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Re: [phenixbb] NAG-NAG link definition seems to have no effect
by Benjamin Stauch 12 Jun '14

12 Jun '14

Thanks for your quick reply! However now I get the following error message, "Fatal problems interpreting model file: NUmber of atoms with unkown nonbonded energy type symbols: 3 Please edit the model file to resolve the problems nd/org supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Alternatively, to continue despite this problem use: stop_for_unknown=False" the log file says, Monomer Library directory: "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib" Total number of atoms: 11298 Number of models: 1 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain A and resname NAG and resid 401 residue_selection_2: chain A and resname ASN and resid 74 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain A and resname NAG and resid 401 residue_selection_2: chain A and resname NAG and resid 402 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain B and resname NAG and resid 401 residue_selection_2: chain B and resname ASN and resid 74 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain B and resname NAG and resid 401 residue_selection_2: chain B and resname NAG and resid 402 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 319, 4675 Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} Classifications: {'undetermined': 2, 'peptide': 317} Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, 'NH3': 1} Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} Not linked: pdbres="ALA A 317 " segid="A " pdbres="NAG A 401 " segid="A " Not linked: pdbres="NAG A 401 " segid="A " pdbres="NAG A 402 " segid="A " Conformer: "B" Number of residues, atoms: 319, 4675 Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} Classifications: {'undetermined': 2, 'peptide': 317} Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, 'NH3': 1} Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} Not linked: pdbres="ALA A 317 " segid="A " pdbres="NAG A 401 " segid="A " Not linked: pdbres="NAG A 401 " segid="A " pdbres="NAG A 402 " segid="A " bond proxies already assigned to first conformer: 4309 Chain: "B" [...] Chain: "C" [...] Residues with excluded nonbonded symmetry interactions: 26 residue: [...] Number of atoms with unknown nonbonded energy type symbols: 3 "ATOM 5046 HO4 NAG A 401 .*.A H " "ATOM 6215 HD22 ASN B 74 .*.B H " "ATOM 10057 HO4 NAG B 401 .*.B H " Time building chain proxies: 4.05, per 1000 atoms: 0.36 Deleting these atoms (NAG HO4 and ASN HD22) manually doesn't seem to do the trick - as I explicitly want to refine hydrogens I reckon they are added back on. Also it seems BETA1-4 wants to desperately link NAG O4 to NAG O1 which doesn't exist .. Shuld I manually define my NAG-NAG link instead of using the BETA1-4? Thanks again! B 2014-06-12 10:54 GMT+02:00 Benjamin Stauch <bs448c(a)gmail.com>: > Thanks for your quick reply! However now I get the following error message, > > "Fatal problems interpreting model file: NUmber of atoms with unkown > nonbonded energy type symbols: 3 Please edit the model file to resolve the > problems nd/org supply a CIF file with matching restraint definitions, > along with apply_cif_modification and apply_cif_link parameter definitions > if necessary. Alternatively, to continue despite this problem use: > stop_for_unknown=False" > > the log file says, > > > > Monomer Library directory: > "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib" > Total number of atoms: 11298 > Number of models: 1 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain A and resname NAG and resid 401 > residue_selection_2: chain A and resname ASN and resid 74 > apply_cif_link: > data_link: BETA1-4 > mod_id_1: DEL-HO4 > mod_id_2: DEL-O1 > residue_selection_1: chain A and resname NAG and resid 401 > residue_selection_2: chain A