[ccp4bb] arp/warp
Dear all, I am getting an error message when I run arp/warp using CCP4i. */"QUITTING ... ARP/wARP module stopped with an error message: RESTRAINTS *** Look for error message in the file: /home/rafael/MAD/CCP4/2_warpNtrace_build.last.log [1] 11549/* The only error message I can find on the above file is: /*:1: parser error : Document is empty XMLOutputFilename = 'snow_log.xml' ^ Parameter Stream does NOT contain XML, this is the reason for the previous message (parser error). Will try to parse it as a variable file (each line being a 'variableName=value' pair).*/ Any ideas? Cheers, Rafael. -- Rafael Couñago Research Fellow Department of Biochemistry University of Otago 710 Cumberland St Dunedin, New Zealand ph: (03) 479 5148
[ccp4bb] Arp/wARP
Hi, I've installed the entire CCP4 7.1 package (ShelX and arpWarp); however, I can't find the arp/Warp binaries/scripts (e.g. auto_em.sh). Are these not included with the CCP4 package? If not, why not? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Arp/warp error
Dear all I am getting this error while running arp/warp to build DNA/RNA: PHIB is not assigned to an mtz label Input was merged data (.mtz) However no such problem while using arp/warp classic as i chose for automated model building from existing model and not experimental phases. Kindly help how to give PHIB and FOM labels here?? Thanx in advance Monica
[ccp4bb] arp/warp error
I've recently installed arp/warp(7.1) in ccp4 6.2 in linux i686,the problem is whenever I'm trying to run arp/warp navigator or any other programs under arp/warp it gives the error " cannot get environment variable for warpbin" Please help. Thanks in advance. Seema Nath
[ccp4bb] ARP/wARP Solvent
Dear all, I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it couldn't recognize my ligand library file (.cif), which works fine in refmac refinement. Apparently, the error message is: ===> Error: New ligand has been encountered. Stopping now Refmac_5.2.0019: New ligand has been encountered. Stopping now Your coordinate file has a ligand which has either minimum or no description in the library A new ligand description has been added to /tmp/mchu/refmac5_temp1.03957_lib.cif Even if I use the one refmac created after the error, it still can't recognize this new cif file... I also tried to run it from command line, another problem was raised. It couldn't recognize the FP label in my mtz when I used the keyword [fp F_New] [sigfp SIGF_New] [freer FreeR_flag] Error message: Label FP does not match the content of the datafile /home/mchu/ARP_wARP/solvent/L1.mtz Possible mtz labels are: F_New FC FWT DELFWT Does anyone have any idea why and how I can fix it? Thank you so much in advance! Kind regards, Matt -- -- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester --
[ccp4bb] arp/warp ligand
Hi all, I am trying to fit a ligand into density using ARP/wARP 7.0.1 in CCP4 suite 6.0.2 on CCP4interface 1.4.4.2. I get an error message telling me to look for the error in a "##_warp_ligand_details.log". _ Running Refmac5 to refine the protein PDB without the search ligand. After refmac, R = 0.177 (Rfree = 0.000) The difference electron density map has been calculated. Segmentation fault QUITTING ... ARP/wARP module stopped with an error message: MAPREAD_MODE_GRIDMAKER *** Look for error message in the file: 29_warp_ligand_details.log #CCP4I TERMINATION STATUS 0 All done #CCP4I TERMINATION TIME 16 Mar 2009 14:43:30 #CCP4I MESSAGE Task failed *** * Information from CCP4Interface script *** Error during script execution. *** When I look at the details file, all I see at the end is (no error message): ## COORDINATE READING ## Reading apo protein ... done. Identifying N and O atoms for h-bond investigations ... done. Reading clean search ligand(s) ... (PDBfmt) done ___ The details file ends thus, regardless of whether I read in a library file for the ligand or not, the library is one generated from ProDRG or from refmac. Funnily enough, the program ends the same way even using input files that I had used previously, with a previous version of ARP/wARP; input files that worked before. Help, please! Thanks a ton! Sangeetha.
[ccp4bb] ARP/wARP webservice
Dear Colleagues, We are happy to announce a redesigned and extended webservice for remote ARP/wARP execution. In addition to the crystallographic protein chain tracing, many other functionalities of ARP/wARP are now also available online. These include: - classic protein model building starting from phases or from existing model - secondary structure building - nucleotide building - solvent modelling - ligand modelling and identification The webservice offers a registration with an email address, which provides more options to the users. For example, all jobs a user has previously submitted are now in one place, can be easily evaluated, compared or run again with different parameters. The link for the new ARP/wARP webservice is https://arpwarp.embl-hamburg.de. The former link http://cluster.embl-hamburg.de/ARPwARP/remote-http.html continues to function too. The webservice is using the current ARP/wARP version 7.6.1, which has been jointly released with the CCP4 software. The website contains links to related webservices: Auto-Rickshaw for structure solution, ViCi for ligand scaffold hopping and DipCheck for protein model validation. Your feedback, comments and suggestions are welcome. Happy model building! The ARP/wARP team at EMBL Hamburg
[ccp4bb] Arp/wArp error
Dear all, I have a nice MAD map produced by Sharp and would like to trace a chain into it using Arp/wArp. When I input the mtz file via the CCP4i interface, I get the following message: "Cannot extract ARP/wARP asymmetric unit limits The job will fail if run" Well it DOES fail when run! My space group is C2 (given as C121 in the mtz file header), the mtz file is a standard structure factor file generated by CAD (adding Sharp phases to native data which are at a higher resolutino than the MAD data) and I just don't see what is going wrong. I am using CCP4 6.1.2 and Arp 7.0.1, with the CCP4Interface version 2.0.5 running on Mac OSX version 10.5.8. Any advice will be extremely welcome! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr
[ccp4bb] arp/warp installation
Dear all, I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh. All tests pass up to and including refmac version check (see log below). After that, a "Badly formed number" in an if test. What could be the issue? The system is Redhat EL 5.4, tcsh. Thanks. Andreas ld-andf 133% ./install.sh ARP/wARP installer is checking your c-shell... c-shell is installed on your machine at /bin/csh Your login shell is: /bin/tcsh Checking permissions for /dev/null- OK Checking availability of sed command - OK Checking availability of tail command - OK Checking availability of awk command - OK Checking decimal separator- OK Checking ARP/wARP directory path - OK Checking ARP/wARP directory structure - OK Checking java installation- installed version is "1.6.0" Checking java version number - OK Checking python installation - installed version is 2.4.3 Checking python version number- OK Python executables are available in /csb/soft/Linux/src/arp_warp_7.1/byte-code/python-2.4 Checking operating system name- Linux Checking processor type - i686 ARP/wARP version 7.1 executables for this platform are available in /csb/soft/Linux/src/arp_warp_7.1/bin/bin-i686-Linux Installing script and data files for: bin-athlon-Linux bin-i386-Darwin bin-i686-Linux bin-ia64-Linux bin-powerpc-Darwin bin-x86_64-Linux Checking CCP4 & ARP/wARP installation - OK Checking refmac5 installation - installed version is 5.5.0109 Checking refmac5 version number - OK if: Badly formed number. -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] arp/warp
Hi all, I got the same errors as Rafael. Please help. Thanks Peter > Date: Tue, 16 Mar 2010 14:39:10 +1300 > From: rafael.coun...@otago.ac.nz > Subject: [ccp4bb] arp/warp > To: CCP4BB@JISCMAIL.AC.UK > > Dear all, > > I am getting an error message when I run arp/warp using CCP4i. > > */"QUITTING ... ARP/wARP module stopped with an error message: > RESTRAINTS > > *** Look for error message in the file: > /home/rafael/MAD/CCP4/2_warpNtrace_build.last.log > > [1] 11549/* > > > The only error message I can find on the above file is: > > /*:1: parser error : Document is empty > XMLOutputFilename = 'snow_log.xml' > ^ > Parameter Stream does NOT contain XML, this is the reason for the > previous message (parser error). > Will try to parse it as a variable file (each line being a > 'variableName=value' pair).*/ > > Any ideas? > > Cheers, > > Rafael. > > > -- > Rafael Couñago > Research Fellow > Department of Biochemistry > University of Otago > > 710 Cumberland St > Dunedin, New Zealand > ph: (03) 479 5148 _ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969
Re: [ccp4bb] arp/warp
Dear Rafael, dear Li Chan, is this the first time you run arp/warp on that particular computer? Maybe the architecture of the binaries are not the correct ones. You might search for the 'snow' binary (which leaves the empty log file) with the command 'find ./ -name snow' issued from the arp/warp installation directory and then try to execute that file. If you get an error 'could not execute' or 'wrong architecture' you may have to reinstall arp/warp with the correct binaries for your computer. But this is just a guess. On Tue, Mar 16, 2010 at 02:39:10PM +1300, Rafael Counago wrote: > Dear all, > > I am getting an error message when I run arp/warp using CCP4i. > > */"QUITTING ... ARP/wARP module stopped with an error message: > RESTRAINTS > > *** Look for error message in the file: > /home/rafael/MAD/CCP4/2_warpNtrace_build.last.log > > [1] 11549/* > > > The only error message I can find on the above file is: > > /*:1: parser error : Document is empty > XMLOutputFilename = 'snow_log.xml' > ^ > Parameter Stream does NOT contain XML, this is the reason for the > previous message (parser error). > Will try to parse it as a variable file (each line being a > 'variableName=value' pair).*/ > > Any ideas? > > Cheers, > > Rafael. > > > -- > Rafael Couñago > Research Fellow > Department of Biochemistry > University of Otago > > 710 Cumberland St > Dunedin, New Zealand > ph: (03) 479 5148 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] arp/warp
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The other possibility you might need to consider is wether or not you have java running on your machine. "restraints" is in java, and it seems that ARP/wARP stops just when starting restraints. As for the "error" message you're seeing, it is well expected : the exact same text is in all runs of ARP/wARP. Sorry for the very limited answer, Serge. Le 16 mars 2010 à 10:35, Tim Gruene a écrit : > Dear Rafael, dear Li Chan, > > is this the first time you run arp/warp on that particular computer? Maybe the > architecture of the binaries are not the correct ones. > > You might search for the 'snow' binary (which leaves the empty log file) with > the command 'find ./ -name snow' issued from the arp/warp installation > directory > and then try to execute that file. If you get an error 'could not execute' or > 'wrong architecture' you may have to reinstall arp/warp with the correct > binaries for your computer. > > But this is just a guess. > > On Tue, Mar 16, 2010 at 02:39:10PM +1300, Rafael Counago wrote: >> Dear all, >> >> I am getting an error message when I run arp/warp using CCP4i. >> >> */"QUITTING ... ARP/wARP module stopped with an error message: >> RESTRAINTS >> >> *** Look for error message in the file: >> /home/rafael/MAD/CCP4/2_warpNtrace_build.last.log >> >> [1] 11549/* >> >> >> The only error message I can find on the above file is: >> >> /*:1: parser error : Document is empty >> XMLOutputFilename = 'snow_log.xml' >> ^ >> Parameter Stream does NOT contain XML, this is the reason for the >> previous message (parser error). >> Will try to parse it as a variable file (each line being a >> 'variableName=value' pair).*/ >> >> Any ideas? >> >> Cheers, >> >> Rafael. >> -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (Darwin) iEYEARECAAYFAkufUjQACgkQlz6UVQtc2uzuVQCgytLJxlRimrWQOcVJqRX2GSx5 hX0AmwWPoX4pLwm4EktmTAl+ncQp58od =WAVY -END PGP SIGNATURE-
Re: [ccp4bb] arp/warp
Dear Raphael and others who experienced this, in some rare cases we have seen that the 'restraints' module of ARP/wARP can have a malfunction. If this is the case for your data, then the best you can do at the moment - while the fix is not there - is to deactivate the use of this module in the ccp4 interface of ARP/wARP: Under 'ARP/wARP flow parameters' it's the first item 'Use conditional restraints for free atoms'. Then rerun your job. Regards, Gerrit. On 3/16/10 2:39 AM, Rafael Counago wrote: Dear all, I am getting an error message when I run arp/warp using CCP4i. */"QUITTING ... ARP/wARP module stopped with an error message: RESTRAINTS *** Look for error message in the file: /home/rafael/MAD/CCP4/2_warpNtrace_build.last.log [1] 11549/* The only error message I can find on the above file is: /*:1: parser error : Document is empty XMLOutputFilename = 'snow_log.xml' ^ Parameter Stream does NOT contain XML, this is the reason for the previous message (parser error). Will try to parse it as a variable file (each line being a 'variableName=value' pair).*/ Any ideas? Cheers, Rafael.
Re: [ccp4bb] arp/warp
Dear Rafael, We have seen this already twice, it is a bug, sorry. The fix is being made and, when ready within a day or two, we will announce it. With best regards, Victor Rafael Counago wrote: Dear all, I am getting an error message when I run arp/warp using CCP4i. */"QUITTING ... ARP/wARP module stopped with an error message: RESTRAINTS *** Look for error message in the file: /home/rafael/MAD/CCP4/2_warpNtrace_build.last.log [1] 11549/* The only error message I can find on the above file is: /*:1: parser error : Document is empty XMLOutputFilename = 'snow_log.xml' ^ Parameter Stream does NOT contain XML, this is the reason for the previous message (parser error). Will try to parse it as a variable file (each line being a 'variableName=value' pair).*/ Any ideas? Cheers, Rafael.
Re: [ccp4bb] Arp/warp error
Dear Monica, On Jun 16, 2014, at 10:39 AM, Monica Mittal wrote: > Dear all > I am getting this error while running arp/warp to build DNA/RNA: > PHIB is not assigned to an mtz label > Input was merged data (.mtz) > However no such problem while using arp/warp classic as i chose for automated > model building from existing model and not experimental phases. > > Kindly help how to give PHIB and FOM labels here?? When you use the ARP/wARP interface and load/browse your .MTZ file, the labels Fobs, PHIB, Sigma, FOM are automatically detected and placed. If you want to select different ones available in your MTZ file, please use the corresponding dropdown menu. First make sure that your MTZ file is correct and contains these labels. You can check that by using "mtzdmp" command for example, which should be available in your system because is part of CCP4. Best regards, Ioan -- Dr. Ioan Vancea European Molecular Biology Laboratory c/o DESY Notkestrasse 85, 22607 Hamburg, Germany Email: ivan...@embl-hamburg.de
[ccp4bb] ARP/wARP 7.0 error
Hi all,
I am trying to use the new ARP/wARP to build a model starting from a
partially refined structure for the phases using the "Use pdb file as it is"
option. When I run the program it quits after/during the first REFMAC cycle
with the following message:
ERROR ('IndexError', ('list index out of range',), [' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CArc.py", line 78, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line 43, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line 107, in
_parse\n'])
--
ERROR => Ending JOB
--
I'm relatively sure I have everything installed properly, but it seems the
program is trying to reference scripts that do not exist (i.e. there is no
/Users/gerrit on my system and therefore no python scripts in
/Users/gerrit/CProg/ARP_svn/pyWARP/). Any help that you could provide would
be appreciated. Thanks in advance.
