Re: [ccp4bb] Convert .cif to mtz
HI Eric, I havent yet done the scala ,i have just indexed and integrated the data in d*trek. I tried converting the .cif in Dtrek2mtz but thats failed. Thanks Madhu
Re: [ccp4bb] Convert .cif to mtz
Madhu, I just noticed that your message said you "indexed and integrated" your data. Did you scale it with d*trek too (that needs to be done before using Dtrek2mtz) or are you looking to use the integrated d*trek reflections for subsequent scaling in ccp4 with scala? Eric On Thu, 23 Jun 2011, Eric Larson wrote: Hi Madhu, D*trek is what you processed your data with. In the ccp4i gui, select the program "Dtrek2mtz" and then in the field that says "convert scaled data output from ... ", select "d*trek" from the pull down menu. Go to http://www.ccp4.ac.uk/html/dtrek2mtz.html for more information. good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Fri, 24 Jun 2011, Madhu shankar Madhu shankar wrote: HI, I indexed and integrated data from RAXIS(Rigaku) detector on 'Crystalclear'. It gave me a .cif file as output.I am not able to read this file in ccp4 to carry out rest of the analysis in ccp4. I want to know how to convert this cif file to MTZ. Thanks Madhu
Re: [ccp4bb] Convert .cif to mtz
Hi Madhu, D*trek is what you processed your data with. In the ccp4i gui, select the program "Dtrek2mtz" and then in the field that says "convert scaled data output from ... ", select "d*trek" from the pull down menu. Go to http://www.ccp4.ac.uk/html/dtrek2mtz.html for more information. good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Fri, 24 Jun 2011, Madhu shankar Madhu shankar wrote: HI, I indexed and integrated data from RAXIS(Rigaku) detector on 'Crystalclear'. It gave me a .cif file as output.I am not able to read this file in ccp4 to carry out rest of the analysis in ccp4. I want to know how to convert this cif file to MTZ. Thanks Madhu
Re: [ccp4bb] Convert .cif to mtz
Easiest way: CCP4i Reflection Data Utilities Convert to MTZ -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Madhu shankar Madhu shankar Sent: Thursday, June 23, 2011 5:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Convert .cif to mtz HI, I indexed and integrated data from RAXIS(Rigaku) detector on 'Crystalclear'. It gave me a .cif file as output.I am not able to read this file in ccp4 to carry out rest of the analysis in ccp4. I want to know how to convert this cif file to MTZ. Thanks Madhu
[ccp4bb] Convert .cif to mtz
HI, I indexed and integrated data from RAXIS(Rigaku) detector on 'Crystalclear'. It gave me a .cif file as output.I am not able to read this file in ccp4 to carry out rest of the analysis in ccp4. I want to know how to convert this cif file to MTZ. Thanks Madhu
[ccp4bb] cif-file with restraints for HC4
is there someone out there who worked out a cif-file WITH restraints for the central p-hydroxy-cinnamoyl chromophore (HC4) in photoactive yellow protein? I'd appreciate a copy. Thanks very much Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: m-schm...@uwm.edu http://users.physik.tu-muenchen.de/marius/
Re: [ccp4bb] Y-Chi2 running out of chart
Dear colleagues, thank you all for your help! I really appreciate it. I did perform a lysozyme test after the repair. I collected ~50 degree (99%). Everything seems to be fine. Maybe I should have done it for an entire round. As for the current collection, as I suspended, it did go out of the chart but then came down to normal. Overall Rmerge is 7.9% (4% square). As Zbyszek and others mention, it is probably due to imperfect crystal and also uneven cooling. If our field engineer discovers anything else, I'll post it here. Thanks again for your help. On Wed, Jun 22, 2011 at 9:00 PM, Artem Evdokimov wrote: > As a follow up to the excellent suggestions made by others I would suggest > that a close examination of x-file headers may reveal abnormalities in e.g. > crystal orientation -- suspecting an unlocked or drifting goniostat. It may > also indicate a precession around the phi, which should also manifest itself > in a systematic deviation of average intensities (i.e. scale factors) in a > similar pattern (assuming uneven illumination of the crystal). Sometimes the > precession is caused by a bubble or a tiny chunk of ice trapped under the > pin, it can melt unevenly and re-align the pin a few minutes into the run > (something similar used to happen a lot at one or two beam lines and it > drove me nuts until I figured out the need to re-align the crystal after the > initial screening). > > Artem > > On Wed, Jun 22, 2011 at 11:22 AM, bie gao wrote: > >> Dear Colleagues, >> >> I'm collecting a dataset on our recently repaired Rigaku home source. >> Crystal diffracts to 2.2A. Indexing seems to be all fine. However, during >> integration, I realize Y-Chi2 is increasing constantly (from 2 to 4.5, >> almost linear) within 60 degree collection, whereas X-Chi2 stays the same. >> An image is attached. There are still another 60 degree to go. Although the >> prediction fits the images well so far, I'm afraid the Y-Chi2 will >> eventually run out of the chart. >> My question is could it be related to any hardware malfunctioning, i.e., >> goniometer, image plates, etc, which may be a side effect of the recent >> major repair? Or what else it can be? >> >> Thanks, >> Bing >> > >