and resname NAG and resid 402 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain B and resname NAG and resid 401 > residue_selection_2: chain B and resname ASN and resid 74 > apply_cif_link: > data_link: BETA1-4 > mod_id_1: DEL-HO4 > mod_id_2: DEL-O1 > residue_selection_1: chain B and resname NAG and resid 401 > residue_selection_2: chain B and resname NAG and resid 402 > Model: "" > Number of chains: 4 > Chain: "A" > Number of atoms: 5075 > Number of conformers: 2 > Conformer: "A" > Number of residues, atoms: 319, 4675 > Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} > Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} > Classifications: {'undetermined': 2, 'peptide': 317} > Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, > 'NH3': 1} > Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} > Not linked: > pdbres="ALA A 317 " segid="A " > pdbres="NAG A 401 " segid="A " > Not linked: > pdbres="NAG A 401 " segid="A " > pdbres="NAG A 402 " segid="A " > Conformer: "B" > Number of residues, atoms: 319, 4675 > Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} > Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} > Classifications: {'undetermined': 2, 'peptide': 317} > Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, > 'NH3': 1} > Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} > Not linked: > pdbres="ALA A 317 " segid="A " > pdbres="NAG A 401 " segid="A " > Not linked: > pdbres="NAG A 401 " segid="A " > pdbres="NAG A 402 " segid="A " > bond proxies already assigned to first conformer: 4309 > Chain: "B" > [...] > Chain: "C" > [...] > Residues with excluded nonbonded symmetry interactions: 26 > residue: > [...] > Number of atoms with unknown nonbonded energy type symbols: 3 > "ATOM 5046 HO4 NAG A 401 .*.A H " > "ATOM 6215 HD22 ASN B 74 .*.B H " > "ATOM 10057 HO4 NAG B 401 .*.B H " > Time building chain proxies: 4.05, per 1000 atoms: 0.36 > > > Deleting these atoms (NAG HO4 and ASN HD22) manually doesn't seem to do > the trick - as I explicitly want to refine hydrogens I reckon they are > added back on. Also it seems BETA1-4 wants to desperately link NAG O4 to > NAG O1 which doesn't exist .. Shuld I manually define my NAG-NAG link > instead of using the BETA1-4? > > Thanks again! > > B > > > > 2014-06-12 2:12 GMT+02:00 Nathaniel Echols <nechols(a)lbl.gov>: > > On Wed, Jun 11, 2014 at 5:05 PM, Benjamin Stauch <bs448c(a)gmail.com> wrote: >> >>> I want to refine a model that has two NAGs linked to an Asn - the sugars >>> are already part of my initial coordinate file, but upon refinement the >>> link between the NAGs gets lost. I have defined a cif_link file as follows >>> that I load (using the GUI), >>> >>> apply_cif_link { >>> data_link = "NAG-ASN" >>> residue_selection_1 = "chain A and resname NAG and resid 401" >>> residue_selection_2 = "chain A and resname ASN and resid 74" >>> } >>> apply_cif_link { >>> data_link = "BETA1-4" >>> residue_selection_1 = "chain A and resname NAG and resid 401" >>> residue_selection_2 = "chain A and resname NAG and resid 402" >>> } >>> >> >> Okay, I think this may be part of the problem - you are missing the outer >> "scope" for these parameter blocks, so they are not processed correctly. >> If you change "apply_cif_link" to >> "refinement.pdb_interpretation.apply_cif_link" in both places it may fix >> the problem. >> >> Refinement doesn't crash or produce errors as far as I can see, however >>> when checking the MolProbity output after refinement, it complains of >>> missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant) >>> >> >> Sorry, this is actually my bug (those atoms should not be included in >> covalently linked sugars), and I think I still have an email complaining >> about this in my inbox from late 2012. I need to overhaul that bit of code >> anyway so I will see if Nigel and I can come up with something smarter. >> >> -Nat >> > >