Craig
--
Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630
[ccp4bb] ARP/wARP 7.0 error
Dear CCP4BB members, I am using the loop building module of new arp/warp 7.0 version in RHEL. I am sure during installation everthing went well. But when I try to run the program the following error occured. I think the problem is somewhere in the xml file format. Any help is highly appreciated! Thanks Karthik (Sorry for the long log file) -- #CCP4I VERSION CCP4Interface 1.4.4.2 #CCP4I SCRIPT LOG loopy #CCP4I DATE 24 Jul 2007 09:20:39 #CCP4I USER vijay #CCP4I PROJECT v3 #CCP4I JOB_ID 8 #CCP4I SCRATCH /tmp/vijay #CCP4I HOSTNAME localhost.localdomain #CCP4I PID 28599 ## This script run with the command ## # /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop -paramfile=/tmp/vijay/v3_8_1_com.tmp loop - WRNG* : CConfig::processStream File isn't in proper XML format loop - WRNG* : Couldn't read XML parameter file for warp::CConfig. loop - WRNG* : CConfig::processStream Handling parameter file as non-xml. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.msg , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.xml , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 8 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 4 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : loopy , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/AAbis_extension.XYZ , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 20 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 0.74 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1. , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/syminfo.lib , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 19 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 60.489 112.116 133.838 90.00 90.00 90.00 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 0 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/set_1200_2C_my_0.3b_cos_log.llh , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/set_1200_2N_my_0.3b_cos_log.llh , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 3.8 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 0 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 378 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 0 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 26 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : -4.5 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1. , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1. , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1. , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 0 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1 , Was not considered. loop - WRNG* : CCo
[ccp4bb] arp/warp in p22121
Dear All, I am trying to build a molecular replacement model in arp/warp in space group P22121. Refmac alone seems to be fine with refining the model in P22121; but arp/warp fails, as far as I can see at the first Refmac refinement stage. In the log-file it says "this space group is not supported". I am wondering whether arp/warp needs the Hermann-Mauguin convention space group P21212. I suppose I will need to reindex in P21212 in order to use arp/warp? (the diffraction data were indexed in XDS, scaled in SCALA, and then run through CAD to change the space group from P222 to P22121). I am using arp/warp via the ccp4i interface. Also, arp/warp gives the following message when I load the mtz file "cannot extract arp/warp asymmetric unit limits, the job will fail if run." (i did run arp/warp successfully with other mtz-files). Thank you in advance for any comments! Florian
Re: [ccp4bb] arp/warp error
Hello Seema, I believe this error occurs because ARP/wARP has not been setup within the startup file for the shell that you are using. For instance, if you use bash (the default under most Linux distributions) you need to add the following line to the .bashrc file in your home directory: source /path/to/arpwarp/arpwarp_setup.bash If this doesn't fix the problem, or my instructions are unclear, please don't hesitate to contact me directly. Saul Hazledine On Jul 19, 2011, at 1:51 PM, Seema Nath wrote: > I've recently installed arp/warp(7.1) in ccp4 6.2 in linux i686,the problem > is whenever I'm trying to run arp/warp navigator or any other programs under > arp/warp it gives the error " cannot get environment variable for warpbin" > Please help. > Thanks in advance. > > Seema Nath
Re: [ccp4bb] ARP/wARP Solvent
Dear Matt, have you tried the 'input a user-defined library file' check box under 'refmac parameters' in the gui? Else try the keyword 'extralibrary' when using the 'auto_solvent.sh' script from the command line. Both options define a string 'LIB_IN mylib.cif' that is passed on to refmac. When using the auto_solvent.sh script, please omit the '[' and ']' characters. Type e.g.: auto_solvent.sh datafile L1.mtz protein L1.pdb fp F_New sigfp SIGF_New extralibrary refmac5_templ.03957_lib.cif I hope this will help. Regards, Gerrit. Matthew Chu wrote: Dear all, I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it couldn't recognize my ligand library file (.cif), which works fine in refmac refinement. Apparently, the error message is: ===> Error: New ligand has been encountered. Stopping now Refmac_5.2.0019: New ligand has been encountered. Stopping now Your coordinate file has a ligand which has either minimum or no description in the library A new ligand description has been added to /tmp/mchu/refmac5_temp1.03957_lib.cif Even if I use the one refmac created after the error, it still can't recognize this new cif file... I also tried to run it from command line, another problem was raised. It couldn't recognize the FP label in my mtz when I used the keyword [fp F_New] [sigfp SIGF_New] [freer FreeR_flag] Error message: Label FP does not match the content of the datafile /home/mchu/ARP_wARP/solvent/L1.mtz Possible mtz labels are: F_New FC FWT DELFWT Does anyone have any idea why and how I can fix it? Thank you so much in advance! Kind regards, Matt
Re: [ccp4bb] ARP/wARP Solvent
Thanks Damian, but I have been using my library file for refmac refinement and it works fine. And I can't find the line "Unrecognized atom type", but presumably, if it works in refmac refinement, why not in Arp/wArp? Yes Gerrit, the "[" and "]" should not be there.so auto_solvent.sh can recognize my mtz fp, etc. BUT I did check the box 'input a user-defined library file' in GUI and the command 'extralibrary' in the script, and again, it fails to read my library file or the one refmac just created, but obviously the extralibrary command works fine? Here is the log: Working directory/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ Job ID is set to 20090108_114504 X-ray data file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1.mtz Protein file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1.pdb Extralibrary file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//refmac5_temp1.10491_lib.cif TLS input file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1_TLS.tls Creating directory /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504 Output solvent file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/L1_solvent.pdb mtz labels taken: F_New SIGF_New FreeR_flag Parameter file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/arp_warp_solvent.par Job launched in /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504 The log file is /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/L1_warp_solvent_details.log But ERROR: Important, Important, Important! Your coordinate file has a ligand which has either minimum or no description in the library A new ligand description has been added to /tmp/mchu/refmac5_temp1.11125_lib.cif Picture of the new ligand can be viewed using postscript file. See above Check description in this file and, if satisfied, use it as the input library Otherwise either edit bond orders manually or use CCP4i Sketcher to view and edit the ligand and create a library entry by running libcheck It is strongly recommended that dictionary entry should be checked carefully before using it If you are happy with the library description then use the keyword (MAKE CHECK NONE) I.e. do not check correctness of the coordinates ===> Error: New ligand has been encountered. Stopping now I really have no idea what is the problem? Any suggestion would be greatly appreciated! Kind regards, Matt 2009/1/8 Damian Ekiert Matt, I had a similar sounding problem once, but it may or may the problem in your case. Do you have any ligands or glycans on your protein that you just added in? I was working on a protein with glycosylations and hadn't yet removed the oxygens from my sugars that would be lost after condensation (e.g., the oxygen that would be lost as water when the first residue was attached to Asn). My suggestion would be to look a little bit higher up in the log file and see if you see any lines saying something like "Unrecognized atom type". I think when there is a discrepancy between the residue name and the names of the atoms in the residue, you can have this problem. Hope that helps. Best, Damian Ekiert 2009/1/8 Gerrit Langer > Dear Matt, > > have you tried the 'input a user-defined library file' check box under > 'refmac parameters' in the gui? Else try the keyword 'extralibrary' when > using the 'auto_solvent.sh' script from the command line. Both options > define a string 'LIB_IN mylib.cif' that is passed on to refmac. > > When using the auto_solvent.sh script, please omit the '[' and ']' > characters. Type e.g.: auto_solvent.sh datafile L1.mtz protein L1.pdb fp > F_New sigfp SIGF_New extralibrary refmac5_templ.03957_lib.cif > > I hope this will help. > Regards, > Gerrit. > > > Matthew Chu wrote: > > Dear all, >> >> I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it >> couldn't >> recognize my ligand library file (.cif), which works fine in refmac >> refinement. >> Apparently, the error message is: >> >> ===> Error: New ligand has been encountered. Stopping now >> Refmac_5.2.0019: New ligand has been encountered. Stopping now >> Your coordinate file has a ligand which has either minimum or no >> description >> in the library >> A new ligand description has been added to >> /tmp/mchu/refmac5_temp1.03957_lib.cif >> >> Even if I use the one refmac created after the error, it still can't >> recognize this new cif file... >> >> I also tried to run it from command line, another problem was raised. It >> couldn't recognize the FP label in my mtz when I used the keyword [fp >> F_New] >> [sigfp SIGF_New] [freer FreeR_flag] >> >> Error message: >> Label FP does not match the content of the datafile >> /home/mchu/ARP_wARP/solvent/L1.mtz >> Possible mtz labels are: F_New FC FWT DELFWT >> >> Does anyone have any idea why and how I can fix it? Thank you so much in >> advance! >> >> Kind regards, >> Matt >> >> >> >> > > --
Re: [ccp4bb] ARP/wARP Solvent
Hi - Its a bug in version 7.0.1 that went (almost) unnoticed ... there was one more complaint a year ago and I had fixed it but there was no release in between. Sorry. Apart from simply doing the solvent building from the REFMAC interface instead (either with arp_warp as since now or with Coot as since CCP4 6.1) I will mail you the fixed file (which might work). Anyone else interested ask me ; the fix will be in the imminent 7.1 release. A. On Jan 8, 2009, at 12:59, Matthew Chu wrote: Thanks Damian, but I have been using my library file for refmac refinement and it works fine. And I can't find the line "Unrecognized atom type", but presumably, if it works in refmac refinement, why not in Arp/wArp? Yes Gerrit, the "[" and "]" should not be there.so auto_solvent.sh can recognize my mtz fp, etc. BUT I did check the box 'input a user-defined library file' in GUI and the command 'extralibrary' in the script, and again, it fails to read my library file or the one refmac just created, but obviously the extralibrary command works fine? Here is the log: Working directory/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ Job ID is set to 20090108_114504 X-ray data file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent// L1.mtz Protein file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent// L1.pdb Extralibrary file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent// refmac5_temp1.10491_lib.cif TLS input file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent// L1_TLS.tls Creating directory /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ 20090108_114504 Output solvent file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ 20090108_114504/L1_solvent.pdb mtz labels taken: F_New SIGF_New FreeR_flag Parameter file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ 20090108_114504/arp_warp_solvent.par Job launched in /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ 20090108_114504 The log file is /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ 20090108_114504/L1_warp_solvent_details.log But ERROR: Important, Important, Important! Your coordinate file has a ligand which has either minimum or no description in the library A new ligand description has been added to /tmp/mchu/ refmac5_temp1.11125_lib.cif Picture of the new ligand can be viewed using postscript file. See above Check description in this file and, if satisfied, use it as the input library Otherwise either edit bond orders manually or use CCP4i Sketcher to view and edit the ligand and create a library entry by running libcheck It is strongly recommended that dictionary entry should be checked carefully before using it If you are happy with the library description then use the keyword (MAKE CHECK NONE) I.e. do not check correctness of the coordinates ===> Error: New ligand has been encountered. Stopping now I really have no idea what is the problem? Any suggestion would be greatly appreciated! Kind regards, Matt 2009/1/8 Damian Ekiert Matt, I had a similar sounding problem once, but it may or may the problem in your case. Do you have any ligands or glycans on your protein that you just added in? I was working on a protein with glycosylations and hadn't yet removed the oxygens from my sugars that would be lost after condensation (e.g., the oxygen that would be lost as water when the first residue was attached to Asn). My suggestion would be to look a little bit higher up in the log file and see if you see any lines saying something like "Unrecognized atom type". I think when there is a discrepancy between the residue name and the names of the atoms in the residue, you can have this problem. Hope that helps. Best, Damian Ekiert 2009/1/8 Gerrit Langer Dear Matt, have you tried the 'input a user-defined library file' check box under 'refmac parameters' in the gui? Else try the keyword 'extralibrary' when using the 'auto_solvent.sh' script from the command line. Both options define a string 'LIB_IN mylib.cif' that is passed on to refmac. When using the auto_solvent.sh script, please omit the '[' and ']' characters. Type e.g.: auto_solvent.sh datafile L1.mtz protein L1.pdb fp F_New sigfp SIGF_New extralibrary refmac5_templ. 03957_lib.cif I hope this will help. Regards, Gerrit. Matthew Chu wrote: Dear all, I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it couldn't recognize my ligand library file (.cif), which works fine in refmac refinement. Apparently, the error message is: ===> Error: New ligand has been encountered. Stopping now Refmac_5.2.0019: New ligand has been encountered. Stopping now Your coordinate file has a ligand which has either minimum or no description in the library A new ligand description has been added to /tmp/mchu/refmac5_temp1.03957_lib.cif Even if I use the one refmac created after the error, it still can't recognize this new cif file... I also tried to run it from comman
Re: [ccp4bb] ARP/wARP Solvent
Thanks, Anastassis, "Solvent" is working now after installing the fixed file. Cheers, Matt 2009/1/8 Anastassis Perrakis > Hi - > Its a bug in version 7.0.1 that went (almost) unnoticed ... there was one > more complaint a year ago and I had fixed it but there was no release in > between. Sorry. > > Apart from simply doing the solvent building from the REFMAC interface > instead (either with arp_warp as since now or with Coot as since CCP4 6.1) I > will mail you the fixed file (which might work). Anyone else interested ask > me ; the fix will be in the imminent 7.1 release. > > A. > > > > On Jan 8, 2009, at 12:59, Matthew Chu wrote: > > Thanks Damian, but I have been using my library file for refmac refinement > and it works fine. And I can't find the line "Unrecognized atom type", but > presumably, if it works in refmac refinement, why not in Arp/wArp? > > Yes Gerrit, the "[" and "]" should not be there.so auto_solvent.sh can > recognize my mtz fp, etc. BUT > I did check the box 'input a user-defined library file' in GUI and the > command 'extralibrary' in the script, and again, it fails to read my library > file or the one refmac just created, but obviously the extralibrary command > works fine? > Here is the log: > > Working directory/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ > Job ID is set to 20090108_114504 > X-ray data file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1.mtz > Protein file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1.pdb > Extralibrary file > /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//refmac5_temp1.10491_lib.cif > TLS input file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1_TLS.tls > Creating directory > /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504 > Output solvent file > /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/L1_solvent.pdb > mtz labels taken: F_New SIGF_New FreeR_flag > Parameter file > /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/arp_warp_solvent.par > Job launched in > /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504 > The log file is > /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/L1_warp_solvent_details.log > > But ERROR: > Important, Important, Important! > Your coordinate file has a ligand which has either minimum or no > description in the library > A new ligand description has been added to > /tmp/mchu/refmac5_temp1.11125_lib.cif > Picture of the new ligand can be viewed using postscript file. See above > Check description in this file and, if satisfied, use it as the input > library > Otherwise either edit bond orders manually or use CCP4i Sketcher to view > and edit the ligand > and create a library entry by running libcheck > It is strongly recommended that dictionary entry should be checked > carefully before using it > If you are happy with the library description then use the keyword (MAKE > CHECK NONE) > I.e. do not check correctness of the coordinates > ===> Error: New ligand has been encountered. Stopping now > > I really have no idea what is the problem? > Any suggestion would be greatly appreciated! > > Kind regards, > Matt > > > > > 2009/1/8 Damian Ekiert > Matt, > > I had a similar sounding problem once, but it may or may the problem in > your case. Do you have any ligands or glycans on your protein that you just > added in? I was working on a protein with glycosylations and hadn't yet > removed the oxygens from my sugars that would be lost after condensation > (e.g., the oxygen that would be lost as water when the first residue was > attached to Asn). My suggestion would be to look a little bit higher up in > the log file and see if you see any lines saying something like > "Unrecognized atom type". I think when there is a discrepancy between the > residue name and the names of the atoms in the residue, you can have this > problem. > > Hope that helps. > > Best, > > Damian Ekiert > > > 2009/1/8 Gerrit Langer > >> Dear Matt, >> >> have you tried the 'input a user-defined library file' check box under >> 'refmac parameters' in the gui? Else try the keyword 'extralibrary' when >> using the 'auto_solvent.sh' script from the command line. Both options >> define a string 'LIB_IN mylib.cif' that is passed on to refmac. >> >> When using the auto_solvent.sh script, please omit the '[' and ']' >> characters. Type e.g.: auto_solvent.sh datafile L1.mtz protein L1.pdb fp >> F_New sigfp SIGF_New extralibrary refmac5_templ.03957_lib.cif >> >> I hope this will help. >> Regards, >> Gerrit. >> >> >> Matthew Chu wrote: >> >> Dear all, >>> >>> I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it >>> couldn't >>> recognize my ligand library file (.cif), which works fine in refmac >>> refinement. >>> Apparently, the error message is: >>> >>> ===> Error: New ligand has been encountered. Stopping now >>> Refmac_5.2.0019: New ligand has been encountered. Stopping now >>> Your coordinate file has a ligand which has either
Re: [ccp4bb] arp/warp ligand
Dear Sangeetha, what you noticed is a bug that appears under particular circumstances. Sorry for your inconvenience. From your logfile excerpt I think that this bug has been observed before and been fixed. The next release will include the fixed version, however useless this might sound to you now. So if you are in urgent need to get the software running now, please contact me in a private communication and send me details about your case and your computing environment and we will see what we can do. Greetings from Hamburg, Gerrit.