Re: [ccp4bb] Refmac5: put restraint on only peptide bonds
External distance restraints have type type 0 - replace what is generated by refmac type 1 - use if there is no restraint for this type. Only one restraint per atom pair type 2 - there may be many restraints per atom pair. Refmac will choose the restraint that is the closest to current interatomic distance I hope it answers to you question. Cheers Garib On 23 Jun 2011, at 14:21, Ed Pozharski wrote: > On Thu, 2011-06-23 at 16:49 +0900, Masaki UNNO wrote: >> Dear all >> Is it possible to put restraint on only peptide bonds? I would like >> to put restraint on O-N bond lengths, Ca-O-N angles, and O=O-N angles. >> Could you teach me how to do it, if possible? >> Masaki UNNO, Ph.D. > > One could create a monomer library with a set of alternative amino acids > (you'd rename them in the PDB-file too). Then, modeling a library after > the standard one, you assign alternative atom types and have a limited > set of defined bonds/angles. This would be quite painful to do though. > > I wonder what will happen if you run unrestrained refinement yet provide > external distance restraints as described in refmac manual? Will the > external restraints be ignored? If not, then I'd think this is a better > approach. If yes, then maybe you can do the trick by using very high > weight matrix parameter (approaching the unrestrained refinement) and > correspondingly high external weight scale value. > > Cheers, > > Ed. > > > > -- > "Hurry up before we all come back to our senses!" > Julian, King of Lemurs
Re: [ccp4bb] Homology modelling
I suspect what your colleague wants is not a whole slew of homology models, but for you to take a look at variable residues, see what they are doing in the structure, and make comments like The tyrosine is H-bonding the ligand, so mutating to phenylalanine may weaken the binding or change specificity, the Ile is in a hydrophobic patch and mutating to Leu probably won't have much effect, or the Ile is in a hydrophobic patch at the bottom of the active site cleft, so mutating to Ala may allow a larger substrate to be accommodated. If (s)he doesn't feel coonfident doing that for himself, he probably wouldn't feel confident drawing conclusions from the homology models either. Simon Kolstoe wrote: Dear ccp4bb, One of my colleagues is interested in how a certain protein differs between species. He's done a blast search, collected all the aligned sequences, and "emailed them to the crystallographer to tell him the implications of the sequence changes". Although I am not at all confident that I can predict any implications based upon sequence differences, I thought I could at least have a try by mapping the different species sequences onto the existing structure and then regularising it just to see what happens (and then perhaps looking at buried surface area, electrostatics, subunit interfaces etc.). I know the program chainsaw can mutate the sequence based on an alignment, however I can't stop it pruning non-conserved residues. Does anyone know of another program that I could use to do this step? Similarly if anyone knows other software tools/methods I could use to try and work out the implications of sequence changes I would be grateful for advice. Thanks, Simon
Re: [ccp4bb] Refmac5: put restraint on only peptide bonds
On Thu, 2011-06-23 at 16:49 +0900, Masaki UNNO wrote: > Dear all > Is it possible to put restraint on only peptide bonds? I would like > to put restraint on O-N bond lengths, Ca-O-N angles, and O=O-N angles. > Could you teach me how to do it, if possible? > Masaki UNNO, Ph.D. One could create a monomer library with a set of alternative amino acids (you'd rename them in the PDB-file too). Then, modeling a library after the standard one, you assign alternative atom types and have a limited set of defined bonds/angles. This would be quite painful to do though. I wonder what will happen if you run unrestrained refinement yet provide external distance restraints as described in refmac manual? Will the external restraints be ignored? If not, then I'd think this is a better approach. If yes, then maybe you can do the trick by using very high weight matrix parameter (approaching the unrestrained refinement) and correspondingly high external weight scale value. Cheers, Ed. -- "Hurry up before we all come back to our senses!" Julian, King of Lemurs
Re: [ccp4bb] Homology modelling