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NAG-NAG link definition seems to have no effect
by Benjamin Stauch 12 Jun '14

12 Jun '14

Hi Phenix, apologies for the beginner question, and I do realise that there are some related threads already but nothing so far has helped me to solve this problem. I want to refine a model that has two NAGs linked to an Asn - the sugars are already part of my initial coordinate file, but upon refinement the link between the NAGs gets lost. I have defined a cif_link file as follows that I load (using the GUI), apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = "chain A and resname NAG and resid 401" residue_selection_2 = "chain A and resname ASN and resid 74" } apply_cif_link { data_link = "BETA1-4" residue_selection_1 = "chain A and resname NAG and resid 401" residue_selection_2 = "chain A and resname NAG and resid 402" } when checking the .geo file phenix.refine outputs, I do not see any restraints between Asn and NAG, nor NAG and NAG. There might be some clues in the refine.log file: Build ligand and use monomer library to name atoms : NAG Using monomer library entry NAG as template which I guess looks good, and then something like this which could be where things are going wrong: Monomer Library directory: "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib" Total number of atoms: 11298 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 319, 4675 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2, 'peptide': 317} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} Not linked: pdbres="ALA A 317 " segid="A " pdbres="NAG A 401 " segid="A " Not linked: pdbres="NAG A 401 " segid="A " pdbres="NAG A 402 " segid="A " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Refinement doesn't crash or produce errors as far as I can see, however when checking the MolProbity output after refinement, it complains of missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant) Furthermore there's still a HO4 attached to the O4 of NAG ... while the BETA1-4 should care to delete it .. however the mon_lib reads BETA1-4 . DEL-HO4 pyranose . DEL-O1 pyranose glycosidic_bond_beta1-4 which doesn't seem entirely relevant for my case? Any help would be appreciated Thanks! Ben

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Using .fcf file with Phenix
by Rex Palmer 10 Jun '14

10 Jun '14

Can I run Phenix with a .fcf file and a .pdb file? If not how can I convert .fcf to the correct format? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com

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Run PHENIX commands on GUI verison?
by 李翔 09 Jun '14

09 Jun '14

Hi, I currently can only access to PHENIX with my laptop which has a Windows system (GUI). I want to run some commands for generating restraints for my models such as: iotbx.show_distances MR.1.pdb > contacts.distances, phenix.secondary_structure_restraints model.pdb Is there a way I can run commands in GUI version or can I run the above commands in the GUI version? Thanks for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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B-factors for some sidechains were not refined well
by Zhou, Tongqing (NIH/VRC) [E] 09 Jun '14

09 Jun '14

Dear colleagues, I am refining one structure at 1.94 A with phenix.refine with individual b, TLS, and xyz. The Rwork and Rfree are now at 16.1 and 19.8%. But when inspecting the maps, I noticed that the sidechain tip of some residues showed positive density and the b-factor for those atoms were very high while those for the other atoms of the same residues were normal; The b-factors for newly added ligands were also not refined well showing high b-value and positive density at the same time; the disulfide bonds also show positive density and high B. The occupancy were all set to 1. Please give suggestions. Thanks! Best regards, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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launching MR jobs from the command line.
by Francis Reyes 04 Jun '14

04 Jun '14

Hi all, For the moment (1.9-1692) phenix.automr still works from the command line but I received a note that it's a 'Deprecated program' . ************************************************************************ WARNING - DEPRECATED PROGRAM Please note: the command-line AutoMR tool and associated GUI have been deprecated and will be removed in future releases. We recommend that you use phenix.mrage or phenix.phaser, both of which are available in the GUI. The program will resume execution in 5 seconds. ************************************************************************ phenix.mrage doesn't resolve to anything, and phenix.phaser runs the phaser binary. Is there a new way to launch MR jobs from the command line (which had all the PHIL friendly goodies that automr had?) ? Thanks, F

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difference map peak in coot not showing all peaks?
by Murpholino Peligro 04 Jun '14

04 Jun '14

In coot I have set the map contour level to 5.0 rmsd and I do Validate -> Difference Map Peaks ... and the new window shows me where the peaks are...but not all of them. For example, see screenshot attached. (there are peaks above sg cys80 and sg cy64, both appear in the visual window in coot but only one of them, cys80, in the listing. If I understand clearly, they should both appear in the visual window and in the listing because I have the same filter (5.0 rmsd). Right? Now...the peaks values are from Phenix doing a Isomorphous Difference Map ... So I do not know if this is from Coot or from Phenix.

