Re: [ccp4bb] research paper
Jung-Hoon, This is a so-called WaReZ request, which could get you banned a lot of webfora. Of course, we are all guilty of it at some occasions. The best way to get an article is to ask the authors, they are allowed give away free copies (depending on the journal I guess). Hooray, for authors who pay open access fees. Cheers, Robbie Date: Thu, 28 Jul 2011 12:23:10 -0400 From: f...@bernstein-plus-sons.com Subject: Re: [ccp4bb] research paper To: CCP4BB@JISCMAIL.AC.UK The article is available for purchase for $40. Journals cannot survive without funding which can come from many sources - subscriptions, author payment to make the article open-access, etc. But asking someone to provide a 'free' copy without Acta's permission is tantamount to theft. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** * Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 = On Thu, 28 Jul 2011, Ed Pozharski wrote: On Thu, 2011-07-28 at 14:35 +, Jung-Hoon Lee wrote: Acta Cryst D63 (2007), 550-554. I can't believe Cornell has no access to Acta D. -- Hurry up before we all come back to our senses! Julian, King of Lemurs
[ccp4bb] Serious error in Pointless versions 1.5.x, sincere apologies
Summary There is a serious error in all the 1.5.x versions of Pointless for certain cases, fixed now in version 1.6.1 available now from our ftp site. The wrong 1.5.x versions have been distributed by CCP4 in releases 6.1.24 and the recent 6.2.0, but earlier CCP4 releases (6.1.13 and before) contained earlier versions of Pointless (eg 1.4.x versions) which do not suffer from this bug. However I know that people have installed 1.5.x versions from our ftp site. I would like to apologise for problems caused by this error mea culpa Phil Evans === Corrected versions ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre pointless-1.6.1.linux linux executable pointless-1.6.1.osx10.6 osx 10.6 executable pointless-1.6.1.tar.gz source pointless.html doc === What cases does the bug affect? The bug may scramble the order of symmetry operators relative to the ISYM flags on each observation (see below, technicalities), leading to an incorrect reconstruction of the original hkl indices in Scala or Aimless. This happens for MTZ input files (usually from Mosflm) integrated is the highest point group in higher symmetry lattices, specifically tetragonal 422, hexagonal 622, rhombohedral R32 and cubic 432, when the output file is also in the same point group. In these cases, the output file will be wrong even if Pointless is just copying from input to output (-c or COPY options) The bug does NOT affect: 1) lower symmetry lattices (triclinic, monoclinic, orthorhombic) 2) data input or output in lower than maximum point group symmetry within the same Laue class (eg 4, 3, 321, 23, R3) 3) XDS or other non-MTZ input === How serious is it? Files with scrambled symmetry operators will lead to wrong reconstruction of the original indices which are used in Scala or Aimless to generate beam directions for the SECONDARY absorption correction. Thus the error will have the biggest effect on long wavelength data with substantial absorption, and have much less effect on typical short wavelength data. High multiplicity will also tend to average out the errors. === Technicalities Unmerged MTZ files store for each observation the hkl indices reduced to the asymmetric unit and a flag ISYM which is the index into the list of space group symmetry operators stored in the file. This information can then be used to reconstruct the original hkl indices measured. This bug caused to order of the symmetry operators to be changed without changing the ISYM flags, leading to a wrong reconstruction of original hkl in Scala/Aimless, and hence wrong secondary beam directions for the absorption correction.
