Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot
Hi Fred Well, it is ironic that after acquiring ability to determine a protein structure some times in a few minutes we are still failed my format conversions like 30 years ago :-( Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Jun 1, 2010, at 16:30 , Vellieux Frederic wrote: Hi Christian, Had exactly the same problem (converting an mmCIF file into a PDB). I located and installed CIFTr . The version I have running here is ciftr-v2.053 . I am afraid I can't remember exactly where I downloaded it from. I think it one of the PDB associated files. Fred. Christian Engel wrote: Dear All, I am looking for a ccp4 program that reads in cif-files and converts them into pdb-files, including the CRYST1 card. Can anybody suggest a solution? I didn't find any in ccp4i, e.g. the coordinate utilities. I also tried COOT to read in cif-files (downloaded from the pdb server). For one example it crashed, for others it doesn't colour the bonds properly if Bonds (Colour by Atom) is chosen but shows all bonds in one colour. Is that a known feature? If I save these coordinates in pdb-format and try to read it back, I get an ERROR saying: Wrong ASCII format of an integer. Thanks for any suggestions Christian Engel */Mit freundlichen Grüßen / Best regards / Cordialement/* Dr. Christian Engel Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 020 D-65926 Frankfurt am Main t: +49 69 305 12946 f: +49 69 305 80169 w:_www.sanofi-aventis.de_ 125 Jahre Arzneimittel aus Deutschland von sanofi-aventis * Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias Braun, Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Heinz Riederer *
Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot
My understanding from Gerard K is that the next version of the PDB format will also use unjustified atom names. Unfortunately, following mmdb, I also backed the wrong horse and assumed space-padded atom names were here to stay. A certain amount of re-engineering is going to be required. My current plan (which will be implemented in clipper, but I guess mmdb needs something similar) is to have two modes in the coordinate code: a legacy mode which auto pads atom names on read (which is easy if the element name is present and requires guesswork otherwise). By selecting this mode programs will work without other modification (a 1-line change). The new mode will auto-strip all padding from atom names. Programs which use atom names will need to be modified (mostly find-and-replace). When writing to a file, the atoms names will then need to be padded if and only if the file is in traditional PDB format. PDB files which don't have element names are going to be painful. I can't guarantee 100% compatibility in clipper::MiniMol, so the clipper major version will bump to 3.0. Paul Emsley wrote: As to the colours, that is also due, IMHO to a bug^H^H^H issue in the mmCIF file. The atom names and elements in the mmCIF file are not quoted so they result in simple left-hand justified strings - such as N - whereas from the corresponding PDB file one would get an atom name of N and an element of N. These mmCIF simple strings don't match Coot's (or, i imagine, many other macromolecular file-reading program's) expectation of atom names and elements - hence it is not recognised and is represented in grey.
Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot
You should be able to use the CCP4 utility coord_format though this is not in the GUI: coord_format xyzin ./1ivo.cif xyzout 1ivo.pdb eof END eof This converts at least some of the header, including the CRYST1 card. BUT: 1) slight glitch - you need to specify the full path for the cif file, otherwise it goes looking for a dictionary file 2) loading my first attempt into Coot, I also got the Wrong ASCII format of an integer message. This seems to be because the HETATMs have no residue number - a little text edit solves the problem. I seem to remember that this is deliberate in mmCIF and was the subject of some debate 10 years ago ... 3) yes, all the atom names are left justified, but Coot seems happy with that. This is because the element name is there, which in turn comes from _atom_site.type_symbol in the cif file HTH Martyn On Tue, 2010-06-01 at 15:21 +0200, Christian Engel wrote: Dear All, I am looking for a ccp4 program that reads in cif-files and converts them into pdb-files, including the CRYST1 card. Can anybody suggest a solution? I didn't find any in ccp4i, e.g. the coordinate utilities. I also tried COOT to read in cif-files (downloaded from the pdb server). For one example it crashed, for others it doesn't colour the bonds properly if Bonds (Colour by Atom) is chosen but shows all bonds in one colour. Is that a known feature? If I save these coordinates in pdb-format and try to read it back, I get an ERROR saying: Wrong ASCII format of an integer. Thanks for any suggestions Christian Engel Mit freundlichen Grüßen / Best regards / Cordialement Dr. Christian Engel Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 020 D-65926 Frankfurt am Main t: +49 69 305 12946 f: +49 69 305 80169 w:www.sanofi-aventis.de 125 Jahre Arzneimittel aus Deutschland von sanofi-aventis * Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias Braun, Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Heinz Riederer * -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot
There is a time-honored tradition of PhD students struggling through format conversion issues. Where is the fun and learning opportunity if everything ran smoothly? ;) Cheers, Steve -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Felix Frolow Sent: Wednesday, June 02, 2010 2:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot Hi Fred Well, it is ironic that after acquiring ability to determine a protein structure some times in a few minutes we are still failed my format conversions like 30 years ago :-( Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
[ccp4bb] Postdoctoral position at the Goethe University Frankfurt- Institute of Biochemistry
Post-doc Position at the Institute of Biochemistry at the Goethe University Frankfurt, Germany Robert Tampé and Martin Pos at the Institute of Biochemistry, Goethe University Frankfurt, are looking for an experienced crystallographer at the post-doctoral level to work on structures of membrane multidrug efflux proteins. The labs are well-equipped including robotics to facilitate overproduction and crystallization of membrane proteins and is embedded in the Cluster of Excellence Frankfurt Macromolecular Complexes ( http://www.cef-mc.de www.cef-mc.de). The Institute of Biochemistry is located in the Biocenter on a young and vibrant campus at the outskirts, yet near to the city of Frankfurt. For more information, please visit the web page: http://www.biochem.uni-frankfurt.de/index.php?id=7 http://www.biochem.uni-frankfurt.de/ Interested candidates can send their CV (closing date 21.06.2010) to: mailto:p...@em.uni-frankfurt.de p...@em.uni-frankfurt.de With kind regards, Martin Pos Klaas Martinus Pos, Ph.D. Professor of Membrane Transport Machineries Cluster of Excellence Frankfurt - Macromolecular Complexes Institute of Biochemistry Goethe-University Frankfurt am Main Max-von-Laue-Str. 9 D-60438 Frankfurt am Main Germany Tel: +49-69-798 29251 Fax: +49-69-798 29201 E-Mail: mailto:p...@em.uni-frankfurt.de p...@em.uni-frankfurt.de Website: http://www.biochem.uni-frankfurt.de/index.php?id=7 http://www.biochem.uni-frankfurt.de/index.php?id=7 http://www.sfb807.de/index.php?id=pos http://www.sfb807.de/index.php?id=pos
[ccp4bb] staff scientist position at the EMBL in Hamburg, Germany