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software update
by Edna Patricia Matta, Ms 04 Jun '14

04 Jun '14

Hello everybody, Quick question, do I have to uninstall the old version of the software If I want to have the new one? Thanks a lot, E Edna Patricia Matta, MSc. PhD Postdoctoral Fellow McGill University Goodman Cancer Centre 1160 Pine Avenue West, Room 614 Montreal, Quebec, CANADA, H3A 1A3 [http://www.med.mcgill.ca/nahum/images/tel.png] TEL: 1-514-398-7275 [http://www.med.mcgill.ca/nahum/images/fax.png] FAX: 1-514-398-1287

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Submissions for Comput. Cryst. Newsletter
by Nigel Moriarty 02 Jun '14

02 Jun '14

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the July 2014 issue is 16 June 2014 (with some leeway if you are still working on the text). The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Autosol and sequence file
by Stefan Knight 02 Jun '14

02 Jun '14

I don’t seem to have much luck with Phenix these days… Trying to run Autosol from the GUI but the process aborts immediately complaining that a sequence file is required to run Autosol. I have given it a sequence file in fasta format that is recognised as such when added. I’ve also tried instead pasting the sequence into the Crystal info window but that didn’t help. Grateful for any tip on how to convince Phenix it has all it needs to get going ;-). Thanks, Stefan ------------------------------------------------------------------------------------------------------- Stefan D. Knight, PhD Professor of Biology Department of Cell and Molecular Biology, Uppsala University Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala Sweden Voice: +46 (0)18 471 45 54 Fax: +46 (0)18 53 03 96 E-mail: stefan(a)xray.bmc.uu.se ------------------------------------------------------------------------------------------------------- "We trained very hard, but it seemed that every time we were beginning to form into teams, we would be reorganised. I was to learn later in life that we tend to meet any new situation by reorganising - and a wonderful method it can be for creating the illusion of progress while producing confusion, inefficiency and demoralisation." – Gaius Petronius Arbiter (d. AD 66) -------------------------------------------------------------------------------------------------------

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How to add difference map peak value to B-factor column in Phenix-Coot after isomorphous difference map?
by Murpholino Peligro 01 Jun '14

01 Jun '14

Hi all. How to add a difference map peak value to B-factor column in Phenix-Coot after isomorphous difference map? Because what I get (after Phenix Isomorphous Difference Map) is a pdb with the peaks (chain A) and holes (chain B) with their positions given by UNKnown atoms, 1 for occupancy and in the B-column their peak-or-hole value. I would be happy if I could get the actual atoms with positions and the peak-or-hole value in the B-column. Thanks again and again.

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molecular replacement keeping hetatms?
by Murpholino Peligro 27 May '14

27 May '14

Can I do molecular replacement with phenix/phaser, keeping all the waters from the first model from the first data set? >From here ( http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#WATER), I should change all the HOH labels to something like WWW. Then I guess that I should put HOH labels again in the solution model, for the following refinement in phenix.refine. Is that it?... Any suggestions? thanks again!

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(no subject)
by Fulvio Saccoccia 27 May '14

27 May '14

Dear phenix users and developers, in the past I usually used the fix_rotamers=true options to fix some residue issues. Now, this option is lacking (I currently use the dev-1702 version of phenix) but I was wondering if some other option does replace it. In addition, I would like to know better how real_space_refinement works; is there any tutorial or presentation about it? Thanks in advance -- Fulvio Saccoccia, PhD Dept. of Biochemical Sciences Sapienza University of Rome 00185, Rome (Italy) Phone: +39 06 4991 0556 https://www.researchgate.net/profile/Fulvio_Saccoccia/?ev=hdr_xprf

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Workshop announcement @ Inst Pasteur Montevideo - Uruguay : Modern Approaches in Drug Discovery for Neglected Infectious Diseases
by Alejandro Buschiazzo 23 May '14