Re: [ccp4bb] pdb_extact and refmac5.6
Hello, We are currently in the final stages of updating the standalone version of pdb_extract. In the meantime, we encourage users to try the web server version of the program at http://pdb-extract.rcsb.org/ The PDB_extract will: # provide you with an author information form, which can be saved/updated for multiple related entries # assemble coordinate and log files pertaining to your specific experimental methods # allow you to fix the primary sequence of your protein/nucleotide chains to account for unresolved residues # output the coordinate (and structure factor files, if applicable) in mmCIF format for Validation and for deposition at RCSB ADIT or PDBj ADIT. If the web version produces similar errors, please email the log file to use at depo...@deposit.rcsb.org and we will look into it. Sincerely, Jasmine Jan Abendroth wrote: Hi all, we typically use pdb_extract to generate pdb files with a good header. There seems to be an issue with logfiles from refmac5.6.0117, distributed with the current ccp4 version, and pdb_extract. pdb_extract version-3.006 is distributed with ccp4-6.2.0. While reading the refmac log file, pdb_extract chokes with a segmentation fault. When run without reading in the refmac log file, the program complains about the following missing link, both in the linux and osx distribution of ccp4. Can not open file (/usr/local/ccp4/ccp4-6.2.0/ccp4-6.2.0//src/harvest_app_/pdb_extract/pdb-extract-data/mmcif_pdbx_2.items) in get_lines_from_file pdb_extract version-3.010, as downloaded form the rcsb webpage also chokes on the refmac5 logfile with a segmentation fault. Any ideas how to treat the new refmac log files in pdb_extract? Thanks a lot. Jan -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com http://Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com -- Jasmine Young, Ph.D. RCSB Protein Data Bank Assistant Research Professor Lead biocurator Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey 610 Taylor Road Piscataway, NJ 08854-8087 Email: jas...@rcsb.rutgers.edu Phone: (732)-445-0103 Fax:(732)-445-4320
[ccp4bb] Post-doc positions at Colorado State
This is a reposting of Post-doc ad with the full-consideration application deadline next week. Note that there are multiple independent post-docs with projects involving mostly crystallography or mostly biochemistry. === Post-doctoral fellow positions in ubiquitin signaling and RNA virus replication The Peersen and Cohen laboratories at Colorado State University in Fort Collins are recruiting up to three post-doc positions for studies of macromolecular interactions and structure. The positions require a Ph.D. at time of hire with prior experience in protein biochemistry, molecular biology, or biophysical methods. The Peersen lab projects are focused on the structures of viral RNA-dependent RNA polymerases and the assembly of membrane anchored replication centers formed by single stranded RNA viruses. The projects will build on recent studies of viral elongation complexes (Gong Peersen, PNAS 107:22505, Hobdey et al., J. Virology 84:8072) to further our understanding of polymerase function, replication fidelity, and higher order assemblies. Previous experience in X-ray crystallography, RNA biochemistry, membrane systems, or fluorescence methods would be advantageous. The Cohen laboratory position is to study mechanisms of signaling by polyubiquitin. Recent work defined the linkage-specific avidity mechanism for polyubiquitin binding (Sims Cohen, Mol Cell 33:775-783; Sims et al., Nat. Struct. Mol. Biol. 16:883-889). Available projects include studies of polyubiquitin receptor proteins, development of linkage-specific polyubiquitin sensors, and investigation of the role of linkage-specificity in signaling by polyubiquitin in vivo. Candidates should have prior experience in protein biochemistry and molecular biology; familiarity with biophysical methods or mammalian cell culture is desirable. Applications should be received by August 5, 2011 for full consideration. Interested individuals should submit a CV, statement of research and career interests, and contact information for three references at http://www.natsci.colostate.edu/employment/bmbPdoc/ CSU is an EO/EA/AA employer. CSU conducts background checks on all final candidates.
Re: [ccp4bb] Fab:antigen complex crystallization!!!