STAFF SCIENTIST IN BIOLOGICAL X-RAY CRYSTALLOGRAPHY WITH SYNCHROTRON RADIATION European Molecular Biology Laboratory, Hamburg, Germany A position is available at the Structural Biology Unit of the EMBL in Hamburg. The Unit utilises synchrotron radiation at the German Synchrotron Research Centre (DESY) for research in structural biology. EMBL operates synchrotron beamlines at the DORIS-III storage ring (until the end of 2012), which are used by hundreds of external visitors per year as well as local research groups. EMBL is also building an integrated facility for structural biology at the new PETRA III storage ring at DESY, Hamburg, which will include the operation of world-class synchrotron radiation beamlines, providing an ideal research environment for future challenges in structural biology. We are seeking a scientist who will be involved in support of our crystallographic synchrotron beamline facilities initially at DORIS and subsequently at PETRA III. The post holder will be affiliated to the group of Victor Lamzin (http://www.embl-hamburg.de/research/unit/lamzin/index.html) and will be expected to carry out research projects in, e.g.: • Research and technology development for X-ray crystallography • Automation and integration of user-friendly synchrotron radiation data acquisition facilities • Research in structural biology on, e.g. projects of medical relevance, teaming up with ongoing research projects at the EMBL • Collaborations with external research groups on challenging structural biology and technology development projects Applicants should have a PhD in a relevant field, postdoctoral training, significant research accomplishments and expertise in macromolecular crystallography. Excellent communication and social skills and a good command of English are required. An initial contract of 3 years will be offered to the successful candidate. This can be renewed, depending on circumstances at the time of the review. Closing date for applications is 13 June 2010 For further information please look at http://www.embl-hamburg.de/aboutus/jobs/jobs_embl_hamburg/2010/w_10_039/index.html To apply, please email a cover letter, CV (in English) and contact information of three professional references quoting ref. no. W/10/039 in the subject line, to applicat...@embl.de General enquiries may be sent to j...@embl.de
[ccp4bb] About solvent flattening
Hi, I wanted to do solvent flattening for my map using Wang's method. I used CCP4-DM, and now have several questions: 1. DM seems requiring the FOM, so I generated FOM using SIGMAA by providing FP, FC and SIFFP using the following: sigmaa HKLIN in.mtz HKLOUT out-sigmaa.mtz eof title tt labin FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC labout DELFWT=DELFWT FWT=FWT WCMB=WCMB symmetry $spcgrp END eof # I think the output FOM should be in range between 0 to 1; however, it produced FOM between -1 to 1 based on my in.mtz. This leads to complaints by the following DM calculation, and I am not sure whether I could avoid this. 2. My DM script is as follows: # dm HKLIN ./1KP8-NewSharpRescaleB0-sigmaa-oriB.mtz HKLOUT ./1KP8-NewSharpRescaleB0-sigmaa-oriB_dm.mtzdmtest mode - SOLV - NOHIST combine PERT scheme ALL ncycles - 1 solc 0.6 solmask - frac 0.6 - 0.4 - radius 3.0 2 ncsmask LABIN FP = FWT SIGFP = SIGFP PHIO = PHIC FOMO = WCMB LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM FCDM=FCDM PHICDM=PHICDM END dmtest ## I am not sure whether there the above is ok for the purpose of a simple real-space solvent flattening using Wang's method. By the way, my map is at resolution 2.0, and I am not sure what is the best radius for this resolution. 2. Based on Wang's paper (Wang, B. C. (1985) Methods in Enzymology 115, 90-112), the solvent flattening is carried out in real space, and since my goal it simply modify my map, and I don't think I need FOM etc. So, can CCP4 (or anyother packages like Phenix, CNS, UPPSALA...,) provide a simple real-space solvent flattening without too much complications? Thanks a lot for any hints. Best Regards, Hailiang
[ccp4bb] Off-topic: hollow protein crystals
Kurt Krause's group solved a structure from hollow crystals: J. Mol. Biol. 2002 Apr 26;318(2):503-18. The crystal structure of Trichomonas vaginalis ferredoxin provides insight into metronidazole activation. Crossnoe CR, Germanas JP, LeMagueres P, Mustata G, Krause KL. From: Andre Ambrosio andre.ambro...@cebime.org.br Reply-To: Andre Ambrosio andre.ambro...@cebime.org.br Date: Wed, 2 Jun 2010 14:07:14 -0500 To: CCP4BB@JISCMAIL.AC.UK Conversation: [ccp4bb] Off-topic: hollow protein crystals Subject: [ccp4bb] Off-topic: hollow protein crystals Dear all, We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Regards, -Andre.
