- phenixbb - phenix-online.org

B-factors
by Hermella Woldemdihin 05 Aug '10

05 Aug '10

Hi All! Where can I set B-factor for water in phenix.refine on the GUI version of phenix? Thanks!

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r-work and r-free for specific resolution range(s)
by Kay Diederichs 04 Aug '10

04 Aug '10

Hi, is there a way to get the R-factor statistics from phenix.refine, for a specific resolution range, e.g. 2.5-2.6A ? The reason I ask is that I would like to specify the same resolution range as the data reduction program does. I tried with phenix.reflection_statistics x_map_coeffs.mtz x_data.mtz --low-resolution=2.6 --resolution=2.5 but with the default settings, phenix.refine writes 2FOFCWT and FOFCWT, but not FC . So it looks like I have to re-run phenix.refine and make it write out FC? Or is it easier to run phenix.xmanip for that purpose? thanks, Kay

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MR with 1000+ aa chain
by Meghan Miller 04 Aug '10

04 Aug '10

Hello, I am trying to run AutoMR using a chain that is 1014 amino acids. The output pdb starts back at 0 once it reaches 1000. Is this a bug, or user error? Thanks, Meghan

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Re: [phenixbb] r-work and r-free for specific resolution range(s)
by Kay Diederichs 04 Aug '10

04 Aug '10

> Date: Wed, 4 Aug 2010 10:37:45 -0700 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] r-work and r-free for specific resolution > range(s) > Message-ID: > <AANLkTindW12Anq8iJVq-rh5LWiUyj4rZ52M3iyoy=7j8(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Wed, Aug 4, 2010 at 10:22 AM, Kay Diederichs< > kay.diederichs(a)uni-konstanz.de> wrote: > >> is there a way to get the R-factor statistics from phenix.refine, for a >> specific resolution range, e.g. 2.5-2.6A ? The reason I ask is that I would >> like to specify the same resolution range as the data reduction program >> does. >> > > phenix.refine will print R-factors by resolution shell, but the number of > shells it decides to use varies with the number of reflections - for a > really small structure (e.g. amyloid peptide) you will have only one > resolution shell (the argument being that R-free statistics aren't reliable > if you have very few reflections in the test set). You can set an upper > limit on this (refinement.main.max_number_of_resolution_bins), but it won't > give you ten shells if phenix.refine wants to use, say, five. There may be > another way to get this information that I'm not aware of, but I've always > done it directly in Python. > > I've been working on a project that potentially requires changing > phenix.model_vs_data to report these statistics; my plan was to use the last > of ten shells, since both HKL2000 and SCALA report everything that way > (don't know about XDS since I haven't used it). Is this sensible, or does > it need to be more flexible and accept explicit resolution ranges? (I'm not > actually sure whether this is possible right now, but 10 shells is easy.) > > -Nat Hi Nat, in fact this is a small protein, and phenix.refine only outputs a single resolution shell. phenix.model_vs_data currently does not give R-factors; it would be worthwhile to enhance this, and to have it accept shell limits. XDS has 9 shells whose limits are calculated internally, and one overall. For XSCALE, one can specify up to 20 RESOLUTION_SHELLS . In the meantime, I resort to sftools <<EOF read x_f_model.mtz Y select col R_FREE_FLAGS=0 correl col FOBS FMODEL resolution 2.6 2.5 shells 1 select all select col R_FREE_FLAGS=1 correl col FOBS FMODEL resolution 2.6 2.5 shells 1 stop y where x_f_model was written by phenix.refine . thanks, Kay

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Re: [phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold! (Pavel Afonine)
by Joseph Noel 04 Aug '10