[ccp4bb] Arp/Warp in Ubuntu
Hi, Does anyone know how to Plugging ARP/wARP GUI into CCP4i interface? I followed http://www.embl-hamburg.de/arp-cgi-bin/FAQ7.0_1.pl, but always get a warning "Can not get environment variable for wardoc" with a subsequent Application Error "Error:bad window path name \".warning..." Under Ubuntu, I can find the place for me to input the administrator's code.. Thanks in advance. Yuan SHANG
Re: [ccp4bb] Arp/wArp error
One easy suggestion - try buccaneer and refinement! Eleanor The Arp/warp people will have to fix this.. Anita Lewit-Bentley wrote: Dear all, I have a nice MAD map produced by Sharp and would like to trace a chain into it using Arp/wArp. When I input the mtz file via the CCP4i interface, I get the following message: "Cannot extract ARP/wARP asymmetric unit limits The job will fail if run" Well it DOES fail when run! My space group is C2 (given as C121 in the mtz file header), the mtz file is a standard structure factor file generated by CAD (adding Sharp phases to native data which are at a higher resolutino than the MAD data) and I just don't see what is going wrong. I am using CCP4 6.1.2 and Arp 7.0.1, with the CCP4Interface version 2.0.5 running on Mac OSX version 10.5.8. Any advice will be extremely welcome! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr
Re: [ccp4bb] Arp/wArp error
Dear Jan, that is an annoying thing with Arp/wARP - it sometimes does not recognise some space groups, esp. the monoclinic ones with eg can be called C2 or C121 etc. Run the mtz file again through CAD, use SG 5 or C2. That should work. and it does! Thanks a lot. Let's hope these annoying obstacles can get removed from the path of - otherwise really happy - CCP4 users! Thanks again, Anita Bonne chance Jan On Tue, Dec 1, 2009 at 8:41 AM, Anita Lewit-Bentley wrote: Dear all, I have a nice MAD map produced by Sharp and would like to trace a chain into it using Arp/wArp. When I input the mtz file via the CCP4i interface, I get the following message: "Cannot extract ARP/wARP asymmetric unit limits The job will fail if run" Well it DOES fail when run! My space group is C2 (given as C121 in the mtz file header), the mtz file is a standard structure factor file generated by CAD (adding Sharp phases to native data which are at a higher resolutino than the MAD data) and I just don't see what is going wrong. I am using CCP4 6.1.2 and Arp 7.0.1, with the CCP4Interface version 2.0.5 running on Mac OSX version 10.5.8. Any advice will be extremely welcome! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] Arp/wArp error
Hi all, I ran into that several times in the monoclinic space groups. ARP/wARP does not seem to like the C121 notation, yet likes the C2 notation. Same for P121 vs. P2. Re-assigning the SG eg. in CAD using the correct notation or the SG number is an easy remedy. Cheers Jan On Tue, Dec 1, 2009 at 8:57 AM, Eleanor Dodson wrote: > One easy suggestion - try buccaneer and refinement! > Eleanor > The Arp/warp people will have to fix this.. > > > > Anita Lewit-Bentley wrote: > >> Dear all, >> >> I have a nice MAD map produced by Sharp and would like to trace a chain >> into it using Arp/wArp. When I input the mtz file via the CCP4i interface, I >> get the following message: >> >> "Cannot extract ARP/wARP asymmetric unit limits >> The job will fail if run" >> >> Well it DOES fail when run! >> >> My space group is C2 (given as C121 in the mtz file header), the mtz file >> is a standard structure factor file generated by CAD (adding Sharp phases to >> native data which are at a higher resolutino than the MAD data) and I just >> don't see what is going wrong. >> >> I am using CCP4 6.1.2 and Arp 7.0.1, with the CCP4Interface version 2.0.5 >> running on Mac OSX version 10.5.8. >> >> Any advice will be extremely welcome! >> >> Anita >> >> >> >> Anita Lewit-Bentley >> Unité d'Immunologie Structurale >> CNRS URA 2185 >> Département de Biologie Structurale & Chimie >> Institut Pasteur >> 25 rue du Dr. Roux >> 75724 Paris cedex 15 >> FRANCE >> >> Tel: 33- (0)1 45 68 88 95 >> FAX: 33-(0)1 40 61 30 74 >> email: ale...@pasteur.fr >> >> >> -- -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA http://www.emeraldbiostructures.com work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] Arp/wArp error
On Tue, Dec 01, 2009 at 04:57:38PM +, Eleanor Dodson wrote: > One easy suggestion - try buccaneer and refinement! > Eleanor > The Arp/warp people will have to fix this.. It's also possible that this is due to a ctruncate problem: if the CAD job adds the SHARP MTZ file (with C2) and a MTZ file coming from ctruncate (with 'C121' instead of 'C 1 2 1') you could see that too. See http://www.ccp4.ac.uk/ccp4bin/viewcvs/ccp4/lib/clipper/clipper/ccp4/ccp4_mtz_io.cpp?sortby=date and the changes of 6 weeks ago. So it might be rather something in CCP4/Clipper than ARP/wARP ;-) A simple solution: echo "SYMM C2" | mtzutils hklin cad.mtz hklout cad_fix.mtz Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Arp/wArp error
Dear all, First, I am happy that there is am easy solution. Second, let me clarify that ARP/wARP CCP4i GUI uses standard CCP4i library functions to read in files etc etc. I am sorry to get technical, but what I do is simply: CreateInputFileLine line \ [...lines deleted...] -setfileparam space_group_name SPACE_GROUP \ thus I am relying to the CCP4i libraries to return to me the correct space group name when the user reads in a file. Later on I use the CCP4i library command set space_group [GetSpaceGroupNumber $array(SPACE_GROUP)] that is because ARP/wARP programs want to use space group numbers as input later on. So, whatever the error is with C121 and P121 is not in ARP/wARP. Very likely it is in the GetSpaceGroupNumber function of CCP4i. You can easily check that, since under 'Crystal Parameters' the space group name should be 'P121', but I suspect that for that I get a '0' for space group number... (would be good if somebody sends me such a file so I can check!) Thus, the 'ARP/wARP people' cannot fix, no matter how willing they are. However, I would appreciate if somebody from CCP4 team tells me if there is something wrong in the code, or fixes the CCP4i code if it is indeed broken for that function. Also, yet another solution if anyone runs to this problem, is to run auto_tracing.sh from the command line (it will list a choice of needed keywords) That uses a program by the ARP/wARP team that will figure out the correct space group number from the symmetry operators of the MTZ file and it should run in C121 just like C2. The same is true for the ARP/wARP Hamburg Web Server. Best - Tassos On Dec 1, 2009, at 18:05, Jan Abendroth wrote: Hi all, I ran into that several times in the monoclinic space groups. ARP/ wARP does not seem to like the C121 notation, yet likes the C2 notation. Same for P121 vs. P2. Re-assigning the SG eg. in CAD using the correct notation or the SG number is an easy remedy. Cheers Jan On Tue, Dec 1, 2009 at 8:57 AM, Eleanor Dodson wrote: One easy suggestion - try buccaneer and refinement! Eleanor The Arp/warp people will have to fix this.. Anita Lewit-Bentley wrote: Dear all, I have a nice MAD map produced by Sharp and would like to trace a chain into it using Arp/wArp. When I input the mtz file via the CCP4i interface, I get the following message: "Cannot extract ARP/wARP asymmetric unit limits The job will fail if run" Well it DOES fail when run! My space group is C2 (given as C121 in the mtz file header), the mtz file is a standard structure factor file generated by CAD (adding Sharp phases to native data which are at a higher resolutino than the MAD data) and I just don't see what is going wrong. I am using CCP4 6.1.2 and Arp 7.0.1, with the CCP4Interface version 2.0.5 running on Mac OSX version 10.5.8. Any advice will be extremely welcome! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr -- -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA http://www.emeraldbiostructures.com work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
Re: [ccp4bb] arp/warp installation
The attached slightly modified script fixes that problem Phil install_csh.sh.gz Description: GNU Zip compressed data On 4 Jan 2010, at 11:15, Andreas Förster wrote: > Dear all, > > I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh. All > tests pass up to and including refmac version check (see log below). After > that, a "Badly formed number" in an if test. What could be the issue? > > The system is Redhat EL 5.4, tcsh. > > Thanks. > > > Andreas > > > > ld-andf 133% ./install.sh > > ARP/wARP installer is checking your c-shell... > c-shell is installed on your machine at /bin/csh > Your login shell is: /bin/tcsh > > Checking permissions for /dev/null- OK > Checking availability of sed command - OK > Checking availability of tail command - OK > Checking availability of awk command - OK > Checking decimal separator- OK > Checking ARP/wARP directory path - OK > Checking ARP/wARP directory structure - OK > Checking java installation- installed version is "1.6.0" > Checking java version number - OK > Checking python installation - installed version is 2.4.3 > Checking python version number- OK > Python executables are available in > /csb/soft/Linux/src/arp_warp_7.1/byte-code/python-2.4 > Checking operating system name- Linux > Checking processor type - i686 > ARP/wARP version 7.1 executables for this platform > are available in /csb/soft/Linux/src/arp_warp_7.1/bin/bin-i686-Linux > > Installing script and data files for: > bin-athlon-Linux > bin-i386-Darwin > bin-i686-Linux > bin-ia64-Linux > bin-powerpc-Darwin > bin-x86_64-Linux > > Checking CCP4 & ARP/wARP installation - OK > Checking refmac5 installation - installed version is 5.5.0109 > Checking refmac5 version number - OK > if: Badly formed number. > > > -- >Andreas Förster, Research Associate >Paul Freemont & Xiaodong Zhang Labs > Department of Biochemistry, Imperial College London >http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] arp/warp installation
As Phil realized, the leading zeros in the refmac5 version number were the culprit that broke the original installation script. His modified version works beautifully. Thanks. Andreas On 04/01/2010 11:27, Phil Evans wrote: The attached slightly modified script fixes that problem Phil On 4 Jan 2010, at 11:15, Andreas Förster wrote: Dear all, I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh. All tests pass up to and including refmac version check (see log below). After that, a "Badly formed number" in an if test. What could be the issue? The system is Redhat EL 5.4, tcsh. Thanks. Andreas ld-andf 133% ./install.sh ARP/wARP installer is checking your c-shell... c-shell is installed on your machine at /bin/csh Your login shell is: /bin/tcsh Checking permissions for /dev/null- OK Checking availability of sed command - OK Checking availability of tail command - OK Checking availability of awk command - OK Checking decimal separator- OK Checking ARP/wARP directory path - OK Checking ARP/wARP directory structure - OK Checking java installation- installed version is "1.6.0" Checking java version number - OK Checking python installation - installed version is 2.4.3 Checking python version number- OK Python executables are available in /csb/soft/Linux/src/arp_warp_7.1/byte-code/python-2.4 Checking operating system name- Linux Checking processor type - i686 ARP/wARP version 7.1 executables for this platform are available in /csb/soft/Linux/src/arp_warp_7.1/bin/bin-i686-Linux Installing script and data files for: bin-athlon-Linux bin-i386-Darwin bin-i686-Linux bin-ia64-Linux bin-powerpc-Darwin bin-x86_64-Linux Checking CCP4& ARP/wARP installation - OK Checking refmac5 installation - installed version is 5.5.0109 Checking refmac5 version number - OK if: Badly formed number. -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[ccp4bb] arp/warp: missing 'wilsonb'
Hello, we have been trying to run arp warp 7.1.0 from ccp4-6.1.2 starting from experimental phases. As we hit the run or 'run& view comm script' button, a window appears saying "Can't read 'wilsonb': no such variable" followed by a polite apology and nothing else happens ever after. What might be the cause and the cure of such behaviour? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] ARP/wARP 7.0 error
Hi there -
That error is indeed something totally misleading from python.
Somehow, the error messages get hard-coded at compilation time and
list the directories
that compilation took place at (in this case Gerrit's laptop).
We will try and suppress this message since its totally misleading.
The error message is in the parsing of the Refmac log file
(Garib ... we should indeed do the XML one of these days !)
I think we have seen it before, but if you could send us a gzip of
the whole run dir,
or at least the last refmac log file, we will be able to tell you
exactly.
In a similar case, getting the newest refmac5 from York solved the
problem.
Since I can almost guarantee that any such anomalies are genuine bugs
in ARP/wARP 7.0
(and especially in the 'new' flex-warp module) it might be best to
email directly the authors,
so we can deal with it asap ...
(I am on ccp4bb detox, I read it once a day to avoid shouting to too
many people)
Tassos
On Jul 23, 2007, at 16:24, Craig McElroy wrote:
Hi all,
I am trying to use the new ARP/wARP to build a model starting from a
partially refined structure for the phases using the "Use pdb file
as it is"
option. When I run the program it quits after/during the first
REFMAC cycle
with the following message:
ERROR ('IndexError', ('list index out of range',), [' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CArc.py", line 78, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line 43, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line
107, in
_parse\n'])
--
ERROR => Ending JOB
--
I'm relatively sure I have everything installed properly, but it
seems the
program is trying to reference scripts that do not exist (i.e.
there is no
/Users/gerrit on my system and therefore no python scripts in
/Users/gerrit/CProg/ARP_svn/pyWARP/).
Any help that you could provide would
be appreciated. Thanks in advance.
Craig
--
Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630
Re: [ccp4bb] ARP/wARP 7.0 error
Thank you for the help. It seems as if the new Refmac5 has done the trick.
Thanks
Craig
Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630
Anastassis Perrakis wrote:
Hi there -
That error is indeed something totally misleading from python.
Somehow, the error messages get hard-coded at compilation time and
list the directories
that compilation took place at (in this case Gerrit's laptop).
We will try and suppress this message since its totally misleading.
The error message is in the parsing of the Refmac log file
(Garib ... we should indeed do the XML one of these days !)
I think we have seen it before, but if you could send us a gzip of the
whole run dir,
or at least the last refmac log file, we will be able to tell you
exactly.
In a similar case, getting the newest refmac5 from York solved the
problem.
Since I can almost guarantee that any such anomalies are genuine bugs
in ARP/wARP 7.0
(and especially in the 'new' flex-warp module) it might be best to
email directly the authors,
so we can deal with it asap ...
(I am on ccp4bb detox, I read it once a day to avoid shouting to too
many people)
Tassos
On Jul 23, 2007, at 16:24, Craig McElroy wrote:
Hi all,
I am trying to use the new ARP/wARP to build a model starting from a
partially refined structure for the phases using the "Use pdb file as
it is"
option. When I run the program it quits after/during the first REFMAC
cycle
with the following message:
ERROR ('IndexError', ('list index out of range',), [' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CArc.py", line 78, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line 43, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line 107, in
_parse\n'])
--
ERROR => Ending JOB
--
I'm relatively sure I have everything installed properly, but it
seems the
program is trying to reference scripts that do not exist (i.e. there
is no
/Users/gerrit on my system and therefore no python scripts in
/Users/gerrit/CProg/ARP_svn/pyWARP/).
Any help that you could provide would
be appreciated. Thanks in advance.