Re: [ccp4bb] About solvent flattening
Hi Hailiang, Be sure to include PARTIAL WCMB in your sigmaa script. This option outputs something more like a conventional FOM for use in DM. Also, I would allow DM to run more cycles and suggest starting with default parameters for solvent masking and density levels and then looking at the resulting maps. You have also specified ncsmask parameters without specifying ncs or asking the program to utilize ncs. Try the CCP4i GUI, it avoids many of these technical problems. Best, --Paul --- On Wed, 6/2/10, Hailiang Zhang zhan...@umbc.edu wrote: From: Hailiang Zhang zhan...@umbc.edu Subject: [ccp4bb] About solvent flattening To: CCP4BB@JISCMAIL.AC.UK Date: Wednesday, June 2, 2010, 3:04 PM Hi, I wanted to do solvent flattening for my map using Wang's method. I used CCP4-DM, and now have several questions: 1. DM seems requiring the FOM, so I generated FOM using SIGMAA by providing FP, FC and SIFFP using the following: sigmaa HKLIN in.mtz HKLOUT out-sigmaa.mtz eof title tt labin FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC labout DELFWT=DELFWT FWT=FWT WCMB=WCMB symmetry $spcgrp END eof # I think the output FOM should be in range between 0 to 1; however, it produced FOM between -1 to 1 based on my in.mtz. This leads to complaints by the following DM calculation, and I am not sure whether I could avoid this. 2. My DM script is as follows: # dm HKLIN ./1KP8-NewSharpRescaleB0-sigmaa-oriB.mtz HKLOUT ./1KP8-NewSharpRescaleB0-sigmaa-oriB_dm.mtzdmtest mode - SOLV - NOHIST combine PERT scheme ALL ncycles - 1 solc 0.6 solmask - frac 0.6 - 0.4 - radius 3.0 2 ncsmask LABIN FP = FWT SIGFP = SIGFP PHIO = PHIC FOMO = WCMB LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM FCDM=FCDM PHICDM=PHICDM END dmtest ## I am not sure whether there the above is ok for the purpose of a simple real-space solvent flattening using Wang's method. By the way, my map is at resolution 2.0, and I am not sure what is the best radius for this resolution. 2. Based on Wang's paper (Wang, B. C. (1985) Methods in Enzymology 115, 90-112), the solvent flattening is carried out in real space, and since my goal it simply modify my map, and I don't think I need FOM etc. So, can CCP4 (or anyother packages like Phenix, CNS, UPPSALA...,) provide a simple real-space solvent flattening without too much complications? Thanks a lot for any hints. Best Regards, Hailiang
Re: [ccp4bb] Off-topic: hollow protein crystals
On Wed, Jun 2, 2010 at 12:07 PM, Andre Ambrosio andre.ambro...@cebime.org.br wrote: We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Yes, I had very similar crystals once (PDB ID 2i6f*). They were in the I4 space group, and the lattice formed two solvent channels, one large, one small, which I assumed ran the entire length of the crystal. The chains adjacent to the large solvent channel were poorly ordered and nearly uninterpretable in some datasets, so my best guess is that the hollow crystals were the result of this disorder. Fortunately, it didn't appear to have any effect on the diffraction quality. -Nat (* which still shows To be published, 3 years after we published it - does the PDB not figure this out automatically?)
Re: [ccp4bb] Off-topic: hollow protein crystals
Andre I had same kind of crystal like in your picture. It diffracted around 2.7A. Even I had some crystals where one end was closed. Both hollow crystal or the closed end (part) crystal diffracted same. With regards Syed --- On Thu, 6/3/10, Andre Ambrosio andre.ambro...@cebime.org.br wrote: From: Andre Ambrosio andre.ambro...@cebime.org.br Subject: [ccp4bb] Off-topic: hollow protein crystals To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, June 3, 2010, 12:37 AM Dear all, We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Regards, -Andre.
Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot
Don't you worry, there's a lifetime of learning opportunities. I used to spend almost as much time helping senior PIs with format conversion as new students. Got to love the pdb ho --- From:Soisson, Stephen M stephen_sois...@merck.com Subject: Re: Converting cif-files into pdb-files / reading cif -files into coot There is a time-honored tradition of PhD students struggling through format conversion issues. Where is the fun and learning opportunity if everything ran smoothly? ;) Cheers, Steve
