Re: [ccp4bb] I/sigma for h+k=2n+1 and h+k=2n
From memory - check the documentation mtzutils hklin1 data.mtz RZONE 1 1 0 2 0 lists reflections with h+k = 2n END mtzutils hklin1 data.mtz RZONE 1 1 0 2 1 lists reflections with h+k = 2n+1 END Eleanor This will list all On Tue, 26 Jul 2011 09:51:47 -0400, zhang yu ccp4f...@gmail.com wrote: Hi, I had a dataset which is P21 but with a pseudo-translational symmetry of (1/2, 1/2 ,0). Theoretically the dataset should show systematic weak spots of h+K= 2n+1 compared to h+k= 2n. Is that correct? I would like to have a close look at the reflections. for example, the average I/sigma for reflections with h+k=2n+1 and reflections with h+k=2n. Which software could do this job? A brief tutorial is appreciated. Yu
[ccp4bb] International Conference Multi-Pole Approach to Structural Biology
Dear Colleagues, We are pleased to announce the call for abstracts (posters talks) for: International Conference Multi-Pole Approach to Structural Biology November 16-19, 2011 | Warsaw, Poland The submission deadline for abstracts, to be considered for a talk, is August 31, 2011 Early registration deadline is also August 31, 2011: regular fee: 500 PLN = 125 Euro student fee: 300 PLN = 75 Euro Please see our website for details programme: http://iimcb.genesilico.pl/multipole/ The purpose of the conference is to present and discuss the advances of structural biology. 35 invited lectures will be delivered by accomplished scholars with significant links to Poland, who have had successful scientific careers around the world, working in a general field of structural biology, including biocrystallography and structural bioinformatics. Confirmed speakers include: Alex Wlodawer, Jacek Lubkowski, Krzysztof Appelt, Grzegorz Bujacz, Piotr Zielenkiewicz, Lukasz Lebioda, Marek Brzozowski, Mariusz Jaskolski, Andrzej Joachimiak, Zygmunt Derewenda, Pawel Grochulski, Mirek Cygler, Krzysztof Lewinski, Wladek Minor, Krzysztof Fidelis, Andrzej Kolinski, Adam Liwo, Andrzej Kloczkowski, Krzysztof Ginalski, Jarek Meller, Roman Laskowski, Witek Filipowicz, Marcin Nowotny, Matthias Bochtler, Zbyszek Dauter, Teresa Przytycka, Jacek Blazewicz, Janusz Bujnicki, Krzysztof Wozniak, Andrzej Sokalski, Bogdan Lesyng, Wieslaw Nowak, Marek Cieplak, Zbyszek Otwinowski, and Adam Godzik. Additional talks will be selected from submitted abstracts. We welcome submissions on all aspects of structural biology and bioinformatics, and in other related fields of research. The conference will be entirely in English and we encourage both national and international participants to register and attend. Make plans for your participation now - register today! We would also greatly appreciate if you could forward this announcement to anybody who may be interested, and if you post the poster available at the conference's website at a message board in your institution. Yours sincerely, Janusz Bujnicki on behalf of the Organizing Commiittee P.S. Apologies for possible multiple postings!
Re: [ccp4bb] Modified residue list
Dear Bernhard, Funnily enough we wanted to do precisely that yesterday and the kind folks at the PDBe sent us this csv file (attached, but small). It is the result of a query in the PDBe/chem database of all residues for which the molecule type is amino acid. Other than all the cases you are after it includes names longer than 1-letter which are derived from di-, tri- and tetra-peptides and several X residues which have the alpha-amino acid mainchain but sidechains which cannot be considered to be derived from natural amino acids. Hope this helps, Robert -- Dr. Robert Esnouf, University Research Lecturer and Head of Research Computing, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK Emails: rob...@strubi.ox.ac.uk Tel: (+44) - 1865 - 287783 and rob...@esnouf.comFax: (+44) - 1865 - 287547 table_export.csv Description: MS-Excel spreadsheet
Re: [ccp4bb] small lysozyme crystals?