You might want to have a look at consurf, which maps conservation from an alignment onto a structure. http://consurf.tau.ac.il/ On 23/06/2011, at 6:42 PM, Simon Kolstoe wrote: > Dear ccp4bb, > > One of my colleagues is interested in how a certain protein differs between > species. He's done a blast search, collected all the aligned sequences, and > "emailed them to the crystallographer to tell him the implications of the > sequence changes". > > Although I am not at all confident that I can predict any implications based > upon sequence differences, I thought I could at least have a try by mapping > the different species sequences onto the existing structure and then > regularising it just to see what happens (and then perhaps looking at buried > surface area, electrostatics, subunit interfaces etc.). > > I know the program chainsaw can mutate the sequence based on an alignment, > however I can't stop it pruning non-conserved residues. Does anyone know of > another program that I could use to do this step? > > Similarly if anyone knows other software tools/methods I could use to try and > work out the implications of sequence changes I would be grateful for advice. > > Thanks, > > Simon
Re: [ccp4bb] Homology modelling
You might find the PHYRE server useful. It can also deal with gaps and loops. Can be useful for prepping MR models, too. Roger Rowlett On Jun 23, 2011 4:42 AM, "Simon Kolstoe" wrote: > Dear ccp4bb, > > One of my colleagues is interested in how a certain protein differs between species. He's done a blast search, collected all the aligned sequences, and "emailed them to the crystallographer to tell him the implications of the sequence changes". > > Although I am not at all confident that I can predict any implications based upon sequence differences, I thought I could at least have a try by mapping the different species sequences onto the existing structure and then regularising it just to see what happens (and then perhaps looking at buried surface area, electrostatics, subunit interfaces etc.). > > I know the program chainsaw can mutate the sequence based on an alignment, however I can't stop it pruning non-conserved residues. Does anyone know of another program that I could use to do this step? > > Similarly if anyone knows other software tools/methods I could use to try and work out the implications of sequence changes I would be grateful for advice. > > Thanks, > > Simon
Re: [ccp4bb] MR question
If it is of moderate resolution (3 ish), uncheck automatic weighting in RefMac and constrain to 0.007-0.01. You're probably over-fitting your data. -Joe Joseph M. Watts, Ph.D. Research Scientist Syngenta Biotechnology, Inc.
[ccp4bb] postgraduate studentship available
Dear ccp4bb, Apologies for the off-topic posting, but I would be grateful if you could bring the availability of the PhD studentship detailed below to anyone who may be interested. Funding restrictions dictate that the position is open to EU nationals who are normally domiciled in the UK. Many thanks Jim Spencer A PhD position will shortly be available (from 1st October 2011 or as soon as possible thereafter) in the laboratory of Dr J. Spencer in the School of Cellular and Molecular Medicine, University of Bristol, UK. The student will use a variety of structural (X-ray crystallography) and biophysical (enzyme inhibition assays, fluorescence and isothermal titration calorimetry) methods to study the interaction of metallo-beta-lactamases (MBLs) with a range of small molecule inhibitors. MBLs protect host bacteria, particularly Gram-negative species responsible for healthcare-associated infections, from almost all beta-lactam (pencillin and related) antibiotics, including carbapenems, the most effective current treatments for such infections. The studentship is funded for three years by the UK Medical Research Council and forms part of a larger collaborative network of laboratories in the UK and Canada that aims to develop new countermeasures for MBLs as a basis for improved treatments for infections by antibiotic-resistant Gram-negative bacteria. Applicants should have, or be about to obtain, a first or upper second class degree in a biomedical science (e.g. Microbiology, Biochemistry etc.) or a related discipline. Informal enquiries are welcome to Dr. Spencer (jim.spen...@bristol.ac.uk; (44) (0) 117 331 2084). Applications for postgraduate study may be made on online: http://www.bristol.ac.uk/prospectus/postgraduate/2011/intro/apply.html. Information on postgraduate study at the University of Bristol is available at: http://www.bristol.ac.uk/prospectus/postgraduate/2011 -- Dr. James Spencer, Lecturer in Microbiology School of Cellular and Molecular Medicine Medical Sciences Building University of Bristol University Walk Bristol BS8 1TD jim.spen...@bristol.ac.uk http://www.bristol.ac.uk/cellmolmed/staff/spencer.html -- Tel: (44) (0) 117 331 2084 Fax: (44) (0) 117 331 2091
[ccp4bb] P-CUBE workshop on Workshop on Advances in Protein Crystallization and 2nd P-CUBE User Meeting, 5 - 9 September 2011, Zurich, Switzerland