Craig
--Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630
Re: [ccp4bb] ARP/wARP 7.0 error
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Karthik; Indeed the problem seems to lie in the XML produced by the CCP4 GUI which is very likely to contain a first (or few initial) line(s) which makes "loop" to believe it has to deal with NON-XML input while indeed the input is XML... Hence (as stated by the first warning) it turns to the fall-back 'plain-text' format for parsing the parameter file but then it is confused as soon as it encounters the body of the file which is NOT "plain-text" but XML. One thing you should try is to : 1. look at the parameter file in an editor (file /tmp/vijay/ v3_8_1_com.tmp) 2. If as mentioned above it contains a few plain text lines at the beginning, delete them. 3. Also you have to check that the loop which is defined by " C104<8>C112 " should indeed be " C104<8>C112 " (because plain < and > are not valid in XML, unless marking a tag). (indeed this alone would produce the error you see). 4. Then re-run loop : /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop - paramfile=/tmp/vijay/v3_8_1_com.tmp Last remark : We had some trouble while testing on 64b x86 (AMD or intel x86 processor running in 64b mode). If you encounter more troubles we are very interested in your feed-back. In the meantime (if encountering 'Illegal Instruction' or other kind of core-dump), you can run using the x86 32bit version which is likely to run also on your computer : /home/programs/linux/arp_warp_7.0/bin/bin-i686_64-Linux/loop - paramfile=/tmp/vijay/v3_8_1_com.tmp Please do not hesitate to send any more question, bug report... Cheers; Serge. Le 28 juil. 07 à 13:59, Karthikeyan S. a écrit : Dear CCP4BB members, I am using the loop building module of new arp/warp 7.0 version in RHEL. I am sure during installation everthing went well. But when I try to run the program the following error occured. I think the problem is somewhere in the xml file format. Any help is highly appreciated! Thanks Karthik (Sorry for the long log file) -- #CCP4I VERSION CCP4Interface 1.4.4.2 #CCP4I SCRIPT LOG loopy #CCP4I DATE 24 Jul 2007 09:20:39 #CCP4I USER vijay #CCP4I PROJECT v3 #CCP4I JOB_ID 8 #CCP4I SCRATCH /tmp/vijay #CCP4I HOSTNAME localhost.localdomain #CCP4I PID 28599 ## This script run with the command ## # /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop -paramfile=/tmp/vijay/v3_8_1_com.tmp loop - WRNG* : CConfig::processStream File isn't in proper XML format loop - WRNG* : Couldn't read XML parameter file for warp::CConfig. loop - WRNG* : CConfig::processStream Handling parameter file as non-xml. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.msg , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.xml , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 8 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 4 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : loopy , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/ AAbis_extension.XYZ , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 20 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 0.74 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1. , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/syminfo.lib , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 19 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 60.489 112.116 133.838 90.00 90.00 90.00 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 0 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : 1 , Was not considered. loop - WRNG* : CConfig::readLine Invalid line read from parameter file : /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linu
Re: [ccp4bb] ARP/wARP 7.0 error
Hi - On 28 Jul 2007, at 13:59, Karthikeyan S. wrote: Dear CCP4BB members, I am using the loop building module of new arp/warp 7.0 version in RHEL. I am sure during installation everthing went well. But when I try to run the program the following error occured. I think the problem is somewhere in the xml file format. I am afraid you run in a weird bug ... Look at the following line from the file you sent: C104<8>C112 , Was not considered. In the script file we do try and substitute '<' and '>' with 'lt' and 'gt', since <,> are invalid XML characters. Somehow, that does not happen in your system and at least one more system we know of. This line should look like C104<4>C112 if you edit it in the file you sent and then rerun from the command line (copying from your log file) /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop - paramfile=/tmp/vijay/v3_8_1_com.tmp it should work. If anyone has a clue why the substitution works in some systems but in some does not, please help us ! A user has seen it once before, but I cant reproduce in OSX, FC5 ... Any clues would be appreciated. Tassos
Re: [ccp4bb] ARP/wARP 7.0 error
Hi, Thanks for the suggestions. I tried by changing the the line with the suggested line and rerun the program from command prompt both in 32 and 64 bit version, but it gave the following error. -- ### ### ARP/wARP Program Suite: LOOP BUILDING 0.1 Krista Joosten (17-11-2005) ### ### F77 lib: V. Lamzin ### Copyright 2005 , NKI, A. Perrakis Laboratory # ### Starting time : Mon Jul 30 09:31:00 2007 MIGHT ABORT NOW, error message is : ERROR** : Couldn't find any loop to build Quitting now... encountered an error (exception) : N4warp4CMsgE Message is : Couldn't find any loop to build Ending time : Mon Jul 30 09:31:01 2007 CPU usage loop building: 0.49s. --- May be this error could be a trival one, I am not able to get what exactly mission, as I run this loop module first time. I am also enclosing the input file I used. -- INPUT FILE -- /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.msg /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.xml 8 4 loopy /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/AAbis_extension.XYZ 20 0.74 1. /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/syminfo.lib 19 60.489 112.116 133.838 90.00 90.00 90.00 1 0 1 /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/set_1200_2C_my_0.3b_cos_log.llh /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/set_1200_2N_my_0.3b_cos_log.llh 3.8 0 378 1 0 1 26 -4.5 1. 1. 1. 0 1 1 0.1 0.1 0 0 1 1 0 100 0.3 6 2 0.7 -1.5 50 15 5 C104<8>C112 PNHVTYSGD 1 /home/vijay/divya/ps39_3/refinement/cns/denzo1/04_model.pdb /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/ps39_3_refmac4.mtz /tmp/vijay/ps39_3_loopy1.map FWT PHWT 0 1 5 /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac 04_model_loop /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac 04_model_proposed 0 1. 0. > Hi - > > > On 28 Jul 2007, at 13:59, Karthikeyan S. wrote: > >> Dear CCP4BB members, >> >> I am using the loop building module of new arp/warp 7.0 version in >> RHEL. I >> am sure during installation everthing went well. But when I try to >> run the >> program the following error occured. I think the problem is >> somewhere in >> the xml file format. > > I am afraid you run in a weird bug ... > > Look at the following line from the file you sent: > >> C104<8>C112 , Was not considered. > > In the script file we do try and substitute '<' and '>' with 'lt' and > 'gt', since <,> are invalid XML characters. > Somehow, that does not happen in your system and at least one more > system we know of. > > This line should look like > > C104<4>C112 > > if you edit it in the file you sent and then rerun from the command line > (copying from your log file) > > /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop - > paramfile=/tmp/vijay/v3_8_1_com.tmp > > it should work. > > If anyone has a clue why the substitution works in some systems but > in some does not, please help us ! > A user has seen it once before, but I cant reproduce in OSX, FC5 ... > Any clues would be appreciated. > > Tassos >
Re: [ccp4bb] arp/warp in p22121
Hi - ARP/wARP only likes standard space groups, like P21212, P22121 is not-standard ... oh well ... (Eleanor is complaining about it for about 13 years ... but never mind that she is right) Just re-index your sg to be P21212 (refl. utilities, reindex, in ccp4i). Choose 'Entering reflection transformation' P22121 to become P21212 you need h=l k=k l=-h set SG to p21212 if you are too lazy redo the Molrep or a nice brain teaser is to apply the correct transformation to your PDB (PDBSET will do that for you) and you are ready to go with ARP/wARP A. PS. depending on cell axes length, and given that convention wants the smaller 21 axis first, the formally correct transformation above might be h=k k=l l=h (in other words if your CURRENT b axis is smaller than your current c axis its the one above. if the CURRENT c axis is smaller than b, the use the one on top) PS2 I think i got the - right, you need to be sure you do not invert the hand - reindex will complain if I was wrong, in which case get rid/add a the '-' sign ;-) On Sep 18, 2007, at 12:28, Florian Schmitzberger wrote: Dear All, I am trying to build a molecular replacement model in arp/warp in space group P22121. Refmac alone seems to be fine with refining the model in P22121; but arp/warp fails, as far as I can see at the first Refmac refinement stage. In the log-file it says "this space group is not supported". I am wondering whether arp/warp needs the Hermann-Mauguin convention space group P21212. I suppose I will need to reindex in P21212 in order to use arp/warp? (the diffraction data were indexed in XDS, scaled in SCALA, and then run through CAD to change the space group from P222 to P22121). I am using arp/warp via the ccp4i interface. Also, arp/warp gives the following message when I load the mtz file "cannot extract arp/warp asymmetric unit limits, the job will fail if run." (i did run arp/warp successfully with other mtz-files). Thank you in advance for any comments! Florian
Re: [ccp4bb] arp/warp in p22121
Dear Florian, ARP/wARP supports 65 space groups where proteins crystallise and it indeed uses the Hermann-Mauguin convention as given in the International Tables. The space group P22121 (number 3018 in the CCP4 symop.lib) is not supported by ARP/wARP. The standard for it would be number 18, P21212. The easiest is to re-index your data. The error message 'cannot extract asymmetric unit limits' should then also disappear. Victor PS. Actually, Tassos has already replied while I was typing this message. Florian Schmitzberger wrote: Dear All, I am trying to build a molecular replacement model in arp/warp in space group P22121. Refmac alone seems to be fine with refining the model in P22121; but arp/warp fails, as far as I can see at the first Refmac refinement stage. In the log-file it says "this space group is not supported". I am wondering whether arp/warp needs the Hermann-Mauguin convention space group P21212. I suppose I will need to reindex in P21212 in order to use arp/warp? (the diffraction data were indexed in XDS, scaled in SCALA, and then run through CAD to change the space group from P222 to P22121). I am using arp/warp via the ccp4i interface. Also, arp/warp gives the following message when I load the mtz file "cannot extract arp/warp asymmetric unit limits, the job will fail if run." (i did run arp/warp successfully with other mtz-files). Thank you in advance for any comments! Florian
Re: [ccp4bb] arp/warp in p22121
> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Victor Lamzin > Sent: 18 September 2007 12:48 > To: [EMAIL PROTECTED]; CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] arp/warp in p22121 > > Dear Florian, > > ARP/wARP supports 65 space groups where proteins crystallise and it > indeed uses the Hermann-Mauguin convention as given in the > International > Tables. The space group P22121 (number 3018 in the CCP4 symop.lib) is > not supported by ARP/wARP. The standard for it would be number 18, > P21212. The easiest is to re-index your data. IMHO, gratuitous permutation of the cell axes in the data & co-ordinates is certainly not always an easy option since it's a real pain to have datasets around with different indexings: it causes endless confusion, particularly as in one case I had in P22121 where the a & b cell lengths were very close so it wasn't obvious just by looking at the files whether they had been re-indexed or not! The problem is specifically that ARP/wARP *doesn't* support the IUCr convention as given in IT (Vol. A, >= 1983 edition, Table 9.3.4.1, p.758 in 5th ed.) regarding choice of cell in primitive orthorhombic space groups, and I suspect in centred monoclinic ones also. AFAIK ARP/wARP and pointless are the only two CCP4 programs that currently don't fully support the IUCr convention (though I suppose you could argue that ARP/wARP isn't technically a CCP4 program). It seems to me that the IUCr cell choice convention has a perfectly rational basis: the cell is chosen at the time the images are indexed solely on the basis of the assigned Bravais lattice symmetry, and provided that no problems with pseudo-symmetry are discovered later on it should never normally need to be changed thereafter. Systematic absences (not including absences due to centred lattices) have no influence on the choice of cell for the simple reason that they are not always reliable indicators of the true space group (particularly screw-axis absences). Assignment of the space-group symbol often does not occur until the heavy-atom Patterson or translation function solution stage, and I don't see the sense in being forced to permute the cell axes at that stage. It seems to me that a design goal of 'user-friendly' software should be to minimise the opportunity for the user to make obvious blunders which can waste a lot of time to sort out (even if it means making life a little more difficult for the programmer)! -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] arp/warp in p22121
The problem is specifically that ARP/wARP *doesn't* support the IUCr convention as given in IT (Vol. A, >= 1983 edition, Table 9.3.4.1, p.758 in 5th ed.) regarding choice of cell in primitive orthorhombic space groups, and I suspect in centred monoclinic ones also. AFAIK ARP/wARP and pointless are the only two CCP4 programs that currently don't fully support the IUCr convention Phaser doesn't "support" the IUCr convention, and if it was used for the original MR in this case (I don't know whether it was or not), then it would have caused the "problem". We have had user requests to change the output to the IUCr convention, but other people get confused if the axes are permuted. So the choice will be made an output option - Frank von Delft suggested the keyword "IUCR [ON/OFF]"! Vote for your choice of default now... Airlie McCoy
Re: [ccp4bb] arp/warp in p22121
I'm confused now, sticking to the IUCr convention should not require any axis permutation. My beef is specifically against unnecessary axis permutations! Surely it's when the program doesn't support the convention that you are forced to permute the axes? Besides I did solve a structure in P22121 with Phaser so I'm even more confused! -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Airlie McCoy > Sent: 19 September 2007 15:09 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] arp/warp in p22121 > > >The problem is specifically that ARP/wARP *doesn't* support the IUCr > >convention as given in IT (Vol. A, >= 1983 edition, Table > 9.3.4.1, p.758 > >in 5th ed.) regarding choice of cell in primitive orthorhombic space > >groups, and I suspect in centred monoclinic ones also. > AFAIK ARP/wARP > >and pointless are the only two CCP4 programs that currently > don't fully > >support the IUCr convention > > Phaser doesn't "support" the IUCr convention, and if it was > used for the > original MR in this case (I don't know whether it was or > not), then it > would have caused the "problem". We have had user requests to > change the > output to the IUCr convention, but other people get confused > if the axes > are permuted. So the choice will be made an output option - > Frank von Delft > suggested the keyword "IUCR [ON/OFF]"! Vote for your choice > of default > now... > > Airlie McCoy > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] arp/warp in p22121