04 Aug '10

Thanks Pavel! I will wait and see what Ralf says regarding defining the symmetry operator. If I am using the GUI for phenix.refine should I create a new file with the bond definition you mention and include it as one of the starting files or should I edit the Refine_*.eff file that gets created and insert it somewhere there? ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________ On Aug 4, 2010, at 10:22 AM, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: DTT mediated disulfide crosslink across a > crystallographic two-fold! (Joseph Noel) > 2. Re: high average b-factor vs. Wilson B (Gino Cingolani) > 3. Re: high average b-factor vs. Wilson B (Frank von Delft) > 4. Re: DTT mediated disulfide crosslink across a > crystallographic two-fold! (Pavel Afonine) > 5. Re: high average b-factor vs. Wilson B (Pavel Afonine) > 6. r-work and r-free for specific resolution range(s) > (Kay Diederichs) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 4 Aug 2010 04:53:25 -0700 > From: Joseph Noel <noel(a)salk.edu> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] DTT mediated disulfide crosslink across a > crystallographic two-fold! > Message-ID: <91F9FC5E-00E4-454C-AB99-2DD353BDC4A5(a)salk.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Ralf and Pavel, > > Unfortunately, Phenix didn't recognize a disulfide bond should exist between the sulfur atoms of DTT and the side chain sulfur atom of the cysteine residue in question. I position everything well in the Fo-Fc and 2Fo-Fc maps and ensured the two sulfurs were approximately 2.1 A apart. However, after refinement the DTT molecule moved so the two sulfurs in question where nearly 3 A away. Maybe this is because it is a mixed disulfide between a DTT molecule and a side-chain Cys rather then what most programs expect which is a disulfide between two Cys residues. Is it possible I need to define the complete chemical entity as a hetatm (the disulfide linked Cys residue? Is there a way to specify that a covalent bond should exist between the SG atom of the Cys in question and the S atoms of DTT with DTT lying across the crystallographic two-fold given its internal 2-fold symmetry? > > Joe > ___________________________________________________________ > Joseph P. Noel, Ph.D. > Investigator, Howard Hughes Medical Institute > Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics > The Salk Institute for Biological Studies > 10010 North Torrey Pines Road > La Jolla, CA 92037 USA > > Phone: (858) 453-4100 extension 1442 > Cell: (858) 349-4700 > Fax: (858) 597-0855 > E-mail: noel(a)salk.edu > > Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 > Web Site (HHMI): http://hhmi.org/research/investigators/noel.html > ___________________________________________________________ > >

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04 Aug '10

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Re: [phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold!
by Joseph Noel 04 Aug '10

04 Aug '10

Hi Ralf and Pavel, Unfortunately, Phenix didn't recognize a disulfide bond should exist between the sulfur atoms of DTT and the side chain sulfur atom of the cysteine residue in question. I position everything well in the Fo-Fc and 2Fo-Fc maps and ensured the two sulfurs were approximately 2.1 A apart. However, after refinement the DTT molecule moved so the two sulfurs in question where nearly 3 A away. Maybe this is because it is a mixed disulfide between a DTT molecule and a side-chain Cys rather then what most programs expect which is a disulfide between two Cys residues. Is it possible I need to define the complete chemical entity as a hetatm (the disulfide linked Cys residue? Is there a way to specify that a covalent bond should exist between the SG atom of the Cys in question and the S atoms of DTT with DTT lying across the crystallographic two-fold given its internal 2-fold symmetry? Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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DTT mediated disulfide crosslink across a crystallographic two-fold!
by Joseph Noel 03 Aug '10

03 Aug '10

Hi Phenix Users, I have found a beautifully ordered DTT molecule stretching across a crystallographic two-fold and linking two symmetry related cysteine side chains. Since part of this molecule sits on across the two-fold (special position) I will specify the occupancy as 0.5. I am hoping to get some information on how easy (or how difficult) it is to specify this arrangement in Phenix for refinement since it is covalent and sitting across a crystallographic two-fold (and presumably stabilizing the lattice). Will ReadySet build the appropriate CIF file if I build the DTT into the density and give it a 0.5 occupancy? Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Re: [phenixbb] Adequate size for Free R test set?
by Joseph Noel 03 Aug '10