23 May '14

Dear Colleagues: We are pleased to announce the Workshop: "Modern Approaches in Drug Discovery for Neglected Infectious Diseases" at the Institut Pasteur de Montevideo (Uruguay). *Dates:* November 3rd - 8th, 2014 *Venue**: *Institut Pasteur de Montevideo (Montevideo, Uruguay) *Invited speakers:* Wim Hol (University of Washington, Seattle, USA), Paul Michels (University of Edinburgh, Edinburgh, UK), Celerino Abad-Zapatero (University of Illinois at Chicago, Chicago, USA), Hugo Cerecetto (UdelaR), Marcelo Comini (IP Montevideo), Sergio Pantano (IP Montevideo), Alejandro Buschiazzo (IP Montevideo)* * *Aim:* The general aim of this International Workshop is to train students in state-of-the-art approaches for drug discovery and rational design, with special emphasis on target-based methods. The course will provide with a multidisciplinary view, with invited professors covering a diverse set of subjects : protein crystallography, in silico methods for molecular simulations, medicinal chemistry and biology of neglected infectious diseases.** For details of the activity please see the preliminary program. <http://www.pasteur.edu.uy/images/program_v.5-5-14.2.pdf> The course will be in English. This activity is supported by the /Center for Structural Biology of the MERCOSUR /(CeBEM <http://www.cebem.org.ar/>), jointly with the /United Nations University Biotechnology Programme for Latin America and the Caribbean/ (UNU - BIOLAC <http://unu.edu/about/unu-system/biolac>). * **Applicants:* Graduate students and young research scientists are encouraged to apply. 24 students will be selected among the applications. The Course will provide financial support for the students, covering registration fees, and for the case of those coming from abroad, all local expenses (lodging, per diem and local transportation). /* The application deadline is September 8th, 2014. The results will be announced by September 30th.*/ The application form, activity program, contact information and other details can be found at the web site of the course <http://www.pasteur.edu.uy/index.php/en/teaching/courses/54-ensenanza/cursos…> Please address further inquiries toSBDD_course(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Three positions open at the MAX IV Laboratory
by Marjolein Thunnissen 23 May '14

23 May '14

The MAX IV facility, the largest and most ambitious Swedish investment in research infrastructure, will be the brightest source of x-rays worldwide and will replace the existing laboratory, which today consists of the storage rings MAX I, II and III. The new MAX IV facility will become operational in June 2016. To extend the suite of already funded beamlines, MAX IV Laboratory is planning the next set of beam lines. Therefore The MAX IV laboratory in Lund has opened two positions within the life-science division. We are looking for two beamline scientists, one for the biomedical imaging beamline MEDMAX and one for the microfocus beamline MicroMAX. For both these positions the scientist will be overseeing the development, construction and commissioning of the MedMAX, respectively MicroMAX beamline from its conceptual stage to full operation. Both beam lines are planned to be cutting edge beam lines, fully exploiting the excellent properties of the MAX IV 3GeV storage ring. In addition we are also looking for a software engineer to be engaged in the design of the MX software infrastructure at the beamline for protein crystallography which is under construction, BioMAX. More information on these positions can be found at https://www.maxlab.lu.se/positions and the links within this page, or from our Life-Sciences director Tomas Lundqvist . best regards Marjolein Thunnissen [cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC] Marjolein Thunnissen Science Coordinator MX MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/>

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Integrated Structural Biology, PhD program at the IGBMC
by Alexandre OURJOUMTSEV 21 May '14

21 May '14

Dear all, kind reminder for PhD fellowship opportunities at the International PhD program of the IGBMC, notably for Integrated Structural Biology. Deadline for applications is 3rd of june 2014: http://phdprogramme.igbmc.fr/ Interested candidates are invited to visit the home pages of the teams of the Integrated Structural Biology department at http://www.igbmc.fr/research/department/3/ Please feel free to contact the group leaders for further information about the projects. Best regards, Bruno Klaholz Sacha Urzhumtsev

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any idea what is this? (unidentifiable blob in electron density map)
by Murpholino Peligro 21 May '14

