- phenixbb - phenix-online.org

Geometry Restraints
by Mario Sanches 20 Apr '12

20 Apr '12

I am refining a low resolution structure (2.9A) using phenix.refine. As I continue the refinement Rwork/Rfree are dropping but my geometry statistics in general are very bad. My clashscore is getting worst and the RMS(angle) is really high. I have tried to play with the "wxc_scale" parameter and also ran phenix selecting the "Optimize X-ray/ADP weight" option. All attempts end with a RMS(angle) of ~3.8 and a Clashscore of ~190. Is there a known procedure to deal with this? I feel that my geometry weighing term is too loose but I don't know exactly how to tighten it other than decreasing the wxc_scale parameter. I have gone and manually corrected bad positions before but given the low resolution nature of the structure the clashes tend to be reestablished during refinement. Thank you in advance for your help, -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches

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inverting a set of phase angles
by Mooers, Blaine H.M. (HSC) 19 Apr '12

19 Apr '12

Does phenix have a reflection file utility for correctly inverting a set of phase angles? Blaine Mooers Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-mooers(a)ouhsc.edu<mailto:[email protected]> webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…

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torsion NCS and SA
by dirk.reinert＠boehringer-ingelheim.com 19 Apr '12

19 Apr '12

Dear all, Is it safe to use torsion NCS (refinement.ncs.type="torsion") and torsion SA (refinement.main.simulated_annealing_torsion= "true") as a default? Thanks for advice, Dirk --- Dr. Dirk Reinert Boehringer Ingelheim Pharma GmbH & Co. KG Dept. Lead Identific. and Optim. Sup. Ge Tel.: +49 (7351) 54-97892 Fax: +49 (7351) 83-97892 mailto:[email protected] Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein; Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender), Ursula Fuggis-Hahn, Ralf Gorniak, Michael Klein, Dr. Martin Wanning; Vorsitzender des Aufsichtsrates: Prof. Dr. Dr. Andreas Barner; Sitz: Ingelheim am Rhein; Registergericht Mainz: HR B 23260 Diese E-Mail ist vertraulich zu behandeln. Sie kann besonderem rechtlichen Schutz unterliegen. Wenn Sie nicht der richtige Adressat sind, senden Sie bitte diese E-Mail an den Absender zurück, löschen die eingegangene E-Mail und geben den Inhalt der E-Mail nicht weiter. Jegliche unbefugte Bearbeitung, Nutzung, Vervielfältigung oder Verbreitung ist verboten. / This e-mail is confidential and may also be legally privileged. If you are not the intended recipient please reply to sender, delete the e-mail and do not disclose its contents to any person. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited.

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Can the Update Waters routine ignore specified waters?
by John Pascal 19 Apr '12

19 Apr '12

Hello All, While using Update Waters in the phenix GUI, several waters that have been defined around a metal binding site are removed. I am happy with the placement of these waters - can I specify somewhere that Update Waters should leave them alone? and that their positions, etc. are still refined during the run? Thanks. Best Regards, John -- *John M. Pascal, PhD* Assistant Professor Department of Molecular Biology & Biochemistry Kimmel Cancer Center Thomas Jefferson University 233 South 10th Street, BLSB Room 804 Philadelphia, PA 19107 Email: John.Pascal(a)KimmelCancerCenter.org <mailto:[email protected]> Phone: (215) 503-4596 Fax: (215) 923-2117

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(no subject)
by Tom Burnley 19 Apr '12

19 Apr '12

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Re: [phenixbb] Bulk Solvent
by Nathaniel Echols 17 Apr '12

