PhD >> >> -- >> >> 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] Phenix refine distorting a sidechain despite correct density
Hi Folmer, I would choose to not do the real space refinement in phenix.refine during > the last rounds of refinement of a model, when sidechain positions are > essentially correct. > by design it is supposed to place and fit side chains as good as possible, satisfying both map fit and geometry criteria (such as rotameric states and NCIs). If it does not perform up to your expectations it is best to report this to us and I will make sure the issue is taken care of immediately. I wonder if you wouldn't mind explaining your choice and if possible argue it with specific examples (preferable all done off mailing list as this gets way too narrow and specific!). -Thanks! Pavel 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] Phenix refine distorting a sidechain despite correct density
Dear Igor There's a phenix bulletin board for question like this, which is where you should post the question. ( I crosspost here) I would choose to not do the real space refinement in phenix.refine during the last rounds of refinement of a model, when sidechain positions are essentially correct. I hope this helps Folmer tor. 3. dec. 2020 05.48 skrev Igor Petrik : > I am refining a 1.71A X-ray structure with phenix refine. I have > everything modelled in - ~150 residues in the ASU and a heme - and my > R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out > that two of my sidechains have distorted geometries. One is a His, and > looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct > geometry, but the actual coordinates that phenix refine produce don't lie > in that density; there are significant difference map peaks showing that > the coordinates are in the wrong place. If I use real space refine in Coot > to put the coordinates back into the correct density and refine it again in > phenix, they get distorted again. > > What settings in phenix should I check to try to get it to properly refine > the coordinates? > > Thanks, > - Igor Petrik, PhD > > -- > > 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] Phenix refine distorting a sidechain despite correct density
Igor There is a Phenix BB for your Phenix related questions. You can subscribe here. http://www.phenix-online.org/mailman/listinfo/phenixbb In the meantime, please send the Phenix version and OS to myself and Pavel privately and I'm sure we can help. We may also need the inputs (privately, of course) so please forward them also, if possible. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Dec 2, 2020 at 8:48 PM Igor Petrik wrote: > I am refining a 1.71A X-ray structure with phenix refine. I have > everything modelled in - ~150 residues in the ASU and a heme - and my > R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out > that two of my sidechains have distorted geometries. One is a His, and > looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct > geometry, but the actual coordinates that phenix refine produce don't lie > in that density; there are significant difference map peaks showing that > the coordinates are in the wrong place. If I use real space refine in Coot > to put the coordinates back into the correct density and refine it again in > phenix, they get distorted again. > > What settings in phenix should I check to try to get it to properly refine > the coordinates? > > Thanks, > - Igor Petrik, PhD > > -- > > 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/
[ccp4bb] Phenix refine distorting a sidechain despite correct density
I am refining a 1.71A X-ray structure with phenix refine. I have everything modelled in - ~150 residues in the ASU and a heme - and my R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out that two of my sidechains have distorted geometries. One is a His, and looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct geometry, but the actual coordinates that phenix refine produce don't lie in that density; there are significant difference map peaks showing that the coordinates are in the wrong place. If I use real space refine in Coot to put the coordinates back into the correct density and refine it again in phenix, they get distorted again. What settings in phenix should I check to try to get it to properly refine the coordinates? Thanks, - Igor Petrik, PhD 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/