21 May '14

1) 2FOFCWT PH2FOFCWT bue map (front1.png) (process: XDS->Aimless within CCP4i->MR with Phaser->Phenix.refine/coot->Phenix-refine-withwaters/coot) 2) FWT PHWT purple map (front2.png) (Output from Aimless and calculate Fs with refmac within coot with last pdb from 1st line) What do I have in the crystal? NaCl, Sodium acetate, water, lysozyme and some complexes (~ 400 daltons) that chelate Cu2+ Is there like a gallery of crazy-looking blobs that are explained with something ....real and possible? (that would be great help for the newb) Thanks in advance. links to screenshots right here: https://www.dropbox.com/s/rzjepvr8genolxi/front1.png https://www.dropbox.com/s/0iycf4lh5y726x4/front2.png https://www.dropbox.com/s/xx5kvgn91p763ei/faraway.png (1.0 rmsd for both maps above and 3.5 for the "red and green maps")

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phenix.rna_validate and the MolProbity web server report different bond angle violations
by Huw Jenkins 20 May '14

20 May '14

Hi, I’ve recently been using phenix.erraser to help correct RNA geometry errors and finding it very useful. However, it appears that the geometry validation statistics reported by phenix.rna_validate with respect to bond angle outliers are very different from those reported by the MolProbity web server. As an example - if I run phenix.rna_validate on 1u8d (as used in the documentation for phenix.erraser) the following outliers are reported: RNA Validation ----------------------------------------------- Pucker Outliers: #residue:delta_angle:is_delta_outlier:epsilon_angle:is_epsilon_outler G A 15 :74.054:no:103.458:yes U A 48 :119.081:yes:283.965:no U A 63 :90.366:yes:74.220:yes ----------------------------------------------- Bond Length Outliers: #residue:atom_1:atom_2:num_sigmas ----------------------------------------------- Angle Outliers: #residue:atom_1:atom_2:atom_3:num_sigmas C A 39 : C5': C4': C3':-5.294 U A 63 : O3': C3': C2':-4.402 ----------------------------------------------- Suite Outliers: #suiteID:suite:suiteness:triaged_angle G A 16 :!!:0.000:epsilon-1 U A 48 :!!:0.000:delta U A 49 :!!:0.000:delta-1 A A 64 :!!:0.000:epsilon-1 The MolProbity web server reports the same pucker and suite outliers but flags up many more angle violations: A 39 C worst is C5'-C4'-C3': 10.588 σ A 63 U worst is O3'-C3'-C2': 8.803 σ A 54 C worst is C5'-C4'-C3': 7.883 σ A 49 U worst is C2'-C1'-N1: 5.416 σ A 62 G worst is C2'-C1'-N9: 4.946 σ A 15 G worst is O3'-C3'-C2': 4.825 σ A 22 U worst is C5'-C4'-C3': 4.785 σ A 64 A worst is C4'-C3'-O3': 4.648 σ A 65 A worst is C2'-C1'-N9: 4.582 σ A 44 A worst is C4'-C3'-C2': 4.395 σ As the number of sigmas for the angle violations are different between phenix.rna_validate and MolProbity I guess they’re using different target distributions (not just reporting at a different sigma cut-off) but I’ve no idea which is more valid. Hopefully there is a simple explanation! Thanks, Huw

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Postdoctoral Fellow: Data Processing and Merging in Serial Crystallography
by Kay Diederichs 19 May '14