Hi Sue It's certainly true that the convention in the 1935 and 1952 editions of IT Volume 1 *appeared* to be the 'standard setting' convention that you describe because only the 'standard' settings were listed, and this was the way that many crystallographers interpreted it (actually only macromolecular crystallographers, the small molecule people stick to the IUCr convention), so this is probably where you're coming from. However the 1983 edition of Volume A clarified the situation and made it clear that this was never the intention, so all the conventional settings are now shown on the SG diagram pages. P22121 & P21221 certainly are defined in IT Vol. A - look on the diagram page for SG no. 18 & you'll see them. The 'standard symbol' for a space group is merely the heading on the page used only for indexing purposes, so space groups P22121, P21221 and P21212 all have the same standard symbol P21212; hence the standard symbol is not unique and can't be used to unambiguously define the space group. The 'standard setting' is merely the space group setting that has the same name as the standard symbol. Even if that weren't true do we really want to be still sticking to a convention that was abandoned 25 years ago and doesn't a later convention override an earlier one anyway? Actually the convention in use is not the issue anyway, I don't care which convention is used as long as all programs use the same convention! - then I'll never need to permute axes (just as fundamentally I don't care which co-ordinate format is used as long as all programs use the same one, then I'll never need to reformat). So Mosflm uses the IUCr convention (i.e. a<=b<=c for primitive orthorhombic), and therefore any program which doesn't support that convention for any space group forces you to permute the axes completely unnecessarily. -- Ian > -Original Message- > From: Sue Roberts [mailto:[EMAIL PROTECTED] > Sent: 19 September 2007 16:38 > To: Ian Tickle > Subject: Re: [ccp4bb] arp/warp in p22121 > > Hi Ian > > But there's an older convention, which is to use the space groups > settings defined in the International Tables - and P22121 is not a > standard setting. > > Sue > > > On Sep 19, 2007, at 8:18 AM, Ian Tickle wrote: > > > I'm confused now, sticking to the IUCr convention should not > > require any > > axis permutation. My beef is specifically against unnecessary axis > > permutations! Surely it's when the program doesn't support the > > convention that you are forced to permute the axes? > > > > Besides I did solve a structure in P22121 with Phaser so > I'm even more > > confused! > > > > -- Ian > > > >> -Original Message- > >> From: [EMAIL PROTECTED] > >> [mailto:[EMAIL PROTECTED] On Behalf Of Airlie McCoy > >> Sent: 19 September 2007 15:09 > >> To: CCP4BB@JISCMAIL.AC.UK > >> Subject: Re: [ccp4bb] arp/warp in p22121 > >> > >>> The problem is specifically that ARP/wARP *doesn't* > support the IUCr > >>> convention as given in IT (Vol. A, >= 1983 edition, Table > >> 9.3.4.1, p.758 > >>> in 5th ed.) regarding choice of cell in primitive > orthorhombic space > >>> groups, and I suspect in centred monoclinic ones also. > >> AFAIK ARP/wARP > >>> and pointless are the only two CCP4 programs that currently > >> don't fully > >>> support the IUCr convention > >> > >> Phaser doesn't "support" the IUCr convention, and if it was > >> used for the > >> original MR in this case (I don't know whether it was or > >> not), then it > >> would have caused the "problem". We have had user requests to > >> change the > >> output to the IUCr convention, but other people get confused > >> if the axes > >> are permuted. So the choice will be made an output option - > >> Frank von Delft > >> suggested the keyword "IUCR [ON/OFF]"! Vote for your choice > >> of default > >> now... > >> > >> Airlie McCoy > >> > >> > > > > > > Disclaimer > > This communication is confidential and may contain privileged > > information intended solely for the named addressee(s). It may not > > be used or disclosed except for the purpose for which it has been > > sent. If you are not the intended recipient you must not review, > > use, disclose, copy, distribute or take any action in > reliance upon > > it. If you have received t
Re: [ccp4bb] arp/warp in p22121
On second reading maybe I misunderstood what you were saying. If Phaser reads an MTZ file which doesn't conform to the convention (e.g. a<=b<=c NOT true in primitive orthorhombic) then it certainly should not by default permute the axes on output, I agree that that certainly would cause confusion. However Phaser does accept an MTZ file which does conform (e.g. P22121 a<=b<=c) and doesn't (and shouldn't) permute the axes. So I vote for a default of preserving the input convention whatever it is, and I definitely vote against all axis permutations unless a) it's absolutely necessary (e.g. for consistency with other datasets), and b) the user specifically requests it (and really really means it!). -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Airlie McCoy > Sent: 19 September 2007 15:09 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] arp/warp in p22121 > > >The problem is specifically that ARP/wARP *doesn't* support the IUCr > >convention as given in IT (Vol. A, >= 1983 edition, Table > 9.3.4.1, p.758 > >in 5th ed.) regarding choice of cell in primitive orthorhombic space > >groups, and I suspect in centred monoclinic ones also. > AFAIK ARP/wARP > >and pointless are the only two CCP4 programs that currently > don't fully > >support the IUCr convention > > Phaser doesn't "support" the IUCr convention, and if it was > used for the > original MR in this case (I don't know whether it was or > not), then it > would have caused the "problem". We have had user requests to > change the > output to the IUCr convention, but other people get confused > if the axes > are permuted. So the choice will be made an output option - > Frank von Delft > suggested the keyword "IUCR [ON/OFF]"! Vote for your choice > of default > now... > > Airlie McCoy > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] arp/warp in p22121
So I vote for a default of preserving the input convention whatever it is, and I definitely vote against all axis permutations unless a) it's absolutely necessary (e.g. for consistency with other datasets), and b) the user specifically requests it (and really really means it!). Phew! It makes a change for someone NOT to want a new option in Phaser! Airlie
[ccp4bb] arp/warp 7.0.1 and ccp4i
Hello all, While testing a newly installed ARP/wARP interface (ver. 7.0.1) in ccp4i (ver. 6.1.0) on Ubuntu (8.10) I noticed that the Fobs and Sigma pull-down menus are missing from the ARP/wARP Quick Fold window. This is accompanied by the following error message, which is output in stderr by the ccp4i interface: ERROR CreateLabinLine: unrecognised argument -fileout To remedy this problem one has to edit the warp_albe.tcl file, which is located in $CCP4/ccp4i/tasks directory. Line 325 -fileout XYZOUT DIR_XYZOUT "_helices_" has to be removed. All the best, Petr
[ccp4bb] ARP/wARP and computer platforms
We are collecting information on computer platforms that people would like ARP/wARP to run on. To access the questionnaire please go to http://www.embl-hamburg.de/ARP/platinf_new.shtml Thank you for your cooperation. With best regards, Victor
[ccp4bb] ARP/wARP and computer platforms
We were collecting information on computer platforms that people would like ARP/wARP to run on. 126 people responded with 296 platform choices. The latter grouped as follows: Linux i686 26% Linux x86_64 24% Linux ia644% total Linux54% Mac powerpc 9% Mac Intel 10.48% Mac Intel 10.5 21% total Mac 38% Windows 5% IRIX64 mips 2% Other platforms 1% In addition, we asked about CCP4 version used: CCP4 6.x only98% CCP4 5.x only 2% Both 5.x and 6.x 6% Many thanks for participation in the questionnaire! With best regards, Victor
Re: [ccp4bb] Arp/Warp in Ubuntu
Dear Yuan, Most likely your ARP/wARP settings are not sourced. 1. Quit CCP4i 2. Modify your ./cshrc (or .bashrc) so that it sources CCP4 first and ARP/wARP then. Below is one example of .cshrc: # # Setup CCP4 source /Users/victor/xtal/ccp4/ccp4-6.0.2/include/ccp4.setup # # Setup ARP/wARP source /Users/victor/xtal/arp_warp/arp_warp_7.0.1/arpwarp_setup.csh # 3. Open a new terminal window and start CCP4i. With best regards, Victor SHANG Yuan wrote: Hi, Does anyone know how to Plugging ARP/wARP GUI into CCP4i interface? I followed http://www.embl-hamburg.de/arp-cgi-bin/FAQ7.0_1.pl, but always get a warning "Can not get environment variable for wardoc" with a subsequent Application Error "Error:bad window path name \".warning..." Under Ubuntu, I can find the place for me to input the administrator's code.. Thanks in advance. Yuan SHANG
[ccp4bb] ARP/wARP 7.4 Patch 2 available
Dear colleagues, ARP/wARP 7.4 Patch 2 is available for download on our FTP server, as well. If you were installing ARP/wARP as a joint bundle with CCP4-6.4.0, you can update ARP/wARP via automatic CCP4 update or download the patches from http://www.ccp4.ac.uk/updates/ If you were installing ARP/wARP from a standalone tarball or DMG, please visit www.arp-warp.org with further link to download. After receiving an email with access details to the download area, you can either download full standalone ARP/wARP tarball or DMG, or download only the patch. The README file in the download area (or the FAQ pages on www.arp-warp.org) explain how to apply the patch with a single command. In either case, the installed ARP/wARP will be fully compatible with CCP4-6.4.0. Many thanks for using ARP/wARP, The ARP/wARP team -- Dr. Ioan Vancea European Molecular Biology Laboratory c/o DESY Notkestrasse 85, 22607 Hamburg, Germany Tel: +49 (0)40 89902-340 Email: ivan...@embl-hamburg.de
[ccp4bb] Arp warp 7 error in ccp4i
Dear All :
When I run the new version of arp-warp in the ccp4i interface I got the
following error. Any ideas that what I am doing wrong ??
Thanks for the help.
Francisco
-
ERROR ('IOError', '', [' File
"/usr/local/arp_warp_7.0/flex-wARP-src-214/CArc.py", line 78, in
checkAndProcess\nself.status = self.controller.checkAndProcess()\n', '
File
"/usr/local/arp_warp_7.0/flex-wARP-src-214/CNCSCrudeGenController.py",
line 65, in checkAndProcess\nself._parse(self.logname, self.xmllog,
self.stepmanager.vdict[\'logStream\'])\n', ' File
"/usr/local/arp_warp_7.0/flex-wARP-src-214/CNCSCrudeGenController.py",
line 106, in _parse\nf = open(xmllogname,\'r\')\n'])
--
ERROR => Ending JOB
--
-
Francisco J. Enguita, Ph.D.
Host-pathogen Interactions Group
Macromolecular Crystallography Laboratory
ITQB
EAN, Av. da República
2781-901 Oeiras
Portugal
Phone : +351-21-4469663
Fax : +351-21-4433644
E-mail : [EMAIL PROTECTED]
-
[ccp4bb] ARP/wARP usage at low resolution!
Dear all, May I ask you, if you had cases at low resolution (lets say at least below 2.5 to be generous) that ARP/wARP produced a useful result for you, to send me (... not to the list) a very short email, also mentioning a publication that refers to that result? Thanks in advance, Tassos
[ccp4bb] Arp/WARP for multi-chain complex
Dear All, I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A data, there are three chains (heavy, light chains of antibody and the antigen) in the complex, my question is how to put the sequences in the *.pir file so that it still identifies different chains. It looks like Arp/wArp only accepts *.pir file with one sequence id. Thanks, Tongqing
Re: [ccp4bb] ARP/wARP and computer platforms
Interesting that these questionaire responses are very different from the numbers obained from looking at downloads counts for other cross-platform crystallography software. I wonder if they are more reflective of the currently available ARP-wARP platforms and perhaps the role of administrator- programmer types as the main responders. The open source MIFit distribution (recent data since this was available from Jan 2009) from http://code.google.com/p/mifit/downloads/list logs today at 84 Windows, zipped 84 Linux, gzipped 85 Windows, installer I recall a similar disconnect between CCP4 downloads and BB replies to a questions on optimal hardware platform for crystallographic computing - basically, an antipathy from specific posters towards the Windows OS but a lot of downloads logged. I have come to prefer the laptop crystallography in a Windows enviroment because it is simpler and more efficient for my current work (early stage drug discovery and development using fragment screening and protein structure data) that requires chemistry 'bench' software and tight integration with project reporting and management functions. For the record, I don't see any decision-making issues with crystallographic computing performance on Windows. For example, On a moderately high-end laptop I will typically be able to line-up and auto-process ~8 image data sets/hour (either MOSFLM or d*TREK). A basic structure solution task (MOLREP, 3 rounds of refinement with REFMAC with some water-picking and validation calculations) is usually performed in well under 5 minutes. Cost is a slippery argument since the cost of much of the crystallographic software for commercial use is often several times that of the computer itself and order of magnitude more than a copy of MS Office. Many users might prefer a reliable ready-to-run precompiled executables than potentially dealing with compilation or run-time issues (many useful posts on this BB are about dealing with those!) since not everyone has the knowledge time or desire to work them out. Hope this does not provoke a 'religious war' from the OS zealots - as I indicated I think the optimal OS for crystallography depends more on other factors in your work environment rather than benchmark issues. I would not take this survey to mean that there is no interest in ARP/wARP on Windows - especially as it is one of the more unique programs, perhaps without a direct substitute. As a sidebar, Windows interoperability and reduction of cost/complexity in the crystallographic computing environment is the main reason for preserving arp-waters in CCP4. Thanks John Badger, Director of Structural Biology, Zenobia Therapeutics
[ccp4bb] arp/warp failure on Debian testing
Hello, on two recently installed Linux boxes (PC, i7) with Debian testing (squeeze), arp warp classic does not run but produces the following log-file: --- 8< snip - #CCP4I VERSION CCP4Interface 2.0.5 #CCP4I SCRIPT LOG arp_warp #CCP4I DATE 20 Nov 2009 10:43:14 #CCP4I USER tg #CCP4I PROJECT aparp #CCP4I JOB_ID 3 #CCP4I SCRATCH /tmp/tg #CCP4I HOSTNAME hydra.sheldrick #CCP4I PID 4668 #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 20 Nov 2009 10:43:44 #CCP4I TERMINATION OUTPUT_FILES /net/home/tg/others/ap/3_arp_warp.par aparp /net/home/tg/others/ap/1_wilson.loggraph aparp #CCP4I MESSAGE Task completed successfully --->8 snap -- The gui asks about the Wilson plot, and, when run as 'run and view com file' shows the script for mtzdump. That command executed in from the shell, produces the desired result without failure. On an older installation, but also Debian squeeze, arp warp runs normally. How could I further debug the arp-warp output? One guess would be that some library is missing, but I realised that the binaries are statically linked. The directory /tmp/tg exists and is writable on both computers. Cheers, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] ARP/wARP awk: Command not found.
Hi, auto_tracing.sh “ARP/wARP 8.0 patch 1”, after a few cycles, prints awk: Command not found., and exits a little later with: Data line -- RESOLUTION 20 2.2 Data line -- REMOVE ATOMS 8 CUTSIGMA 1.0 FORCE NEGATIVE MERGE 0.7 Data line -- FIND ATOMS CHAIN Z CUTSIGMA 3.2 RESN DUM This Data Card is not understood: FIND ATOMS CHAIN Z CUTSIGMA 3.2 RESN DUM Looking for keyword ATOM followed by 1 field(s) Cannot accept field shown by arrows: FIND ATOMS ==>CHAIN<== Z CUTSIGMA 3.2 RESN DUM Expected format: FIND ATOMS number CHAIN string CUTSIGMA number/AUTO RESNAM WAT/DUM I do not know if the last error message is related to awk. In any case, awk is available in /usr/bin/awk. Did anyone else experience this issue? If so, is there a workaround? Thanks. Wolfram Tempel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] ARP/WARP won't install - old glibc trouble
Dear CCP4BB, I am unable to install ARP/WARP on a server with Debian 10, it says: Segmentation fault *** ERROR *** This machine cannot run ARP/wARP executables that are statically linked to glibc. *** INSTALLATION OF ARP/wARP 8.0 FAILED *** Modified version exit status 1 -- after some digging I found several old, unsolved issues about that in GitHub, any ideas about how to get around? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] ARP/wARP or Auto-Rickshaw remote services
Dear colleagues, If you are using ARP/wARP or Auto-Rickshaw remote services, we would like to inform you that, as a preparation for the next ARP/wARP version, a few days ago we moved the services to a new, faster and more powerful machine. Almost everything is settled by now, but there are still a few minor issues, which we are working hard to fix as soon as possible. If you still observe random failures and premature stops of some submitted jobs, please resubmit and the job should run successfully. You are also welcome to notify us by an Email in case of problems. We apologise for any inconvenience that this may cause, and thank you for your interest in ARP/wARP. Best regards, ARP/wARP Team -- Dr. Ioan Vancea European Molecular Biology Laboratory c/o DESY Notkestrasse 85, 22607 Hamburg, Germany Tel: +49 (0)40 89902-340 Email: ivan...@embl-hamburg.de
Re: [ccp4bb] Arp warp 7 error in ccp4i
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Francisco;
This looks like a disk access problem. Are you by any chance running
this process from a NFS mounted volume ?
Is this crash reproducible, that is if you "just re-run" the task (in
the CCP4i) will it produce a crash at the exact same spot?
Can you give us more specific information on the machine you are
running flex-wARP ? Which operating system, architecture :
result of 'uname -a'
Maybe the bst is that we sort out this problem using private mails,
and when the cause is identified send a summary to the BB. Would you
agree on this way of doing?
Cordially;
Serge.
Le 15 nov. 07 à 12:02, [EMAIL PROTECTED] a écrit :
Dear All :
When I run the new version of arp-warp in the ccp4i interface I got
the
following error. Any ideas that what I am doing wrong ??
Thanks for the help.
Francisco
-
ERROR ('IOError', '', [' File
"/usr/local/arp_warp_7.0/flex-wARP-src-214/CArc.py", line 78, in
checkAndProcess\nself.status = self.controller.checkAndProcess()
\n', '
File
"/usr/local/arp_warp_7.0/flex-wARP-src-214/CNCSCrudeGenController.py",
line 65, in checkAndProcess\nself._parse(self.logname,
self.xmllog,
self.stepmanager.vdict[\'logStream\'])\n', ' File
"/usr/local/arp_warp_7.0/flex-wARP-src-214/CNCSCrudeGenController.py",
line 106, in _parse\nf = open(xmllogname,\'r\')\n'])
--
ERROR => Ending JOB
--
-
Francisco J. Enguita, Ph.D.
Host-pathogen Interactions Group
Macromolecular Crystallography Laboratory
ITQB
EAN, Av. da República
2781-901 Oeiras
Portugal
Phone : +351-21-4469663
Fax : +351-21-4433644
E-mail : [EMAIL PROTECTED]
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[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 for multi-chain complex
In the absence of a likely, more sensible, answer - I think the trick is/was to
simply put everything in one pir file, but "link" each sequence with a run of
20 or so alanines i.e. sequence A followed by ... sequence B
sequence C.
There may well be a more elegant solution - but I'm fairly sure this worked
previously for us.
With regards,
Tony.
On 19 Apr 2012, at 04:26, "Zhou, Tongqing (NIH/VRC) [E]"
wrote:
> Dear All,
>
> I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A
> data, there are three chains (heavy, light chains of antibody and the
> antigen) in the complex, my question is how to put the sequences in the *.pir
> file so that it still identifies different chains. It looks like Arp/wArp
> only accepts *.pir file with one sequence id.