Dear All, Don't miss out on the P-CUBE workshop and user meeting in Zurich, September 5-9, 2011! Register today under www.p-cube.eu and learn everything about crystallization technologies. The registration deadline is June 30, 2011. See you in Zurich! P-CUBE Management Team *** 2nd P-CUBE User Meeting (5 Sept 2011) Get to know everything about the numerous platforms of P-CUBE and listen to the platform leaders presenting their infrastructure (Protein Expression in Bacterial & Eukaryotic Cells, MultiBac, ESPRIT, DARPins, High-throughput Crystallization, Advanced Microscopy). If you are a former user of one of the platforms, you might even get selected to speak about your data. All the others will have the opportunity to present posters. Workshop on Advances in Protein Crystallization (6-9 Sept 2011) The Workshop on Advances in Protein Crystallization allows you to bring your own protein sample and will cover the following topics: • Properties of macromolecular solutions for structural studies - Polishing methods • Biophysical/biochemical characterization of macromolecular solutions for structural studies • Crystallization of biological macromolecules (Effects of macromolecular solution properties, nucleation and growth, screening strategies, crystallization methods) • Strategies and special approaches to grow crystals (Counter diffusion, seeding, crystal evaluation) Speakers include: Nenad Ban, ETH Zurich (Keynote) Markus Grütter, University of Zurich, CH Andreas Plückthun, University of Zurich, CH Serge Chesnov, UZH/ETH Zurich, CH José Marquez, EMBL Grenoble, FR Patrick Shaw Stewart, Douglas Instruments Ltd, UK Mareike Kurz, University of Zurich, CH Paul Thaw, Molecular Dimensions Ltd, UK To apply for the P-CUBE User Meeting and the workshop please visit our web page at www.p-cube.eu. Scientists applying for the workshop will be asked to submit their CV as well as a letter of motivation. A maximum of 16 participants will be selected for the workshop. The meeting & workshop will be open to scientists from EU Member and/ or Associated States. General Information • There is no registration fee. • Lunch will be paid by P-CUBE. • Accommodation will be covered for workshop participants as well as selected speakers at the user meeting in the Hotel St Josef or Haus Justinus (shared rooms, 5 nights max. workshop, 2 nights max. user meeting). • Participants are responsible for their own travel costs. However, travel costs of speakers at the user meeting will be partially reimbursed (300 € max.). For more information, please contact Petra Lindemann (petra.lindem...@embl.de ) or Jutta Tatzel (j.tat...@bioc.uzh.ch) Dr Mareike Kurz m.k...@bioc.uzh.ch Department of Biochemistry University of Zürich, Irchel Winterthurstrasse 190 8057 Zürich, Switzerland +41446356557
Re: [ccp4bb] Homology modelling
COOT can do this very easily, just use the align and mutate command, cheers, Matt. On 23/06/2011 10:42, Simon Kolstoe wrote: Dear ccp4bb, One of my colleagues is interested in how a certain protein differs between species. He's done a blast search, collected all the aligned sequences, and "emailed them to the crystallographer to tell him the implications of the sequence changes". Although I am not at all confident that I can predict any implications based upon sequence differences, I thought I could at least have a try by mapping the different species sequences onto the existing structure and then regularising it just to see what happens (and then perhaps looking at buried surface area, electrostatics, subunit interfaces etc.). I know the program chainsaw can mutate the sequence based on an alignment, however I can't stop it pruning non-conserved residues. Does anyone know of another program that I could use to do this step? Similarly if anyone knows other software tools/methods I could use to try and work out the implications of sequence changes I would be grateful for advice. Thanks, Simon -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE === Tel: +33 (0) 4.76.88.29.28 Fax: +33 (0) 4.76.88.29.04 http://go.esrf.eu/MX http://go.esrf.eu/Bowler ===
[ccp4bb] Homology modelling
Dear ccp4bb, One of my colleagues is interested in how a certain protein differs between species. He's done a blast search, collected all the aligned sequences, and "emailed them to the crystallographer to tell him the implications of the sequence changes". Although I am not at all confident that I can predict any implications based upon sequence differences, I thought I could at least have a try by mapping the different species sequences onto the existing structure and then regularising it just to see what happens (and then perhaps looking at buried surface area, electrostatics, subunit interfaces etc.). I know the program chainsaw can mutate the sequence based on an alignment, however I can't stop it pruning non-conserved residues. Does anyone know of another program that I could use to do this step? Similarly if anyone knows other software tools/methods I could use to try and work out the implications of sequence changes I would be grateful for advice. Thanks, Simon
[ccp4bb] Refmac5: put restraint on only peptide bonds
Dear all Is it possible to put restraint on only peptide bonds? I would like to put restraint on O-N bond lengths, Ca-O-N angles, and O=O-N angles. Could you teach me how to do it, if possible? Best regards ~ Masaki UNNO, Ph.D. Frotier Research Center for Applied Atomic Sciences, Ibaraki University Ibaraki Quantum Beam Research Center 162-1 Tokai, Shirakata, Naka, Ibaraki 319-1106, Japan Tel: 029-352-3239, Fax: 029-287-7872 E-mail: unn...@mx.ibaraki.ac.jp HP: http://www.fas.ibaraki.ac.jp/?page_id=961 ~
