Re: [ccp4bb] fail to install ccp4i task for arp warp
Dear Jochen and the others, your problem is different from the one described here recently and a different fix will be needed. One major difference is that in your case CCP4 was installed via fink, while I have used the ccp4.ac.uk download pages which as far as I can tell never resulted in an installation with this problem. Thus I have no computer at the moment that reproduces it, sorry. For now to circumvent it - as suggested by Ronan Keegan - please try to install the 'ARP/wARP' task manually into the 'user's local CCP4i' area and not the 'main CCP4i' area of your installation. If this works, could you please tell us? Regards, Gerrit. On 8/31/10 3:56 PM, Jochen Kuper wrote: Dear All, sorry to bother you with this but I just can't figure out what goes wrong ... I am running the latest version of snow leopard on a MBP unibody with the 64bit kernel. I have an up to date fink installation for native 64bit. With this I have installed ccp4 via fink. I have also installed the latest arp warp version (7.1). Both are running nicely individually ... The thing now is that I cannot install the arp warp task in ccp4i. Neither via the original arp warp installation which says it is successful but no tasks show up nor via the ccp4i interface which always ends up with: UnpackTaskArchive: uncompress failed to create /tmp/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /Users/joka/software/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz Needless to say that the packages unpack just fine when I try this without the interface using the same uncompress binary. It does not make a difference whether I use ccp4i with sudo, su or login as root. I am running out of options here and would really appreciate a hint in the right direction ... I have found this in the ccp4bb http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg10117.html but that does not really help. Cheers, Jochen - Dr. Jochen Kuper Rudolf Virchow Center for Biomedical Research Josef Schneider Strasse 2, Haus D15 97070 Wuerzburg +49 (0) 9313180391 jochen.ku...@virchow.uni-wuerzburg.de mailto:jochen.ku...@virchow.uni-wuerzburg.de
Re: [ccp4bb] Fitting high resolution structures to low resolution map
Hallo Peter, if you have CCP4 and ARP/wARP installed, you may just try the 'Quickfold' function under 'model building'. It will try and interpret your map and give you alpha-helices and some strands, too. This secondary structure model can be helpful to locate your known subunits. Regards, Gerrit. On 3/30/10 12:20 AM, Peter Grey wrote: Dear All, I have a crystal (not EM) density map of a very large complex at 4.5A resolution. I have pdb files for homologs of a few of the subunits of this huge complex. I would like to fit these homologs into the density. I have tried without success so far programs that handle phased molecular replacement - MOLREP, ESSENS and FFFEAR. Could you please suggest other programs or servers that can tackle this problem ? Many thanks, Peter
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 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.
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] 3D structure based alignment
Hallo Tânia, you can try 'Rapido' by R. Mosca and T. Schneider at EMBL Hamburg. It is available as a web application under: http://webapps.embl-hamburg.de/rapido/ Best wishes, Gerrit Langer. Tânia Oliveira wrote: Hello, I´m having a problem that I would like to know if someone could help me. I want to do a 3D structure based alignment of my protein with another one. The problem is that my protein has 2 domains, and the structure that I want to superimpose just have one. I can do the structure superimposition by hand, but I´m not being able to do the sequence alignment based on the 3D structure, because the program that I´m using (SSM) starts to superimpose the sequence of my second domain in the beginning of the sequence of my reference model (exactly the same thing that it does with the sequence of the first domain). Do you know if there is any program where I can do this. Thanks in advance, Tânia Oliveira, PhD Student Membrane Protein Crystallography and Microbial Biochemistry Laboratory - ITQB-UNL
Re: [ccp4bb] problem installing arp/warp
Dear Mario, it seems that inside the install script the path variable is not set and therefore the call to refmac5 fails. We are not sure why this happend in your case. The install script was tested with both (t)csh and bash and something in your machine setup was not anticipated by us. Have you run the install.sh utility in the same terminal/shell, in which you later verified your refmac installation by typing 'refmac5 -i'? Could it be that you need to run some setup util for ccp4 manually before? To get you started with ARP/wARP we can send you a taylored install script with some diagnostic output to find a fix. In the meanwhile, can you try to change the line alias runtestrefmac 'refmac5 -i' (line 16 in install_csh.sh) to incorporate the absolute path to the refmac5 binary? Which refmac5 should provide you with this. Regards, Gerrit and Victor. Mario Sanches wrote: Dear all, I am trying to install arp/warp and I am stuck with the following error: -- Checking refmac5 installation - refmac5: Command not found. *** ERROR *** Cannot execute refmac5 *** INSTALLATION OF ARP/wARP 7.0.1 FAILED *** -- CCP4 is installed and refmac5 is running. A few more information: The system is Kubuntu 7.10 My shell is bash (tried tcsh as well and got the same error) Typing refmac5 -i returns: -- CCP4 software suite: library version 6.0 CCP4 software suite: patch level 6.0.2 Program: refmac5; version 5.2.0019 -- when I type refmac5 I get: -- ### ### ### ### CCP4 6.0: Refmac_5.2.0019version 5.2.0019 : 06/09/05## ### User: manager Run date: 17/ 3/2008 Run time: 09:45:33 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B $TEXT:Reference1: $$ comment $$ Refinement of Macromolecular Structures by the Maximum-Likelihood Method: G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255 EU Validation contract: BIO2CT-92-0524 $$ $SUMMARY :Reference1: $$ Refmac: $$ :TEXT:Reference1: $$ -- Thank you all in advance for any help.