>
> Thanks,
>
>
> Tongqing
Re: [ccp4bb] Arp/WARP for multi-chain complex
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Tony, dear Tongqing, the way I understand the working mechanism of arp/warp works I do not see the point introducing the polyALA spacer into the sequence. Just concatenate all sequences into one file as though it was one molecule. Cheers, Tim On 04/19/12 08:51, Antony Oliver wrote: > In the absence of a likely, more sensible, answer - I think the > trick is/was to simply put everything in one pir file, but "link" > each sequence with a run of 20 or so alanines i.e. sequence A > followed by ... sequence B > sequence C. > > There may well be a more elegant solution - but I'm fairly sure > this worked previously for us. > > With regards, > > Tony. > > > On 19 Apr 2012, at 04:26, "Zhou, Tongqing (NIH/VRC) [E]" > wrote: > >> Dear All, >> >> I am trying to use Arp/wArp to build an antibody-antigen complex >> with 1.65 A data, there are three chains (heavy, light chains of >> antibody and the antigen) in the complex, my question is how to >> put the sequences in the *.pir file so that it still identifies >> different chains. It looks like Arp/wArp only accepts *.pir file >> with one sequence id. >> >> Thanks, >> >> >> Tongqing > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPj8ZVUxlJ7aRr7hoRAqu6AKDff8lY6Ehj2A8u76UfTgiIcNoqMACfd7Wr 3cDlEfHVVWxASrw9qxMTwMY= =sFT8 -END PGP SIGNATURE-
Re: [ccp4bb] Arp/WARP for multi-chain complex
Dear Tongqing, On Apr 19, 2012, at 5:26 AM, Zhou, Tongqing (NIH/VRC) [E] wrote: > I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A > data, there are three chains (heavy, light chains of antibody and the > antigen) in the complex, my question is how to put the sequences in the *.pir > file so that it still identifies different chains. It looks like Arp/wArp > only accepts *.pir file with one sequence id. You can put the chains into a single *.pir file and separate each chain with 10 Alanines. For instance (assuming the antigen is protein): Heavy_chain_sequence_AA_Light_chain_sequence_AA_Antigen_sequence To do this you need to edit the *.pir file in a text editor. Details on the file format are in the link below: http://www.bioinformatics.nl/tools/crab_pir.html Please contact me if you hit any problems or this suggestion isn't clear. Saul Hazledine
Re: [ccp4bb] Arp/WARP for multi-chain complex
Dear Tony, Tongqing, Tim, Adding some alanine spacer is good for a simple reason - during sequence docking ARP/wARP checks the distance between the ends of the fragments. Imagine you have two chains, 10 residues each. If you concatenate them together, terminal residues belonging to different chains will have consequtive numbers, 10 and 11: 1122 Also imagine ARP/wARP built all residues in both fragments and is about to sequence-dock them. Fortunately (or not) it removes termini, so that you have: ---- Now, if the distance between residue 9 (the last in the first chain) and 12 (the first in the second chain) is longer than about 3.8*(12-9)=11.4 A (the actual formula is a bit more complex), one of the fragments will not be sequence docked and its side chains will be chopped to glycines. Placing a few alaninines (5 to 10) in between the chains will certainly help. On the other hand, one should not add too many alanines overall. ARP/wARP pretends to be clever and tries to figure out the NCS-order automatically. If you added far too many alanines, you may confuse ARP/wARP in thinking that your structure is, say, a trimer rather than a tetramer. There could be of course better ways of sequence-docking for heteromers, but the above is the current status in 'ARP/wARP Classic' protein model building. With best regards, Victor Quoting "Tim Gruene" : -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Tony, dear Tongqing, the way I understand the working mechanism of arp/warp works I do not see the point introducing the polyALA spacer into the sequence. Just concatenate all sequences into one file as though it was one molecule. Cheers, Tim On 04/19/12 08:51, Antony Oliver wrote: In the absence of a likely, more sensible, answer - I think the trick is/was to simply put everything in one pir file, but "link" each sequence with a run of 20 or so alanines i.e. sequence A followed by ... sequence B sequence C. There may well be a more elegant solution - but I'm fairly sure this worked previously for us. With regards, Tony. On 19 Apr 2012, at 04:26, "Zhou, Tongqing (NIH/VRC) [E]" wrote: Dear All, I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A data, there are three chains (heavy, light chains of antibody and the antigen) in the complex, my question is how to put the sequences in the *.pir file so that it still identifies different chains. It looks like Arp/wArp only accepts *.pir file with one sequence id. Thanks, Tongqing - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPj8ZVUxlJ7aRr7hoRAqu6AKDff8lY6Ehj2A8u76UfTgiIcNoqMACfd7Wr 3cDlEfHVVWxASrw9qxMTwMY= =sFT8 -END PGP SIGNATURE-
Re: [ccp4bb] Arp/WARP for multi-chain complex
Thanks Victor - for giving a rational and detailed explanation. I obviously got carried away with the number of alanines to intersperse! With regards, Tony. On 19 Apr 2012, at 16:52, "Victor Lamzin" wrote: > Dear Tony, Tongqing, Tim, > > Adding some alanine spacer is good for a simple reason - during sequence > docking ARP/wARP checks the distance between the ends of the fragments. > > Imagine you have two chains, 10 residues each. If you concatenate them > together, terminal residues belonging to different chains will have > consequtive numbers, 10 and 11: > 1122 > > Also imagine ARP/wARP built all residues in both fragments and is about to > sequence-dock them. Fortunately (or not) it removes termini, so that you have: > ---- > > Now, if the distance between residue 9 (the last in the first chain) and 12 > (the first in the second chain) is longer than about 3.8*(12-9)=11.4 A (the > actual formula is a bit more complex), one of the fragments will not be > sequence docked and its side chains will be chopped to glycines. Placing a > few alaninines (5 to 10) in between the chains will certainly help. > > On the other hand, one should not add too many alanines overall. ARP/wARP > pretends to be clever and tries to figure out the NCS-order automatically. If > you added far too many alanines, you may confuse ARP/wARP in thinking that > your structure is, say, a trimer rather than a tetramer. > > There could be of course better ways of sequence-docking for heteromers, but > the above is the current status in 'ARP/wARP Classic' protein model building. > > With best regards, > Victor > > > > Quoting "Tim Gruene" : > >> -BEGIN PGP SIGNED MESSAGE- >> Hash: SHA1 >> >> Dear Tony, dear Tongqing, >> >> the way I understand the working mechanism of arp/warp works I do not >> see the point introducing the polyALA spacer into the sequence. Just >> concatenate all sequences into one file as though it was one molecule. >> >> Cheers, >> Tim >> >> On 04/19/12 08:51, Antony Oliver wrote: >>> In the absence of a likely, more sensible, answer - I think the >>> trick is/was to simply put everything in one pir file, but "link" >>> each sequence with a run of 20 or so alanines i.e. sequence A >>> followed by ... sequence B >>> sequence C. >>> >>> There may well be a more elegant solution - but I'm fairly sure >>> this worked previously for us. >>> >>> With regards, >>> >>> Tony. >>> >>> >>> On 19 Apr 2012, at 04:26, "Zhou, Tongqing (NIH/VRC) [E]" >>> wrote: >>> Dear All, I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A data, there are three chains (heavy, light chains of antibody and the antigen) in the complex, my question is how to put the sequences in the *.pir file so that it still identifies different chains. It looks like Arp/wArp only accepts *.pir file with one sequence id. Thanks, Tongqing >>> >> >> - -- >> - -- >> Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> >> -BEGIN PGP SIGNATURE- >> Version: GnuPG v1.4.12 (GNU/Linux) >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >> >> iD8DBQFPj8ZVUxlJ7aRr7hoRAqu6AKDff8lY6Ehj2A8u76UfTgiIcNoqMACfd7Wr >> 3cDlEfHVVWxASrw9qxMTwMY= >> =sFT8 >> -END PGP SIGNATURE- >>
Re: [ccp4bb] Arp/WARP for multi-chain complex
Hi Tony, Tim, Victor and Saul, Thank you very much for the help on Arp/wARP setup. I did it with one big pir file last night without inserting the poly Ala, most of the terminal residues at the "sequence junctions" were not fitted or removed as Tony mentioned. I am amazed how well ArpwArp worked overall! Regards, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 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. ** -Original Message- From: Antony Oliver [mailto:antony.oli...@sussex.ac.uk] Sent: Thursday, April 19, 2012 11:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Arp/WARP for multi-chain complex Thanks Victor - for giving a rational and detailed explanation. I obviously got carried away with the number of alanines to intersperse! With regards, Tony. On 19 Apr 2012, at 16:52, "Victor Lamzin" wrote: > Dear Tony, Tongqing, Tim, > > Adding some alanine spacer is good for a simple reason - during sequence > docking ARP/wARP checks the distance between the ends of the fragments. > > Imagine you have two chains, 10 residues each. If you concatenate them > together, terminal residues belonging to different chains will have > consequtive numbers, 10 and 11: > 1122 > > Also imagine ARP/wARP built all residues in both fragments and is about to > sequence-dock them. Fortunately (or not) it removes termini, so that you have: > ---- > > Now, if the distance between residue 9 (the last in the first chain) and 12 > (the first in the second chain) is longer than about 3.8*(12-9)=11.4 A (the > actual formula is a bit more complex), one of the fragments will not be > sequence docked and its side chains will be chopped to glycines. Placing a > few alaninines (5 to 10) in between the chains will certainly help. > > On the other hand, one should not add too many alanines overall. ARP/wARP > pretends to be clever and tries to figure out the NCS-order automatically. If > you added far too many alanines, you may confuse ARP/wARP in thinking that > your structure is, say, a trimer rather than a tetramer. > > There could be of course better ways of sequence-docking for heteromers, but > the above is the current status in 'ARP/wARP Classic' protein model building. > > With best regards, > Victor > > > > Quoting "Tim Gruene" : > >> -BEGIN PGP SIGNED MESSAGE- >> Hash: SHA1 >> >> Dear Tony, dear Tongqing, >> >> the way I understand the working mechanism of arp/warp works I do not >> see the point introducing the polyALA spacer into the sequence. Just >> concatenate all sequences into one file as though it was one molecule. >> >> Cheers, >> Tim >> >> On 04/19/12 08:51, Antony Oliver wrote: >>> In the absence of a likely, more sensible, answer - I think the >>> trick is/was to simply put everything in one pir file, but "link" >>> each sequence with a run of 20 or so alanines i.e. sequence A >>> followed by ... sequence B >>> sequence C. >>> >>> There may well be a more elegant solution - but I'm fairly sure this >>> worked previously for us. >>> >>> With regards, >>> >>> Tony. >>> >>> >>> On 19 Apr 2012, at 04:26, "Zhou, Tongqing (NIH/VRC) [E]" >>> wrote: >>> >>>> Dear All, >>>> >>>> I am trying to use Arp/wArp to build an antibody-antigen complex >>>> with 1.65 A data, there are three chains (heavy, light chains of >>>> antibody and the antigen) in the complex, my question is how to put >>>> the sequences in the *.pir file so that it still identifies >>>> different chains. It looks like Arp/wArp only accepts *.pir file >>>> with one sequence id. >>>> >>>> Thanks, >>>> >>>> >>>> Tongqing >>> >> >> - -- >> - -- >> Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> >> -BEGIN PGP SIGNATURE- >> Version: GnuPG v1.4.12 (GNU/Linux) >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >> >> iD8DBQFPj8ZVUxlJ7aRr7hoRAqu6AKDff8lY6Ehj2A8u76UfTgiIcNoqMACfd7Wr >> 3cDlEfHVVWxASrw9qxMTwMY= >> =sFT8 >> -END PGP SIGNATURE- >>
[ccp4bb] ARP/wARP-8.0 + CCP4-7.0.065 joint release
Dear CCP4 Users We would like to announce the joint release of ARP/wARP version 8.0 and CCP4-7.0.065. ARP/wARP 8.0 provides a considerably improved performance for X-ray crystallographic applications and it is now also capable of interpreting cryo-EM maps at a resolution range 2.0-3.5 Å. Installation and compatibility -Checks for software installation have been enhanced -32 and 64-bit platforms on OSX and Linux are supported -ARP/wARP is fully compatible with the latest versions of CCP4 and Refmac Protein chain tracing -Protein chain tracing has been made faster and its memory handling has been improved -DipCheck conformational space is introduced for the selection of the chain path -NCS restraints are now default at resolution 1.5 Å or lower -Loop closure can now be provided using a new module Loopy2018 Sequence docking and building -Side chain guess and fit can now be accomplished using a new module SEQQY -Handling of large structures has been enhanced and the maximum number of NCS copies increased to 60 -Both mono- and hetero-multimers can now be handled DNA/RNA building -Nucleotide chain tracing is enhanced with the addition of the second algorithm for phosphate detection -Nucleotide chain tracing now proceeds in an iterative manner, as for protein tracing Identification of crystallographic ligands -Energy estimate for protein-ligand bound state is introduced during identification of crystallographic ligands Solvent building -Building of solvent structure exploits advanced features of Refmac including TLS and local NCS restraints. -Solvent update can optionally be turned off providing a tool for model refinement with Refmac. Building models into cryo-EM maps -Protein and protein-nucleic acid models are built with a minimum user input -Map over-sharpening is handled automatically -Partial models can be completed by sequence-docking and loop building -Models can be refined with a combined real- and reciprocal-space protocol -A very fast secondary structure modelling option can be used separately. An update No 65 for the CCP4-7.0 series automatically installs ARP/wARP-8.0 on Mac OS X and Linux computers, where ARP/wARP-7.6 has previously been installed as a part of CCP4 installation. (The directory arp_warp_7.6 is _not_ removed , but CCP4 i1 and i2 are switched to version 8.0). In addition, the update No 65 brings the following changes. * refmac5: correction to LINK records * contact: increase MaxSelectedResidues * dials: inclusion of mock module * pointless: update to 1.11.6 * rabdam: update to 1.4.1 * crank2: fixes and improvements * documentation: correction to freerflag documentation In addition, tarballs and bundles for CCP4 Setup Manager consisting of CCP4-7.0.065 and ARP/wARP 8.0 are available from CCP4 Downloads: http://www.ccp4.ac.uk/download Please report any bugs to c...@stfc.ac.uk. Many thanks for using CCP4 and ARP/wARP. The CCP4 Core Team To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] arp/warp failure on Debian testing
Hi Tim, First, we do not have access to Debian squeeze so I am afraid I cant say much about it. The gui asks about the Wilson plot, and, when run as 'run and view com file' shows the script for mtzdump. The 'run and view command file' will not work with the way that ARP/ wARP Classic (ab)uses ccp4i. That command executed in from the shell, produces the desired result without failure. Could you please clarify which is 'that commend'? Is that something like warp_tracing.sh my_cp4i_par_file_from_above.par or auto_tracing [parameters] On an older installation, but also Debian squeeze, arp warp runs normally. How could I further debug the arp-warp output? One guess would be that some library is missing, but I realised that the binaries are statically linked. Indeed, arp/warp is statically built. But, since the command line run its not the executables. I suspect semething with Tcl/Tk versions maybe. The directory /tmp/tg exists and is writable on both computers. If you send me what exactly you tried from the commend line I am sure we will be able to debug it. A. Cheers, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
Re: [ccp4bb] arp/warp failure on Debian testing
Hello Tassos, 'that command' (sorry about this expression, _I_ should have know how silly a description that is) was the mtzdump. Could you please clarify which is 'that commend'? Is that something like warp_tracing.sh my_cp4i_par_file_from_above.par That's what I was looking for. Issued at the prompt, the shell informs me that /bin/csh is not installed on the system - debian (being a modern distribution ;-) ) does not install tcsh by default. I guess that's going to resolve the issue. Cheers, Tim
Re: [ccp4bb] ARP/WARP won't install - old glibc trouble
Hi Carlos, We had the same problem trying to install ARP/wARP on our Debian 10 machines. TL;DR: you (or your sysadmin, since this requires root access) have to enable vsyscall as follows: echo 'GRUB_CMDLINE_LINUX_DEFAULT="vsyscall=emulate"' >> /etc/default/grub update-grub reboot An explainer (mostly from our sysadmin): vsyscall is a mechanism that accelerates certain system calls in Linux, apparently added as a way to execute specific system calls that don't need any real level of privilege to run. It's currently considered not very secure, which is why it's deactivated in many recent Linux flavors, including apparently Debian 10. The vsyscall = emulate setting seems to be the safest way to have vsyscall enabled while minimizing security vulnerability. Still, it seems like the best way to move forward is to compile the next version of ARP/wARP with the newer version of glibc. (some key insights obtained from this GitHub post and ones around it: https://github.com/microsoft/WSL/issues/1462#issuecomment-274398213 Hope this helps! Art > On Thu, Sep 3, 2020 at 8:34 AM Carlos Kikuti wrote: > >> Dear CCP4BB, >> >> I am unable to install ARP/WARP on a server with Debian 10, it says: >> >> Segmentation fault >> *** ERROR *** >> This machine cannot run ARP/wARP executables that >> are statically linked to glibc. >> >> *** INSTALLATION OF ARP/wARP 8.0 FAILED *** >> Modified version exit status 1 >> >> -- after some digging I found several old, unsolved issues about that in >> GitHub, any ideas about how to get around? >> >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > -- Artem Y. Lyubimov, PhD Staff Scientist SSRL SMB Crystallography 2525 Sand Hill Road mail stop 99 Menlo Park, CA 94025-7015 (415) 325-2057 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] ARP/WARP won't install - old glibc trouble
Dear Art, I am the sysadmin, which is bad news since I am much better as a crystallographer... and I was working on a different issue on the same machine the past week. Our institut has a good firewall so I believe we'll be fine, the installation of Arp/warp was smooth after the modification of grub as you proposed. Thank you very much! Carlos On Fri, Sep 4, 2020 at 9:30 PM Artem Lyubimov wrote: > Hi Carlos, > > We had the same problem trying to install ARP/wARP on our Debian 10 > machines. TL;DR: you (or your sysadmin, since this requires root access) > have to enable vsyscall as follows: > > echo 'GRUB_CMDLINE_LINUX_DEFAULT="vsyscall=emulate"' >> /etc/default/grub > update-grub > reboot > > An explainer (mostly from our sysadmin): > > vsyscall is a mechanism that accelerates certain system calls in Linux, > apparently added as a way to execute specific system calls that don't need > any real level of privilege to run. It's currently considered not very > secure, which is why it's deactivated in many recent Linux flavors, > including apparently Debian 10. The vsyscall = emulate setting seems to > be the safest way to have vsyscall enabled while minimizing security > vulnerability. Still, it seems like the best way to move forward is to > compile the next version of ARP/wARP with the newer version of glibc. (some > key insights obtained from this GitHub post and ones around it: > https://github.com/microsoft/WSL/issues/1462#issuecomment-274398213 > > Hope this helps! > Art > > >> On Thu, Sep 3, 2020 at 8:34 AM Carlos Kikuti wrote: >> >>> Dear CCP4BB, >>> >>> I am unable to install ARP/WARP on a server with Debian 10, it says: >>> >>> Segmentation fault >>> *** ERROR *** >>> This machine cannot run ARP/wARP executables that >>> are statically linked to glibc. >>> >>> *** INSTALLATION OF ARP/wARP 8.0 FAILED *** >>> Modified version exit status 1 >>> >>> -- after some digging I found several old, unsolved issues about that in >>> GitHub, any ideas about how to get around? >>> >>> >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >> > > -- > Artem Y. Lyubimov, PhD > Staff Scientist > SSRL SMB Crystallography > 2525 Sand Hill Road mail stop 99 > Menlo Park, CA 94025-7015 > (415) 325-2057 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
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 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 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?