Thanks everyone, I got my crystals with PEG 8000 at first and after micro-seeding aith PEG 3350.Now I would work with all your suggestions and references with new vigor. ivan On Thu, Jul 28, 2011 at 9:43 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: Ed (and Ivan) Peter Sun and colleagues published two papers where they show that crystallization conditions for protein-protein complexes are strongly biased towards PEG-based rather than high-salt or organic-solvent-based conditions. This includes antibody-antigen complexes. http://www.ncbi.nlm.nih.gov/pubmed/16699187 http://scripts.iucr.org/cgi-bin/paper?do0016 I have heard anecdotally that the same is true of protein-peptide and protein-small molecule complexes, although I don't know of any systematic study. Can anyone shed light on this? I guess we can look in the Marseilles database Best wishes to all Patrick On Thu, Jul 28, 2011 at 2:32 PM, Ed Pozharski epozh...@umaryland.edu wrote: On Thu, 2011-07-28 at 05:07 +0100, Sean Seaver wrote: Spoiler - Fabs like ammonium sulfate. Not really - in my hands the ammonium sulfate was one hit out of 7. While Ivan's question is about Fab complexes with protein antigen, I think it brings up a more general question of protein class-dependent crystallization bias. While some general trends exist for classes of biopolymers (e.g. MPD is number one precipitant for DNA; protein:DNA complexes tend to crystallize in PEG-based conditions), a general idea of assigning a preferred precipitant to a protein class is, imho, pointless. Fabs are a good example - one would think that with half of the protein more or less the same in all instances some general trends should exist. And perhaps they do, as this http://scripts.iucr.org/cgi-bin/paper?S0907444999016224 seems to suggest. But alas, Fab crystallization conditions, once you look into it, appear to be just as diverse as the same for proteins in general. Crystallization conditions may change radically upon point mutation, so why would one expect that a class of proteins sharing some 50% identity will show unusual love for PEG, ammonium sulfate, sodium malonate or any other miracle precipitant? Consider this. Thanks to great engineering at the Douglas Instruments, we can routinely set up ~1000 drops for a given protein. If one of them shows a crystalline shower, we celebrate. To me, the fact that we try wrong crystallization conditions 99.9% of the time, proves that any attempt to predict crystallization conditions beyond vague things like keep pH close to protein pI, sodium malonate is cool, PEG and ammonium sulfate are two most successful precipitants in history of protein crystallography, etc., is futile. Time wasted on looking into what is the most common precipitant for a particular class of proteins is better spent on setting up more trays. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs -- patr...@douglas.co.ukDouglas Instruments Ltd. DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
[ccp4bb] Newbie Installation Question
Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best,
Re: [ccp4bb] Newbie Installation Question
I've had problems too. Some of the files are non-readable, so you need to do a sudo chmod -R a+r * to make them readable. Also it looks like the libraries changed a bit (at least for ADP). Bernie On Fri, July 29, 2011 2:08 pm, Yuri wrote: Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best,
Re: [ccp4bb] Newbie Installation Question
On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote: Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best, It is most likely that your default shell is bash and you are trying to source tsch script, which naturally fails. Try /setup-scripts/sh/ccp4.setup instead. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Newbie Installation Question
I tried that too ... no success On Fri, 29 Jul 2011 15:28:58 -0400, Ed Pozharski wrote: On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote: Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best, It is most likely that your default shell is bash and you are trying to source tsch script, which naturally fails. Try /setup-scripts/sh/ccp4.setup instead. -- Yuri Pompeu
Re: [ccp4bb] Newbie Installation Question