03 Aug '10

Pavel, Thanks so much for the suggestions. They are really helpful! A few questions relative to Phenix. Is there a way to check with Phenix the thin resolution shells? I created Free Rs in Phenix using the thin resolution shells options but removed the 2000 limit and instead used 5%. Maybe I over-did it relative to your reply. Just wondering how to check each of these thin shells. Alternatively, does Phenix ensure one has an adequate number of test reflections in each "thin shell" if this option is set? If so, what should I used for the maximum number of reflections and/or %? Thanks again! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________ On Aug 3, 2010, at 11:02 AM, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: Adequate size for Free R test set? (Pavel Afonine) > 2. Re: follow up on message 2: phenix.maps --Message: not > implemented (amadrona(a)uci.edu) > 3. Re: follow up on message 2: phenix.maps --Message: not > implemented (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 03 Aug 2010 10:38:57 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: phenixbb(a)phenix-online.org > Cc: Joseph Noel <noel(a)salk.edu> > Subject: Re: [phenixbb] Adequate size for Free R test set? > Message-ID: <4C585431.7000107(a)lbl.gov> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Joe, > > I think almost every one has his/her own opinion on this... Here is what > I think: > > 1) The test set should be such that each "relatively thin resolution > shell" receives at least 50 reflections, and we empirically found that > 150 is "good enough" withing phenix.refine framework. > For "relatively thin resolution shell" definition see: > Lunin & Skovoroda. Acta Cryst. (1995). A51, 880-887. "R-free > likelihood-based estimates of errors for phases calculated from atomic > models". > > This basically defines how many test reflections you need. > > 2) It is customary to set aside either 5 or 10% for test set, with the > total maximum 2000. These are all "magic numbers", that I presume more > or less satisfy "1)" so they became widely used. > > 3) Presence of high-order NCS and selecting free-flags using "thin > shells" algorithm is a different story (Acta Cryst. (2006). D62, > 227--238). It is good to do that because it removes the cross-talk > between test and work reflections due to NCS, but at the same time it > invalidates the requirement "1)". So, this is a gray area (for me at least). > > 4) Some people believe that the final refinement run should be done > using all reflections, arguing that taking away 5-10% of test > reflections worsens the maps. There is some truth in this, yes, removing > the data worsens the maps, but: > a) it is noticeable (in a sense that it can reduce the interpretability > of some parts of the map) only in extreme cases of somewhat low > resolution or low completeness data, b) in most of all other cases it is > simply negligible, c) removing reflections randomly has much smaller > effect than removing them systematically (see page #40 here: > http://www.phenix-online.org/presentations/latest/pavel_maps.pdf and > some relevant references in 2010 PHENIX paper in Acta D). However, if > you do that "final run", you will invalidate the final refinement > statistics, Rfree and Rwork, and thus obtained final structure cannot > have the Rfree associated with it anymore. > > Pavel. > > > On 8/3/10 10:04 AM, Joseph Noel wrote: >> Hi Folks, >> >> Its been a while since I personally refined many structures. In the >> past, I used as a default, 5% of my unique reflections for the Free R >> test set. I have a high resolution structure with 150,000 unique >> reflections and noticed that Phenix defaults are 5% or 2000 >> reflections which ever is smaller. What is the current consensus on an >> adequate number of unique reflections to use for cross-validation? >> >> Thanks! >> Joe >> >> P.S. I really, really love Phenix. >> ___________________________________________________________ >> Joseph P. Noel, Ph.D. >> Investigator, Howard Hughes Medical Institute >> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics >> The Salk Institute for Biological Studies >> 10010 North Torrey Pines Road >> La Jolla, CA 92037 USA >> >> Phone: (858) 453-4100 extension 1442 >> Cell: (858) 349-4700 >> Fax: (858) 597-0855 >> E-mail: noel(a)salk.edu <mailto:[email protected]> >> >> Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 >> Web Site (HHMI): http://hhmi.org/research/investigators/noel.html >> ___________________________________________________________ >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > >

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Adequate size for Free R test set?
by Joseph Noel 03 Aug '10

03 Aug '10

Hi Folks, Its been a while since I personally refined many structures. In the past, I used as a default, 5% of my unique reflections for the Free R test set. I have a high resolution structure with 150,000 unique reflections and noticed that Phenix defaults are 5% or 2000 reflections which ever is smaller. What is the current consensus on an adequate number of unique reflections to use for cross-validation? Thanks! Joe P.S. I really, really love Phenix. ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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