James One thing you should be aware of is that bugs growing in the lysozyme stock solution can have a dramatic effect on the number and size of crystals. (Way, way) back in 1993 when I was in David Blow's lab we noticed an ageing effect with the lysozyme stock solution; if we dissolved freeze-dried lysozyme and set up experiments immediately we got a few large crystals. If, however, we did exactly the same thing except that we kept the lysozyme protein stock overnight in an Eppendorf tube (using a certain batch of tubes), then set up experiments the next morning, we grew dozens of small crystals. The effect seemed to be caused by fungi that were growing in the tubes because fungicides eliminated the effect whereas antibiotics didn't, see below. I have often wondered whether people designing e.g. microgravity experiments that are stored for several days before launching are aware of this! Best wishes Patrick See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2142306/ Abstract This work investigates the influence of storage of lysozyme in solution on its crystallization. The crystallization of hen egg-white lysozyme exhibits a storage effect (aging) that depends on the length of time the lysozyme solution is stored, after dissolving from freeze-dried powder, before being brought to crystallization conditions. The number of crystals obtained increases, while their size decreases, as the solution ages. Observations suggest that this effect is due to the presence of fungi that multiply in the stored protein solution. This aging effect was used to control nucleation and determine the number and size of lysozyme crystals to be formed in a given sample. Summary of results 1. Under the particular conditionosf these experiments, growth of lysozyme crystals depends on thep resence of a nucleating agent. 2. Aging of lysozyme in solution gives rise to enhanced nucleation. 3. The aging effect is independent of the source of the lysozyme powder. 4. Filtration or centrifugation prior to aging does not eliminate the aging but lessens the number of crystals grown. 5. The agent responsible for the enhanced nucleation can be removed by centrifugation or filtration even after aging has occurred. 6. Desalting increases aging. 7. Aging is prevented by antifungal agents but is not affected by either class of antibiotics. 8. Aging is eliminated when a filtered solution is stored in a sterile vial. 9. Nucleation (and consequently the number of crystals grown) can be controlled by altering the ratio of freshly filtered and aged protein solution just prior to crystallization. On Tue, Jul 26, 2011 at 6:56 PM, James Holton jmhol...@lbl.gov wrote: Does anyone out there have a protocol of growing HEWL crystals that are all 50-100 microns wide? I gave this project to a summer student recently, thinking it would be easy, but it is turning out to be more difficult than I thought. Keep getting sphereulites instead of small crystals. Yes, I know you can smash a large lysozyme crystal with a hammer, but that is not exactly what I was going for. What I was hoping for was a well-defined protocol for growing reference crystals that stay evenly illuminated in our x-ray beams as they rotate. The beam is 100 um wide. I'm sure someone has done this before? -James Holton MAD Scientist -- patr...@douglas.co.uk Douglas Instruments Ltd. DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090 US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
[ccp4bb] Purity of DNA oligos in protein co-crystal attempts.
Dear all, I am trying to decide on the many variables I need to consider to attempt a co-crystal between a protein I work on and a DNA oligo of ~35nt in length. As well as molar ratio which from the literature I have seen 1.2-1.5 in excess of DNA, I note from the various oligo companies that there are several levels of purity available. I would be very interested to hear from you about your experiences specifically trying VARIOUS purity levels and also the specific company you used? Also, any rationalisation as to what the contaminating entities are which may prevent co-crystallisation would be welcome. If you reply direct to me, I would be happy to provide a digest of responses for the board? Any help/advice/anecdotes would be most appreciated. Cheers, charlie Dr. Charles Allerston Genome Integrity Group Structural Genomics Consortium Nuffield Department of Medicine Old Road Campus University of Oxford OX3 7DQ http://www.sgc.ox.ac.uk/
Re: [ccp4bb] Purity of DNA oligos in protein co-crystal attempts.