Hi, where did you install CCP4? from the path of your setup-script it seems like to be in the root (/) ? It looks like the problem I posted some days before but probably being buried in the middle of the other thread. Since it's more related to this topic so I paste it again, hoping that it can solve your question. I recently found the problem that after finishing the installation of CCP4-6.2.0 on RHEL5, if the installation destination is not the default path (/usr/local/), the ccp4.setup for csh wouldn't take the customized TCLTK path correctly. No matter if I used sh or csh to install the CCP4 package. This would result in programs using wish failed to start (e.g., ccp4i) from csh. Perhaps it's also related to the issue in this thread. The way to solve this problem is to manually edit the ccp4.setup for csh and correct the TCLTK path. If you have no idea you can just copy the correct one in the ccp4.setup for sh. Wei-Chun On Fri, Jul 29, 2011 at 9:08 PM, Yuri yuri.pom...@ufl.edu wrote: Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best, -- Wei-Chun Kao, MSc. TEL: +49-761-203-5277 Institute for Biochemistry and Molecular Biology Albert-Ludwigs-Universitaet Freiburg im Breisgau Stefan-Meier-Str. 17 D-79104 Freiburg im Breisgau Germany
Re: [ccp4bb] Newbie Installation Question
yes, I noticed the default was TCLTK /usr/local/bin. I think it should be /usr/local/username.../tcltkplusplus/bin Even after editing this it doesnt launch. the command not found message is gone though On Fri, 29 Jul 2011 22:02:22 +0200, Wei-Chun Kao wrote: Hi, where did you install CCP4? from the path of your setup-script it seems like to be in the root (/) ? It looks like the problem I posted some days before but probably being buried in the middle of the other thread. Since it's more related to this topic so I paste it again, hoping that it can solve your question. I recently found the problem that after finishing the installation of CCP4-6.2.0 on RHEL5, if the installation destination is not the default path (/usr/local/), the ccp4.setup for csh wouldn't take the customized TCLTK path correctly. No matter if I used sh or csh to install the CCP4 package. This would result in programs using wish failed to start (e.g., ccp4i) from csh. Perhaps it's also related to the issue in this thread. The way to solve this problem is to manually edit the ccp4.setup for csh and correct the TCLTK path. If you have no idea you can just copy the correct one in the ccp4.setup for sh. Wei-Chun On Fri, Jul 29, 2011 at 9:08 PM, Yuri wrote: Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best, -- Wei-Chun Kao, MSc. TEL: +49-761-203-5277 Institute for Biochemistry and Molecular Biology Albert-Ludwigs-Universitaet Freiburg im Breisgau Stefan-Meier-Str. 17 D-79104 Freiburg im Breisgau Germany -- Yuri Pompeu Links: -- [1] mailto:yuri.pom...@ufl.edu
Re: [ccp4bb] Newbie Installation Question
I downloaded the package for RHEL5. My default shell is sh. But I can change environments. I have progrmas that I must run in tcsh. I tried sourcing sh and csh setups. With the csh setup, after I changed the PATH in the ccp4.setup file (originally set to usr/local/bin), I type ccp4 and I get no error. I am a bit at loss with the sh setup I tried sourcing and I get a command not found message, which leads me to think I am not succeding in sourcing it. Someone mentioned something about some files are not readable... I tried running the executables in the /bin directory but nothing happens... Thank you On Fri, 29 Jul 2011 13:53:49 -0700, Iain Kerr wrote: What is the output when you try to launch ccp4i ? Are there any error messages ? Problems with Tcl/Tk will usually return an error about not being able to locate a specific library. Can you launch the programs independent of the GUI ? eg. if you go to where the executables are (CCP4/ccp4-6.2.0/bin) ./mtzdump You should see some output giving the program version etc. and a list of keyword options. If so, the installation is probably OK and as Ed suggested it could be an environment problem. Why don't you outline the specific steps you've taken so far during installation and environment set up - what shell are you using ? did you download the source code or binaries ? what Tcl/Tk version are you using and where did you get it from ? I can help with this, off the board and then if we find a solution you can post it on the BB. Iain On 7/29/2011 12:37 PM, Yuri wrote: I tried that too ... no success On Fri, 29 Jul 2011 15:28:58 -0400, Ed Pozharski wrote: On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote: Dear all, I have just downloaded and installed the ccp4-6.2.0. It says all I should do next is source the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot launch the program... Any help is welcome...(it is probably something really stupid on my part...) Best, It is most likely that your default shell is bash and you are trying to source tsch script, which naturally fails. Try /setup-scripts/sh/ccp4.setup instead. -- Yuri Pompeu