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 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 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?
... 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 > 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 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
Re: [ccp4bb] ARP/wARP install on 6.2.0 & RHEL 6?
Hello, I'm one of the ARP/wARP developers. Sorry for the slow reply - this is down to time differences. I'll install RHEL6 and try the ARP/wARP install and then report back. This may take a day or so though. My suspicion, based on previous bug reports, is that this problem is related to the TCL installation. The UnpackTaskArchive subroutine is part of the CCP4 API: http://www.ccp4.ac.uk/ccp4bin/viewcvs/*checkout*/ccp4/ccp4i/help/programmers/progdocs/install_utils.html#UnpackTaskArchive We've found that the behaviour of this call is dependent on TCL versions and that we have problems installing on 64bit fink (OSX) because the version of TCL. When I download and install CCP4 onto Ubuntu or SUSE I get a big package (>1GB) that contains CCP4 and a compatible version of TCL. The CCP4 installation then adds the following calls to my .bashrc: source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4.setup source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4-others.setup The ccp4-others.setup pulls in the correct TCL environment. Is your installation of CCP4 similar? Thanks for reporting this problem - it will hopefully improve future versions of ARP/wARP. Saul Hazledine On Jul 28, 2011, at 2:31 AM, Jonathan Kay 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?
Hello, My reply is in the text below: On Jul 28, 2011, at 6:00 AM, 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. We're working on improving this. I believe the main issue is that CCP4 has become more user friendly and installs from a DMG, while the ARP/waRP 7.1 install is still showing its Unix command line roots. > He finally got it set up as a local installation, whereupon it promtly > failed. We use Macs a lot here with few problems (and various versions of CCP4) so my first suspicion is that this might be an install problem. > The message said See refmac-last.log but that told us nothing, and indeed > refmac seemed to have worked.. > Would it be possible to send me the install.log that is created in the ARP/wARP install directory? Also, the refmac-last.log that will be created in the directory where ARP/wARP was working? Its probably best if the remaining communication is done by direct email. I'm sorry for the trouble that you are having. I hope we can fix the problem and prevent it happening to others in future. Saul Hazledine
Re: [ccp4bb] ARP/wARP install on 6.2.0 & RHEL 6?
Dear all, I had no problem with Arp/wARP, but I didn't reinstall. Assume ccp4 sits in /installation/directory/ccp4 and arp in /installation/directory/arp_warp_7.1. The new ccp4 doesn't recognize the existing arp because the task interface is not installed. I run ./install.sh in /installation/directory/arp_warp_7.1, and five seconds later, all is good. I hope this is of help for someone. Andreas On 28/07/2011 4:35, Ethan Merritt 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 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 -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] ARP/wARP install on 6.2.0 & RHEL 6?
Hi, 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. Wei-Chun > We've found that the behaviour of this call is dependent on TCL versions > and that we have problems installing on 64bit fink (OSX) because the version > of TCL. When I download and install CCP4 onto Ubuntu or SUSE I get a big > package (>1GB) that contains CCP4 and a compatible version of TCL. The CCP4 > installation then adds the following calls to my .bashrc: > > source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4.setup > source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4-others.setup > > The ccp4-others.setup pulls in the correct TCL environment. Is your > installation of CCP4 similar? > > Thanks for reporting this problem - it will hopefully improve future > versions of ARP/wARP. > > Saul Hazledine > >
Re: [ccp4bb] ARP/wARP install on 6.2.0 & RHEL 6?
My two cents: I am installing arp/warp on my Mac since ages and it works ;-) The only thing you need to make sure is that you grab ownership of the /usr/local directory to you as a user, if you installed ccp4 from dmg. If you do this by eg sudo chown -R me.mygroup $CCP4 Then install.sh should work for arp/warp Package type installation for arp/warp is also possible technically, and it can be made available in the next release if it is agreed between developers that from now we will support system-specific installations and not only an all-in-one package as till now. A. Sent from my iPad On 28 Jul 2011, at 10:06, Saul Hazledine wrote: > Hello, > My reply is in the text below: > > On Jul 28, 2011, at 6:00 AM, 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. > > We're working on improving this. I believe the main issue is that CCP4 has > become more user friendly and installs from a DMG, while the ARP/waRP 7.1 > install is still showing its Unix command line roots. > >> He finally got it set up as a local installation, whereupon it promtly >> failed. > > We use Macs a lot here with few problems (and various versions of CCP4) so > my first suspicion is that this might be an install problem. > >> The message said See refmac-last.log but that told us nothing, and indeed >> refmac seemed to have worked.. >> > > Would it be possible to send me the install.log that is created in the > ARP/wARP install directory? Also, the refmac-last.log that will be created in > the directory where ARP/wARP was working? > > Its probably best if the remaining communication is done by direct email. > > I'm sorry for the trouble that you are having. I hope we can fix the problem > and prevent it happening to others in future. > > Saul Hazledine
[ccp4bb] arp/warp and refmac problem on os x
Hi, I've got a rather weird problem when trying to run arp/warp. When trying to run arp/warp (latest version 7.0.1) it complains that I should install a newer version of Refmac (5.4.0045). The version of Refmac I have installed is 5.4.0066, and thats what is being used if I run Refmac both from terminal or via CCP4i. However, when arp/warp starts to run it magically finds a refmac 5.2.something and uses that. Reinstalling arp/warp did not help, even though the install script showed that I had refmac 5.4.0066 installed... I'm running OS X 10.5.2 and have installed ccp4 and refmac via fink. All other CCP4 programs work fine and Refmac runs normally as well, it's only when it's called from arp/warp that something goes wrong.. All ideas to fix this problem are most welcome. Cheers, Ronnie Berntsson
[ccp4bb] Arp/warp space group P 21 2 21
Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil
Re: [ccp4bb] Arp/warp space group P 21 2
SHELX has been able to handle P 21 2 21 and other such space groups without any problems for the last 38 years! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Tue, 10 Jun 2008, Garib Murshudov wrote: > I think in refmac it has already been fixed (since October or so). refmac 5.4 > and later version should handle all available space groups with their various > disguises. > > Garib > On 10 Jun 2008, at 16:11, Clemens Grimm wrote: > > >seems to be a 'non-standard' setting. Refmac also has problems with this > >spacegroup, reindexing to P21 21 2 fixed the problem for me. > > > >Clemens > > > >Quoting PhilEvans <[EMAIL PROTECTED]>: > > > > >Is there a reason why Arp/warp doesn't like space group P 21 2 21? > > > > > >Phil > > > > > > > > >
Re: [ccp4bb] Arp/warp space group P 21 2
Among very many other great things 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: [EMAIL PROTECTED] Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: On Jun 10, 2008, at 9:40 PM, George M. Sheldrick wrote: SHELX has been able to handle P 21 2 21 and other such space groups without any problems for the last 38 years! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Tue, 10 Jun 2008, Garib Murshudov wrote: I think in refmac it has already been fixed (since October or so). refmac 5.4 and later version should handle all available space groups with their various disguises. Garib On 10 Jun 2008, at 16:11, Clemens Grimm wrote: seems to be a 'non-standard' setting. Refmac also has problems with this spacegroup, reindexing to P21 21 2 fixed the problem for me. Clemens Quoting PhilEvans <[EMAIL PROTECTED]>: Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil
Re: [ccp4bb] arp/warp and refmac problem on os x
On 24 Apr 2008, at 3:38 PM, Ronnie Berntsson wrote: I've got a rather weird problem when trying to run arp/warp. When trying to run arp/warp (latest version 7.0.1) it complains that I should install a newer version of Refmac (5.4.0045). The version of Refmac I have installed is 5.4.0066, and thats what is being used if I run Refmac both from terminal or via CCP4i. However, when arp/warp starts to run it magically finds a refmac 5.2.something and uses that. Reinstalling arp/warp did not help, even though the install script showed that I had refmac 5.4.0066 installed... I'm running OS X 10.5.2 and have installed ccp4 and refmac via fink. All other CCP4 programs work fine and Refmac runs normally as well, it's only when it's called from arp/warp that something goes wrong.. All ideas to fix this problem are most welcome. This is an interesting feature of the Fink CCP4/Refmac installation. When you install the new refmac in Fink, you get an executable called refmac-5.4, which lives in /sw/share/xtal/ccp4-6.0.2/bin. The refmac5 that you get from the terminal lives in /sw/bin and is a symbolic link to this executable. However, in /sw/share/xtal/ccp4-6.0.2/bin there still lurks an executable refmac5, and this is version 5.2.0019. When you run ARP/wARP from the GUI, it seems that this is the executable that it uses - hence the version warnings. In our experience, this also breaks flex-wARP when run through the GUI. Whether this is just a symptom of the way I use Fink to install things, or whether it's a problem for everyone, I don't know. I have a solution to this, although it may not be the most elegant one. I move the old refmac5 out of the way, and create a new symbolic link mv /sw/share/xtal/ccp4-6.0.2/bin/refmac5 /sw/share/xtal/ ccp4-6.0.2/bin/refmac5.old ln -s /sw/share/xtal/ccp4-6.0.2/bin/refmac-5.4 /sw/share/xtal/ ccp4-6.0.2/bin/refmac5 (This is from memory, so the details may not be correct.) Hope this helps, Chris The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] arp/warp and refmac problem on os x
in arp/warp classic the script does not call refmac5 (the first thing in your path) but $CBIN/refmac5 (refmac from the CBIN place) I suspect that you still kept refmac 5.2 in the official CBIN directory and put refmac5 in another location but earlier in your path, so its picked up first ... try refmac5 -i and $CBIN/refmac5 -i I suspect they will give different results. My best guess at least ... A. On Apr 24, 2008, at 16:38, Ronnie Berntsson wrote: Hi, I've got a rather weird problem when trying to run arp/warp. When trying to run arp/warp (latest version 7.0.1) it complains that I should install a newer version of Refmac (5.4.0045). The version of Refmac I have installed is 5.4.0066, and thats what is being used if I run Refmac both from terminal or via CCP4i. However, when arp/warp starts to run it magically finds a refmac 5.2.something and uses that. Reinstalling arp/warp did not help, even though the install script showed that I had refmac 5.4.0066 installed... I'm running OS X 10.5.2 and have installed ccp4 and refmac via fink. All other CCP4 programs work fine and Refmac runs normally as well, it's only when it's called from arp/warp that something goes wrong.. All ideas to fix this problem are most welcome. Cheers, Ronnie Berntsson
Re: [ccp4bb] arp/warp and refmac problem on os x
Thanks for a very quick answer, it indeed solved the problem. Cheers, Ronnie On Apr 24, 2008, at 4:55 PM, Chris Richardson wrote: On 24 Apr 2008, at 3:38 PM, Ronnie Berntsson wrote: I've got a rather weird problem when trying to run arp/warp. When trying to run arp/warp (latest version 7.0.1) it complains that I should install a newer version of Refmac (5.4.0045). The version of Refmac I have installed is 5.4.0066, and thats what is being used if I run Refmac both from terminal or via CCP4i. However, when arp/ warp starts to run it magically finds a refmac 5.2.something and uses that. Reinstalling arp/warp did not help, even though the install script showed that I had refmac 5.4.0066 installed... I'm running OS X 10.5.2 and have installed ccp4 and refmac via fink. All other CCP4 programs work fine and Refmac runs normally as well, it's only when it's called from arp/warp that something goes wrong.. All ideas to fix this problem are most welcome. This is an interesting feature of the Fink CCP4/Refmac installation. When you install the new refmac in Fink, you get an executable called refmac-5.4, which lives in /sw/share/xtal/ ccp4-6.0.2/bin. The refmac5 that you get from the terminal lives in /sw/bin and is a symbolic link to this executable. However, in / sw/share/xtal/ccp4-6.0.2/bin there still lurks an executable refmac5, and this is version 5.2.0019. When you run ARP/wARP from the GUI, it seems that this is the executable that it uses - hence the version warnings. In our experience, this also breaks flex-wARP when run through the GUI. Whether this is just a symptom of the way I use Fink to install things, or whether it's a problem for everyone, I don't know. I have a solution to this, although it may not be the most elegant one. I move the old refmac5 out of the way, and create a new symbolic link mv /sw/share/xtal/ccp4-6.0.2/bin/refmac5 /sw/share/xtal/ ccp4-6.0.2/bin/refmac5.old ln -s /sw/share/xtal/ccp4-6.0.2/bin/refmac-5.4 /sw/share/xtal/ ccp4-6.0.2/bin/refmac5 (This is from memory, so the details may not be correct.) Hope this helps, Chris The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. On Apr 24, 2008, at 4:56 PM, Anastassis Perrakis wrote: in arp/warp classic the script does not call refmac5 (the first thing in your path) but $CBIN/refmac5 (refmac from the CBIN place) I suspect that you still kept refmac 5.2 in the official CBIN directory and put refmac5 in another location but earlier in your path, so its picked up first ... try refmac5 -i and $CBIN/refmac5 -i I suspect they will give different results. My best guess at least ... A.