On Wed, 2011-07-27 at 13:42 +0100, Charles Allerston wrote: I am trying to decide on the many variables I need to consider to attempt a co-crystal between a protein I work on and a DNA oligo of ~35nt in length. In my somewhat limited protein:DNA crystallization experience, the less pure oligos are just fine. I suspect that protein:DNA complex crystallization is just like protein crystallization - every system is different and whatever worked for someone in the past may not be applicable in your case. Basic rules are (may the protein:DNA crystallization experts correct me and expand the list): 1. Keep the DNA length close to whole number of turns. 2. Try blunt ends, single and double overhangs. 3. Slight DNA excess. 4. May try less purified (and thus cheaper) DNA first. Some anecdotes: 1. Everyone knows complex can be purified, but it is rarely done. 2. Screens designed to crystallize protein:DNA complexes are a hoax. 3. Bet on PEG! 4. Don't give up on 10A resolution - just shoot ~1000 crystals and one will give you a nasty twinned 3A dataset. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] small lysozyme crystals?
i wonder if crushing with a hammer maybe a good first step. does streak seeding after that give smaller crystals amongst the range of different size crystals possible. perhaps? either way would be good for the summer student to try out. -- Karthik On Tue, Jul 26, 2011 at 10:55 AM, James Holton jmhol...@lbl.gov wrote: Does anyone out there have a protocol of growing HEWL crystals that are all 50-100 microns wide? I gave this project to a summer student recently, thinking it would be easy, but it is turning out to be more difficult than I thought. Keep getting sphereulites instead of small crystals. Yes, I know you can smash a large lysozyme crystal with a hammer, but that is not exactly what I was going for. What I was hoping for was a well-defined protocol for growing reference crystals that stay evenly illuminated in our x-ray beams as they rotate. The beam is 100 um wide. I'm sure someone has done this before? -James Holton MAD Scientist
[ccp4bb] NXClient on OSX Lion
Those of you who need NXClient should upgrade to NXPlayer, even though it's an alpha release it seems to work fine on Lion for connections to SSRL. NXClient won't work on Lion as it is 32bit PPC Along those lines Kaleidagraph needs to be updated to 4.1.2 then it works fine under Lion. Existing fink builds seem to work, however I can't get fink to compile something right now. But Bill has updated his webpage, which I should take a look at. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] How to build N-terminal PCA?
The residue PCA can be added directly from Coot using File...Get Monomer and choosing "PCA". Once positioned properly, the peptide bond links will be recognized by Coot and Refmac and refinement is no problem. If using CNS, you may have to include the proper parameter and topology files from your favorite source, e.g. HIC-UP. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 7/27/2011 9:38 AM, Huayue Li wrote: Dear all, I have got a problem on building the N-terminal pyroglutamic acid (PCA). I'm afraid I have successfully defined *.top, *.param and *.link files of PCA; and also successfullyoutput *.mtf and *.pdb files. Everything seems right! I can not find any problem within these files. However, when the annealing.inp executed, it did not output *.pdb files. What is the problem? I will attach corresponding files together. Thank you very much! Huayue College of Pharmacy Pusan National University Busan, Korea
Re: [ccp4bb] small lysozyme crystals?
As a bit of an aside, my current reference crystal of choice is a Germanium Oxide with a 51.3Ang cubic cell. see here: http://www.nature.com/nature/journal/v437/n7059/full/nature04097.html It is much more raditation hard than protein so I can do repeated measurements in the synchrotron beam without radiation damage becoming a factor. It is also physically harder than protein crystal making it easy to break up into sizes of choice and there is no worry about keeping it optimally hydrated. Cheers, Danny DLS I24 Micro-focus Beamline
Re: [ccp4bb] How to build N-terminal PCA?
Huayue Li lihua...@naver.com writes: I have got a problem on building the N-terminal pyroglutamic acid (PCA). I'm afraid I have successfully defined *.top, *.param and *.link files of PCA; and also successfully output *.mtf and *.pdb files. Everything seems right! I can not find any problem within these files. However, when the annealing.inp executed, it did not output *.pdb files. What is the problem? I will attach corresponding files together. It just seems to fail mid‐job! Are you sure it’s nothing trivial, like disk space? -- Ian ◎
[ccp4bb] pdb_extact and refmac5.6
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 work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
Re: [ccp4bb] pdb_extact and refmac5.6
Hi Jan, Have you tried using the x.refmac file that is created instead of the log file. It is in cif format and may be in the DepositFiles directory. Hope you are well and talk to you later, 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 Wed, 27 Jul 2011, 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 work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
[ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 27, 2011, at 20:31, Jonathan Kay jp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
On Wednesday, 27 July 2011, you wrote: Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Sure. I hit the same problem trying to install Arp/wARP on Mandriva. The specific error message you quote comes because the install script fails to create the temp directory before trying to unpack into it. You can fix that by creating the directory by hand first. Unfortunately, that doesn't help very much. The next thing that happens is that the ccp4i installer complains that the tarball is not recognized as a ccp4i install tarball. I gave up at that point. Ethan Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 27, 2011, at 20:31, Jonathan Kay jp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan
[ccp4bb] Fab:antigen complex crystallization!!!