19 May '14

The Paul Scherrer Institute PSI is the largest research centre for natural and engineering sciences within Switzerland. We perform cutting-edge research in the fields of matter and materials, energy and environment and human health. By performing fundamental and applied research, we work on sustainable solutions for major challenges facing society, science and economy. PSI is committed to the training of future generations. Therefore about one quarter of our staff are post-docs, post-graduates or apprentices. Altogether PSI employs 1900 people. The Swiss Light Source (SLS) is one of the most advanced radiation sources worldwide. The SLS Macromolecular Crystallography Group operates two high performance undulator beamlines as well as a state-of-the-art bending magnet beamline for protein crystallography. The group is involved in several aspects of protein crystallography including the development of advanced beamline instrumentation and crystallographic methods, as well as structural biology projects in collaboration with the Biomolecular Research Group at PSI and external partners. In collaboration with Prof. Kay Diederichs at University of Konstanz, we are looking for a Postdoctoral Fellow: Data Processing and Merging in Serial Crystallography Your tasks ========== * Serial crystallography with bright micro-focused X-ray beams from both synchrotron and free electron laser sources has brought new opportunities in micro- and nanocrystallography. At the same time, obtaining best diffraction data from hundreds and thousands of crystals presents unprecedented challenges. New statistics based method of multi-crystal merging and analysis need to be developed and validated. * Develop multi-crystal data analysis, processing and merging methods for serial micro- and nanocrystallography at synchrotron radiation (SR) and X-ray free electron laser (XFEL) sources * Actively participate in serial crystallography experiments at both SR and XFEL sources * Implement an automated data merging pipeline at the SLS protein crystallography beamlines Your profile ============ You hold a PhD degree in (bio-)chemistry or physics and have several years of experience in protein crystallography. Working knowledge for data processing programs is a must. Experience in computer programming would be a significant advantage. If you are a good team player with good communication skills and sense of responsibility, this position will offer a great opportunity for you to develop your research career in an exciting and highly multidisciplinary environment. For further information please contact Prof. Kay Diederichs, phone +49 7531 88 40 49 or Dr Meitian Wang, phone +41 56 310 41 75. Please submit your application online (including list of publications and addresses of referees) for the position as a Postdoctoral Fellow (index no. 6112-00) to: Paul Scherrer Institute, Human Resources Management, Miriam Zehnder, 5232 Villigen PSI, Switzerland http://www.psi.ch/pa/offenestellen/0789-1 -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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Sharing a Phenix project via Dropbox
by Derek Logan 19 May '14

19 May '14

Hi, Has anyone ever successfully shared a Phenix project through Dropbox? I tried Googling for info on this without success. I have tried sharing but it doesn't work because Phenix uses the full path to the project, e.g. /Users/derek/Dropbox/project rather than ~/Dropbox/project, which would work for all users sharing the project. I tried manually editing project.phil in the .phenix directory, but at the end of a run of phenix.refine it was overwritten again. Is there somewhere (job_history.phil?) I can replace /Users/derek with ~ so that it the change will be permanent? I think that this would be a very effective way for me to set up a project being run by one of my PhD students involving people from at least 3 labs that could have opinions on the refinement! /Derek P.S. We are all using Macs.

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phenix.real_space_refine
by Gino Cingolani 16 May '14

16 May '14

Hi all, I'm trying to refine a pdb against an EM map using phenix.real_space_refine using default parameters (e.g. phenix.real_space_refine model1.pdb map.ccp4). The program starts OK but quickly stops with the following output (see below) Any thoughts? Thanks so much! Gino ########################################################################### Add C-beta restraints ********************* Adding C-beta torsion restraints... num c-beta restraints: 11832 ------------------------------------------------------------------------------- Getting target map ****************** Traceback (most recent call last): File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 494, in <module> o = run(sys.argv[1:]) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 273, in __init__ self.caller(func = self.get_target_map, prefix="Getting target map") File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 298, in caller func(prefix=prefix) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 372, in get_target_map number_of_macro_cycles = self.params.refinement.macro_cycles) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 153, in extract_target_map_data_and_crystal_gridding crystal_symmetry = inputs.xray_structure.crystal_symmetry()) File "/usr/local/phenix-dev-1615/cctbx_project/mmtbx/utils/__init__.py", line 3094, in structure_factors_from_map use_sg = True) File "/usr/local/phenix-dev-1615/cctbx_project/cctbx/miller/__init__.py", line 1309, in structure_factors_from_map assert map.focus_size_1d() > 0 and map.nd() == 3 and map.is_0_based() AssertionError ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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NCS in mr_rosetta
by Stefan Knight 15 May '14