17 Apr '12

Garib's response below, since the server wouldn't let him post. ---------- Forwarded message ---------- From: Garib N Murshudov <garib(a)MRC-LMB.CAM.AC.UK> To: "Steiner, Roberto" <roberto.steiner(a)kcl.ac.uk> Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> Date: Tue, 17 Apr 2012 18:11:24 +0100 Subject: Re: [phenixbb] Bulk Solvent Dear all I cannot say much without data. Only thing I can say that there were some problems in some of the versions in 5.5, and there are some improvements in recent versions. 5.7 series may perform better. Before claiming that improvement is due to particular feature I would do a little bit more analysis. regards Garib On 17 Apr 2012, at 18:03, Steiner, Roberto wrote: difference density on the backbone can also arise (more often) due to suboptimal ADP refinement/restraints..or a bug in a particular build.. best wishes roberto PS I cc-ed this email to Garib in case he's got some info specific for 5.5.0102 On 17 Apr 2012, at 17:22, Timothy Springer wrote: As I said, I cant say that, it is a guess based on two facts. 1) Looking at the output of refinement steps, and seeing that the largest decrease in R during refinement comes in the bulk solvent correction step. 2) It is also based on the common occurrence in the Refmac but not Phenix maps of negative difference density on backbone. This is a symptom of errors in bulk solvent correction. Tim On Apr 17, 2012, at 12:06 PM, Steiner, Roberto wrote: Hi Tim, How can you say the difference is really down to bulk solvent correction? there's several other parameters that affect differences in R factors.... Just curious R On 17 Apr 2012, at 16:27, Timothy Springer wrote: no, it just takes me two years to write up sometimes--- So this is a historical question. But there is a ref in that powerpoint to following ref. If this was implemented in Phenix and not Refmac 2 years ago, I should cite it. Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):850-5. Epub 2005 Jun 24. A robust bulk-solvent correction and anisotropic scaling procedure. Afonine PV, Grosse-Kunstleve RW, Adams PD. Source Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720, USA. pafonine(a)lbl.gov Tim On Apr 17, 2012, at 11:18 AM, Jeff Headd wrote: Hi Tim, If you are using Phenix 1.5.2, that would not have had the new bulk-solvent model that Pavel is talking about. Are you using that old of a version for your tests? Jeff On Tue, Apr 17, 2012 at 8:07 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > > Hi Tim, > > this is because recently (a few weeks ago) we introduced a novel bulk-solvent model and a new overall anisotropic scaling procedure. > > Some detailed overview is here: > > http://www.phenix-online.org/presentations/PhenixSantaFe2012_PA.pdf > > This is going to be published soon. > > Pavel > > > On 4/17/12 7:59 AM, Timothy Springer wrote: > > In one of the structures I have refined, I found phenix 1.5_2 gave 1 to 1.5% lower Rfree and Rwork than REFMAC 5.5.0102. > Can I propose in a publication that "We attribute these differences to methods for handling bulk solvent in PHENIX that are less adversely affected by deficiencies in the crystallographic data."? > This is a guess, because there is a large contribution to refinement from bulk solvent, rather than factual information. I did cross-refinement, and found it going from structures refined in REfmac to Phenix, and vice versa. The Phenix maps looked better, too. > Is this a reasonable suggestion, and would there be a relevant reference? > Tim > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb <ATT00001..c> Roberto Steiner, PhD Group Leader Randall Division of Cell and Molecular Biophysics King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.steiner(a)kcl.ac.uk _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb <ATT00001..c> Roberto Steiner, PhD Group Leader Randall Division of Cell and Molecular Biophysics King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.steiner(a)kcl.ac.uk Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: garib(a)mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk

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Bulk Solvent
by Timothy Springer 17 Apr '12

17 Apr '12

In one of the structures I have refined, I found phenix 1.5_2 gave 1 to 1.5% lower Rfree and Rwork than REFMAC 5.5.0102. Can I propose in a publication that "We attribute these differences to methods for handling bulk solvent in PHENIX that are less adversely affected by deficiencies in the crystallographic data."? This is a guess, because there is a large contribution to refinement from bulk solvent, rather than factual information. I did cross-refinement, and found it going from structures refined in REfmac to Phenix, and vice versa. The Phenix maps looked better, too. Is this a reasonable suggestion, and would there be a relevant reference? Tim

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Re: [phenixbb] Sugar woes
by Matthew J. Whitley 17 Apr '12