Re: [ccp4bb] Arp/warp space group P 21 2 21
seems to be a 'non-standard' setting. Refmac also has problems with this spacegroup, reindexing to P21 21 2 fixed the problem for me. Clemens Quoting PhilEvans <[EMAIL PROTECTED]>: Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil
Re: [ccp4bb] Arp/warp space group P 21 2 21
Probably because it's not a standard notation. The standard notation is P21212. I would reindex and run again. Klaus PhilEvans wrote: Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil -- Dr. Klaus Piontek Albert-Ludwigs-University Freiburg Institute of Organic Chemistry and Biochemistry, Room 401 H Albertstrasse 21 D-79104 Freiburg Germany Phone: ++49-761-203-6036 Fax: ++49-761-203-8714 Email: [EMAIL PROTECTED] Web: http://www.chemie.uni-freiburg.de/orgbio/w3platt/
Re: [ccp4bb] Arp/warp space group P 21 2 21
Dear Phil, One reason has been simplicity - many ARP/wARP modules operate with space group number only. For space group 18 this would mean P21212. Using space group name might be less robust - I remember some compatibility problems when CCP4 introduced spaces into space group names, this broke some of the parsers, including simple-minded ones from ARP/wARP. If there is, however, a strong wish for ARP/wARP to support 'unconventionally' indexed space groups - then we will certainly try to introduce it. With best regards, Victor PhilEvans wrote: Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil
Re: [ccp4bb] Arp/warp space group P 21 2 21
I should expand a bit: on this BB last year Ian Tickle pointed out that the IUCr "standard" for primitive orthorhombic space groups is to have a <= b <= c, irrespective of which axes are 2s or 2(1)s. Thus eg space group 18 in its "standard" setting may be P 2 21 21, P 21 2 21 or P21 21 2: the last of these is the "reference" setting. Similarly , space group C2 should be reindexed as I2 if this gives a smaller beta angle. Ralf Grosse-Kunstleve has recently pointed this out to me as well. I have changed Pointless (from version 1.2.12) to follow this convention, though it is a user-settable option to use the reference setting. It does seem sensible to follow the standard convention. If you are picking up the space group from an MTZ file, it is unambiguous, similarly from the space group name in a PDB file. I think Arp/warp should allow whatever setting is in the input file. Phil On 10 Jun 2008, at 16:44, Victor Lamzin wrote: Dear Phil, One reason has been simplicity - many ARP/wARP modules operate with space group number only. For space group 18 this would mean P21212. Using space group name might be less robust - I remember some compatibility problems when CCP4 introduced spaces into space group names, this broke some of the parsers, including simple-minded ones from ARP/wARP. If there is, however, a strong wish for ARP/wARP to support 'unconventionally' indexed space groups - then we will certainly try to introduce it. With best regards, Victor PhilEvans wrote: Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil
Re: [ccp4bb] Arp/warp space group P 21 2 21
Victor 'P 21 2 21' *is* the conventional indexing if a <= b <= c, i.e. it's the setting agreed for deposition of crystal structures by the IUCr and the US National Institute of Standards & Technology (NIST) since 1983: it just doesn't seem to have been agreed by a dwindling number of individual program authors. AFAIK Arp/Warp is the only significant program relevant to PX which doesn't recognise the complete set of conventional settings (as defined in $CLIBD/syminfo.lib and symop.lib). In this case, the transformed setting 'P 21 21 2' (corresponding to the unconventional cell a <= c <= b) is called the 'standard' setting and is the reference symbol used for example as the title of the relevant page in ITC vol A, since for convenience the alternate settings 'P 2 21 21', 'P 21 2 21' and 'P 21 21 2' are all shown on the same page. > seems to be a 'non-standard' setting. Refmac also has > problems with this > spacegroup, reindexing to P21 21 2 fixed the problem for me. > > Clemens I've not had any trouble with this spacegroup when using a recent version of Refmac/CCP4: are you by any chance using an old version (either of Refmac or CCP4)? If not could you post the relevant error message so the problem can be identified & fixed, as it certainly ought to work. Re-indexing is usually not a viable option for us as it causes a lot of pain with our automated processing: if re-indexing really becomes unavoidable then it means we have to delete all the processed data for that crystal and other datasets of the same crystal form, then start all over again from data processing (i.e. from the MOSFLM/D*trek step), so that all datasets & co-ordinates associated with a project in the database are indexed the same way. Having datasets around with different indexings (particularly as happened once if 2 of the cell lengths are very similar) is a recipe for chaos! Anyone trying to automate structure solution would likely run into the same problem, unless of course they anticipated this eventuality in the database design. So yes, making all software accept the internationally recognised conventions could save us a lot of work! -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Victor Lamzin > Sent: 10 June 2008 16:45 > To: PhilEvans > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Arp/warp space group P 21 2 21 > > Dear Phil, > > One reason has been simplicity - many ARP/wARP modules operate with > space group number only. For space group 18 this would mean P21212. > Using space group name might be less robust - I remember some > compatibility problems when CCP4 introduced spaces into space group > names, this broke some of the parsers, including > simple-minded ones from > ARP/wARP. > > If there is, however, a strong wish for ARP/wARP to support > 'unconventionally' indexed space groups - then we will > certainly try to > introduce it. > > With best regards, > Victor > > > > PhilEvans wrote: > > Is there a reason why Arp/warp doesn't like space group P 21 2 21? > > > > Phil > > > > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Arp/warp space group P 21 2 21
I think in refmac it has already been fixed (since October or so). refmac 5.4 and later version should handle all available space groups with their various disguises. Garib On 10 Jun 2008, at 16:11, Clemens Grimm wrote: seems to be a 'non-standard' setting. Refmac also has problems with this spacegroup, reindexing to P21 21 2 fixed the problem for me. Clemens Quoting PhilEvans <[EMAIL PROTECTED]>: Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil
Re: [ccp4bb] Arp/warp space group P 21 2 21
yes, actually my experience with P 21 2 21 dates back to midyear 2007. Retesting with the current refmac version runs fine. Clemens Quoting Ian Tickle <[EMAIL PROTECTED]>: Victor 'P 21 2 21' *is* the conventional indexing if a <= b <= c, i.e. it's the setting agreed for deposition of crystal structures by the IUCr and the US National Institute of Standards & Technology (NIST) since 1983: it just doesn't seem to have been agreed by a dwindling number of individual program authors. AFAIK Arp/Warp is the only significant program relevant to PX which doesn't recognise the complete set of conventional settings (as defined in $CLIBD/syminfo.lib and symop.lib). In this case, the transformed setting 'P 21 21 2' (corresponding to the unconventional cell a <= c <= b) is called the 'standard' setting and is the reference symbol used for example as the title of the relevant page in ITC vol A, since for convenience the alternate settings 'P 2 21 21', 'P 21 2 21' and 'P 21 21 2' are all shown on the same page. seems to be a 'non-standard' setting. Refmac also has problems with this spacegroup, reindexing to P21 21 2 fixed the problem for me. Clemens I've not had any trouble with this spacegroup when using a recent version of Refmac/CCP4: are you by any chance using an old version (either of Refmac or CCP4)? If not could you post the relevant error message so the problem can be identified & fixed, as it certainly ought to work. Re-indexing is usually not a viable option for us as it causes a lot of pain with our automated processing: if re-indexing really becomes unavoidable then it means we have to delete all the processed data for that crystal and other datasets of the same crystal form, then start all over again from data processing (i.e. from the MOSFLM/D*trek step), so that all datasets & co-ordinates associated with a project in the database are indexed the same way. Having datasets around with different indexings (particularly as happened once if 2 of the cell lengths are very similar) is a recipe for chaos! Anyone trying to automate structure solution would likely run into the same problem, unless of course they anticipated this eventuality in the database design. So yes, making all software accept the internationally recognised conventions could save us a lot of work! -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Victor Lamzin Sent: 10 June 2008 16:45 To: PhilEvans Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Arp/warp space group P 21 2 21 Dear Phil, One reason has been simplicity - many ARP/wARP modules operate with space group number only. For space group 18 this would mean P21212. Using space group name might be less robust - I remember some compatibility problems when CCP4 introduced spaces into space group names, this broke some of the parsers, including simple-minded ones from ARP/wARP. If there is, however, a strong wish for ARP/wARP to support 'unconventionally' indexed space groups - then we will certainly try to introduce it. With best regards, Victor PhilEvans wrote: > Is there a reason why Arp/warp doesn't like space group P 21 2 21? > > Phil > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Arp/warp space group P 21 2 21
Thanks very much to everybody for useful discussion on space groups, axes and ARP/wARP. I would particularly refer to the argument on space group uncertainty in data processing and a need to have convenient means to screen various space groups and axes settings for, e.g. automated molecular replacement. Thanks again and best regards, Victor - This mail sent through IMP: http://horde.org/imp/
Re: [ccp4bb] Arp/warp space group P 21 2 21
Dear Victor I'm glad that you see the desirability of updating Arp/warp to allow any setting. I'm a recent convert to this idea myself Best wishes Phil On 11 Jun 2008, at 09:17, [EMAIL PROTECTED] wrote: Thanks very much to everybody for useful discussion on space groups, axes and ARP/wARP. I would particularly refer to the argument on space group uncertainty in data processing and a need to have convenient means to screen various space groups and axes settings for, e.g. automated molecular replacement. Thanks again and best regards, Victor - This mail sent through IMP: http://horde.org/imp/
[ccp4bb] ARP/WARP - Can not get environment variable for warpdoc
I installed CPP4 version 6.1.1 on a Linux laptop which is running ubuntu. Following which I also installed ARP/WARP 7.0.1 version.However, when I attempt to launch ARP/WARP using the CCP4I GUI interface, I get the following message Can not get environment variable for warpdoc. Could someone please help me with fixing this problem. Thanks Sridhar
Re: [ccp4bb] arp/warp in p22121: what to do in Pointless
I think this is only a problem in the primitive orthorhombic system (at least I assume people don't want hexagonal axes along a, A & B centred lattices etc, although there is no reason in principle why not). Following some earlier discussions with Ian, Pointless now honours (and preserves) a reference file (HKLREF) in eg P 2 21 21, and also explicit reindex operations, but an initial indexing will still enforce the "standard" setting eg P 21 21 2, because I accept the "reference" setting from the cctbx library ie suppose you have a crystal which when indexed with a <= b <= c and Pointless decides unambiguously for the sake of argument) that the axis along a is a 2-fold and the other two are 2(1) screws, ie space group P 2 21 21. At present this will be reindexed to the "standard" setting P 21 21 2, but is that what you want, or should it be left as acriterion takes precedence? Phil On 19 Sep 2007, at 17:54, Ian Tickle wrote: Hi Sue It's certainly true that the convention in the 1935 and 1952 editions of IT Volume 1 *appeared* to be the 'standard setting' convention that you describe because only the 'standard' settings were listed, and this was the way that many crystallographers interpreted it (actually only macromolecular crystallographers, the small molecule people stick to the IUCr convention), so this is probably where you're coming from. However the 1983 edition of Volume A clarified the situation and made it clear that this was never the intention, so all the conventional settings are now shown on the SG diagram pages. P22121 & P21221 certainly are defined in IT Vol. A - look on the diagram page for SG no. 18 & you'll see them. The 'standard symbol' for a space group is merely the heading on the page used only for indexing purposes, so space groups P22121, P21221 and P21212 all have the same standard symbol P21212; hence the standard symbol is not unique and can't be used to unambiguously define the space group. The 'standard setting' is merely the space group setting that has the same name as the standard symbol. Even if that weren't true do we really want to be still sticking to a convention that was abandoned 25 years ago and doesn't a later convention override an earlier one anyway? Actually the convention in use is not the issue anyway, I don't care which convention is used as long as all programs use the same convention! - then I'll never need to permute axes (just as fundamentally I don't care which co-ordinate format is used as long as all programs use the same one, then I'll never need to reformat). So Mosflm uses the IUCr convention (i.e. a<=b<=c for primitive orthorhombic), and therefore any program which doesn't support that convention for any space group forces you to permute the axes completely unnecessarily. -- Ian -Original Message- From: Sue Roberts [mailto:[EMAIL PROTECTED] Sent: 19 September 2007 16:38 To: Ian Tickle Subject: Re: [ccp4bb] arp/warp in p22121 Hi Ian But there's an older convention, which is to use the space groups settings defined in the International Tables - and P22121 is not a standard setting. Sue On Sep 19, 2007, at 8:18 AM, Ian Tickle wrote: I'm confused now, sticking to the IUCr convention should not require any axis permutation. My beef is specifically against unnecessary axis permutations! Surely it's when the program doesn't support the convention that you are forced to permute the axes? Besides I did solve a structure in P22121 with Phaser so I'm even more confused! -- Ian -----Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Airlie McCoy Sent: 19 September 2007 15:09 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] arp/warp in p22121 The problem is specifically that ARP/wARP *doesn't* support the IUCr convention as given in IT (Vol. A, >= 1983 edition, Table 9.3.4.1, p.758 in 5th ed.) regarding choice of cell in primitive orthorhombic space groups, and I suspect in centred monoclinic ones also. AFAIK ARP/wARP and pointless are the only two CCP4 programs that currently don't fully support the IUCr convention Phaser doesn't "support" the IUCr convention, and if it was used for the original MR in this case (I don't know whether it was or not), then it would have caused the "problem". We have had user requests to change the output to the IUCr convention, but other people get confused if the axes are permuted. So the choice will be made an output option - Frank von Delft suggested the keyword "IUCR [ON/OFF]"! Vote for your choice of default now... Airlie McCoy Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee
Re: [ccp4bb] arp/warp in p22121: what to do in Pointless
Phil, For the record, the program XPREP - widely used by small molecule crystallographers but also useful for macromoleculess - always makes the conventional cell (in this example P 21 21 2) the default (i.e. what you get if you always hit ), and writes out new .hkl and .ins files in this setting unless the user forces it to do otherwise (the .ins file is used for solving the structure with direct methods and contains the cell corresponding to the new .hkl file). There are three cases where it is intentionally made less awkward for the user to choose an alternative setting if she/he so wishes: 1. Primitive rhombohedral rather than the hexagonal cell with three times the volume. Unlike the situation for macromolecules, where some older programs do not work with the primitive rhombohedral cell, the primitive cell is quite often chosen for small molecules. 2. The space group I2 rather than C2 if it results in a beta angle much closer to 90 degrees (or when it is desired to compare the structure with a structure - possibly another crystalline phase of the same compound - in say I222). The same applies to other C-centred monoclinic cells, e.g. Cc <-> Ia etc. (but Fd is discouraged). 3. The setting P21/n rather than P21/c if it results in a beta angles much closer to 90 etc. These three 'unconventional' settings are also generally accepted by the checking software, databases and journals. To cover all reasonable non-standard settings, XPREP actually understands 413 different space groups! Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Mon, 24 Sep 2007, Phil Evans wrote: > I think this is only a problem in the primitive orthorhombic system (at least > I assume people don't want hexagonal axes along a, A & B centred lattices etc, > although there is no reason in principle why not). > > Following some earlier discussions with Ian, Pointless now honours (and > preserves) a reference file (HKLREF) in eg P 2 21 21, and also explicit > reindex operations, but an initial indexing will still enforce the "standard" > setting eg P 21 21 2, because I accept the "reference" setting from the cctbx > library > > ie suppose you have a crystal which when indexed with a <= b <= c and > Pointless decides unambiguously for the sake of argument) that the axis along > a is a 2-fold and the other two are 2(1) screws, ie space group P 2 21 21. > > At present this will be reindexed to the "standard" setting P 21 21 2, but is > that what you want, or should it be left as a precedence? > > Phil > > > On 19 Sep 2007, at 17:54, Ian Tickle wrote: > > > Hi Sue > > > > It's certainly true that the convention in the 1935 and 1952 editions of > > IT Volume 1 *appeared* to be the 'standard setting' convention that you > > describe because only the 'standard' settings were listed, and this was > > the way that many crystallographers interpreted it (actually only > > macromolecular crystallographers, the small molecule people stick to the > > IUCr convention), so this is probably where you're coming from. However > > the 1983 edition of Volume A clarified the situation and made it clear > > that this was never the intention, so all the conventional settings are > > now shown on the SG diagram pages. P22121 & P21221 certainly are > > defined in IT Vol. A - look on the diagram page for SG no. 18 & you'll > > see them. > > > > The 'standard symbol' for a space group is merely the heading on the > > page used only for indexing purposes, so space groups P22121, P21221 and > > P21212 all have the same standard symbol P21212; hence the standard > > symbol is not unique and can't be used to unambiguously define the space > > group. The 'standard setting' is merely the space group setting that > > has the same name as the standard symbol. Even if that weren't true do > > we really want to be still sticking to a convention that was abandoned > > 25 years ago and doesn't a later convention override an earlier one > > anyway? > > > > Actually the convention in use is not the issue anyway, I don't care > > which convention is used as long as all programs use the same > > convention! - then I'll never need to permute axes (just as > > fundamentally I don't care which co-ordinate format is used as long as > > all programs use the same one, then I'll never need to reformat). So > > Mosflm uses the IUCr convention (i.e. a<=b<=c for primitive > > orthorho