15 May '14

Hi, Is there some way to make mr_rosetta use information about NCS present in the data? I have data from a crystal in sg P21 with a clear 3-fold axis perpendicular to the two-fold screw (as seen in self rotation function), and most likely 6 molecules in the asymmetric unit, but none of the mr_rosetta solutions that have appeared so far show 3-fold symmetry, and it doesn’t seem like the ncs is used in the search. The only info about ncs in mr_rosetta I have been able to find online pertains to extracting NCS from search models or mr_rosetta assembled models. Thanks, Stefan ------------------------------------------------------------------------------------------------------- Stefan D. Knight, PhD Professor of Biology Department of Cell and Molecular Biology, Uppsala University Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala Sweden Voice: +46 (0)18 471 45 54 Fax: +46 (0)18 53 03 96 E-mail: stefan(a)xray.bmc.uu.se ------------------------------------------------------------------------------------------------------- "We trained very hard, but it seemed that every time we were beginning to form into teams, we would be reorganised. I was to learn later in life that we tend to meet any new situation by reorganising - and a wonderful method it can be for creating the illusion of progress while producing confusion, inefficiency and demoralisation." – Gaius Petronius Arbiter (d. AD 66) -------------------------------------------------------------------------------------------------------

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fem command/memory error
by Matteo Colombo 14 May '14

14 May '14

Hi Pavel, I downloaded the last released version of phenix (phenix-1.9-1692) and I would like to run the "feature enhanced map" command. However, when I run it I got the following Memory Error that I didn't have in the previous version of phenix. r_work: 0.1867 r_free: 0.2372 Max B subtracted from atoms and used to sharpen map: 20.0 b_sharp: 25.0 FEM loop: done so far: 10%Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 120, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 99, in run sharp=params.sharp, signal_threshold=params.signal_threshold) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 112, in __init__ progress_counter = progress_counter) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 204, in fem_loop weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 276, in fem_loop_ weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 234, in one_iteration m = get_map(mc=mc_wa, cg=crystal_gridding) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 20, in get_map fourier_coefficients = mc) File "/usr/local/phenix-1.9-1692/cctbx_project/cctbx/miller/__init__.py", line 4357, in __init__ conjugate_flag=True) MemoryError My OS is Ubuntu precise 12.04 LTS, system 32 bit Thanks in advance Matteo -- Matteo Colombo PhD Groupe Extremophile et grands assemblages moléculaire Institut de Biologie Structural J. P. Ebel 6, rue Jules Horowitz F-38027 GRENOBLE Cedex 1

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Re: [phenixbb] Non bonded contacts
by Mark A Saper 14 May '14

14 May '14

Pavel, Your suggestion of setting the alt-loc the same for the two residues in order to avoid the non-bonded contact restraint is not working yet. Do the residues need to be in the same chain Thanks, Mark On May 12, 2014, at 12:23 PM, Mark A Saper <saper(a)umich.edu> wrote: > Hi Pavel, > > I'll try that. I have a PLP cofactor and a lysine. I refined with them forming a Schiff base but the maps had large delta F indicating that the PLP ring was being pulled out of density. So now I am modeling it as PLP and Lys. But there is some bridging density. I want to see how close the Lys would extend if it didn't see the PLP. > > Thanks, > Mark > > On May 9, 2014, at 8:25 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Mark, >> >>> Is there a straightforward way to turn off non-bonded restraints between 2 residues? I see the restraints in the .geo file. Thanks. >> >> you can asigne them diferent altloc identifiers and then they will not see each other via non-bonded interactions. >> If these two residues in question are symmetry mates then there is a keyword for this: custom_nonbonded_symmetry_exclusions . >> >> Also, I wonder why you want to do this? >> >> Pavel >> >

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Using command-line Phenix from the Mac graphical installer
by Nathaniel Echols 13 May '14

13 May '14

A public service announcement: the graphical installer gives you access to all of the same tools as the command-line installer. The only differences are a) the location, and b) we remove some of the bulkier data files that are not required for normal operation. (Which means that the graphical installation is actually about 300MB smaller.) Instructions are here: https://www.phenix-online.org/version_docs/1.9-1692/install-setup-run.html#… In general, I recommend that all (64-bit) Mac users run the graphical installer unless you absolutely need Phenix to go somewhere other than /Applications. (I know that some of you are already aware of this, but I've had to make this same suggestion twice already today, and the command-line installer is more work to support, thank you Apple.) -Nat

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