17 Apr '12

Hi Simon, I have been struggling with very similar issues over the last few weeks, but I (finally!) got it to work appropriately using just the procedure you described. In my case, I was trying to fit and refine a pentasaccharide consisting of MAN and BMA. Adapting what I did to your case, I would suggest the following steps: After loading NAG and MAN monomers into Coot and manually placing them into the electron density in approximately correct positions, save the coordinates and then manually delete the appropriate hydrogens and oxygen from the PDB file. You specifically stated that you did NOT remove the hydrogens, but I found it to be absolutely necessary to delete these atoms, even though my feeling is that Phenix is supposed to remove automatically the appropriate atoms based on the type of glycosidic linkage specified (although I could be wrong on that). In fact, I just deleted all hydrogen atoms from the sugars for purposes of refinement, knowing that I could add them back in later if desired. To determine the appropriate atoms for removal from the coordinate file in order to form the desired glycosidic linkage, run the command phenix.where_mon_lib_list_cif and then look in the specified file for the type of glycosidic linkage you want. For Beta1-2, you get this: BETA1-2 . DEL-HO2 pyranose . DEL-O1 pyranose glycosidic_bond_beta1-2 This means that, in your example, > apply_cif_link { > data_link = "BETA1-2" > residue_selection_1 = chain Z and resname NAG and resid 5 > residue_selection_2 = chain Z and resname MAN and resid 4 > } you should delete the O1 atom from Man 4 of chain Z and the HO2 atom from Nag 5 of chain Z. If the PDB file contains an O1 for Man4 or an HO2 for Nag5, the refinement will fail, and I think that's the cause of the error you're receiving. If everything works as desired, the result should be that C1 of MAN will be connected to O2 of NAG, thus the 1-2 linkage. If you then load the appropriate .CIF files into Coot and/or Phenix, you should be able to refine the sugars as desired. Alpha2-6 links are not included in the mon_lib_list.cif file. If you want to refine such a linkage, my (admittedly limited) understanding is that, unfortunately, you'd have to manually create a CIF file containing the appropriate restraints - bond lengths, angles, etc. Hope you find something useful in all this. I was was ready to pull out my hair several times over the past few weeks, but now that I got it to work, it doesn't seem so bad anymore. Best of luck. Matthew --- Matthew J. Whitley, Ph.D. Postdoctoral Research Fellow Angela Gronenborn Lab Department of Structural Biology University of Pittsburgh School of Medicine On Apr 17, 2012, at 11:00 AM, phenixbb-request(a)phenix-online.org wrote: > > > Message: 6 > Date: Tue, 17 Apr 2012 11:18:57 +0100 > From: Simon Kolstoe <s.kolstoe(a)ucl.ac.uk> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Sugar woes > Message-ID: <7BD08A7C-5B94-4448-8E8A-CBA4437E00B6(a)ucl.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Hi phenixbb, > > Every couple of years I come to build a sugar chain into a protein structure and hope the process is less painful than last time, however it seems things still are not smooth yet! > > I'm trying to build a fairly standard sugar chain onto a protein and am encountering many problems. What I am doing is using coot to get the coordinates for each sugar using the "File-> Get monomer" option and then putting the appropriate link in my phenix.refine .def file after renumbering the sugars. For example: > > apply_cif_link { > data_link = "BETA1-2" > residue_selection_1 = chain Z and resname NAG and resid 5 > residue_selection_2 = chain Z and resname MAN and resid 4 > } > apply_cif_link { > data_link = "BETA1-4" > residue_selection_1 = chain Z and resname GAL and resid 6 > residue_selection_2 = chain Z and resname NAG and resid 5 > } > > For some reason I keep getting the following error: > > --------------- > > Chain: "Z" > Number of atoms: 220 > Number of conformers: 1 > Conformer: "" > Sorry: Traceback (most recent call last): > File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1042, in apply_mod > mod_mon = self.monomer.apply_mod(mod_mod_id) > File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/cif_types.py", line 399, in apply_mod > result.delete_atom_in_place(mod_atom.atom_id) > File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/cif_types.py", line 316, in delete_atom_in_place > raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) > RuntimeError: delete_atom_in_place: unknown atom_id: HO2 > apply_mod failure: > pdbres="NAG Z 5 " segid="Z " > comp id: NAG-b-D > mod id: DEL-HO2 > > ------------------ > > I haven't deleted the hydrogens that came with the sugars so what I thought it was doing was trying to delete an atom that isn't there, however adding a dummy atom with the name HO2 didn't work - any ideas? > > Also it seems happy with BETA1-4 links but not ALPHA2-6 links? How do I specify this link? > > Thanks, > > Simon

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Sugar woes
by Simon Kolstoe 17 Apr '12

17 Apr '12

Hi phenixbb, Every couple of years I come to build a sugar chain into a protein structure and hope the process is less painful than last time, however it seems things still are not smooth yet! I'm trying to build a fairly standard sugar chain onto a protein and am encountering many problems. What I am doing is using coot to get the coordinates for each sugar using the "File-> Get monomer" option and then putting the appropriate link in my phenix.refine .def file after renumbering the sugars. For example: apply_cif_link { data_link = "BETA1-2" residue_selection_1 = chain Z and resname NAG and resid 5 residue_selection_2 = chain Z and resname MAN and resid 4 } apply_cif_link { data_link = "BETA1-4" residue_selection_1 = chain Z and resname GAL and resid 6 residue_selection_2 = chain Z and resname NAG and resid 5 } For some reason I keep getting the following error: --------------- Chain: "Z" Number of atoms: 220 Number of conformers: 1 Conformer: "" Sorry: Traceback (most recent call last): File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1042, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/cif_types.py", line 399, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/cif_types.py", line 316, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: HO2 apply_mod failure: pdbres="NAG Z 5 " segid="Z " comp id: NAG-b-D mod id: DEL-HO2 ------------------ I haven't deleted the hydrogens that came with the sugars so what I thought it was doing was trying to delete an atom that isn't there, however adding a dummy atom with the name HO2 didn't work - any ideas? Also it seems happy with BETA1-4 links but not ALPHA2-6 links? How do I specify this link? Thanks, Simon

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Phaser-MR issues?
by Noinaj, Nicholas (NIH/NIDDK) [F] 15 Apr '12

15 Apr '12

Hi, I just installed the latest installer (1036) and having issues with Phaser-MR. i have a multi-domain structure (6-domains) and trying to search for the domains individually but starting with the most conserved first using the Direct search method. However, my issues are... 1- Phaser-MR appears to still be using the 'automatically determined search order' instead of the order I have selected despite me having this turned OFF 2- Phaser-MR appears to still be using the 'FAST method' despite me having DIRECT method chosen Anyone else seeing this or could i be doing something wrong here? Thanks in advance for any feedback! Cheers, Nick

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