Hi everyone, I have been trying to crystallize Fab:antigen complex( 50kda:90kDa) complex and initially got needle clusters which after microseeding gave me single crystals but they are very small and I could not repeat the results. I have been using HEPES buffer at pH 6.8 to do the final SEC purification step of the complex before setting trays. I was wondering whether there are some other buffers (that one could suggest eg tris-hcl etc) which have given decent positive results when crystallizing Fab complexes.Though I have gone through individual papers (case by case) to get some idea, It would be great if anyone could direct me to a comprehensive literature towards studying the crystatllization conditions of Fab complexes. Equally, people who have considerable experience could suggest a list of must do steps for such problems which have routinely been practiced in their lab Also what is a good storage condition for the excess complex that you want to use later? I would really appreciate any suggestion,help, direction. Thanks ivan
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
A plea from West Australia too. I was sitting with someone yesterday who was trying to install it on a Mac , and finding it a nightmare. He finally got it set up as a local installation, whereupon it promtly failed. The message said See refmac-last.log but that told us nothing, and indeed refmac seemed to have worked.. Can someone - either CCP4 or arp-warp people check this out? Eleanor On Wed, 27 Jul 2011 20:35:50 -0700, Ethan Merritt merr...@u.washington.edu wrote: On Wednesday, 27 July 2011, you wrote: Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Sure. I hit the same problem trying to install Arp/wARP on Mandriva. The specific error message you quote comes because the install script fails to create the temp directory before trying to unpack into it. You can fix that by creating the directory by hand first. Unfortunately, that doesn't help very much. The next thing that happens is that the ccp4i installer complains that the tarball is not recognized as a ccp4i install tarball. I gave up at that point. Ethan Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 27, 2011, at 20:31, Jonathan Kay jp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan
Re: [ccp4bb] Fab:antigen complex crystallization!!!
Dear Ivan, If you take a look at the MPCD ( http://www.cinam.univ-mrs.fr/mpcd/ ) and search for Fab it brings up 172 crystallization conditions. The names should help you narrow down, which conditions are of a complex. Hopefully, you can use those conditions to help you decide, which direction you want to head. Spoiler - Fabs like ammonium sulfate. Take Care, Sean P212121 http://store.p212121.com/
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
... strange, I have not seen any problems installing ARPwARP 7.1 on a new CCP6-6.2.0 install on - linux centos - os-x snow leopard, here I initially ran into write permissions issues and wound up changing the ownership of the /Applications/ccp4-6.2.0 directory Cheers Jan On Jul 27, 2011, at 9:00 PM, ccp4 wrote: A plea from West Australia too. I was sitting with someone yesterday who was trying to install it on a Mac , and finding it a nightmare. He finally got it set up as a local installation, whereupon it promtly failed. The message said See refmac-last.log but that told us nothing, and indeed refmac seemed to have worked.. Can someone - either CCP4 or arp-warp people check this out? Eleanor On Wed, 27 Jul 2011 20:35:50 -0700, Ethan Merritt merr...@u.washington.edu wrote: On Wednesday, 27 July 2011, you wrote: Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Sure. I hit the same problem trying to install Arp/wARP on Mandriva. The specific error message you quote comes because the install script fails to create the temp directory before trying to unpack into it. You can fix that by creating the directory by hand first. Unfortunately, that doesn't help very much. The next thing that happens is that the ccp4i installer complains that the tarball is not recognized as a ccp4i install tarball. I gave up at that point. Ethan Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 27, 2011, at 20:31, Jonathan Kay jp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
