[ccp4bb] Pseudo-translation?
Dear all, I have an orthorhombic crystal (pointless suggests most likely space groups P 2 21 21 or P 2 21 2) with two molecules expected in the asymmetric unit. Analyzing the native Patterson map I found the following peaks (in fractional coordinates): CELL 63.0400 117.2500 133.6500 90. 90. 90. ATOM1 Ano 0. 0. 0. 111.03 0.0 BFAC 20.0 ATOM2 Ano 0.0102 0.0416 0. 15.98 0.0 BFAC 20.0 ATOM3 Ano 0. 0.5000 0.00376.21 0.0 BFAC 20.0 ATOM4 Ano 0.0669 0.0850 0.5.86 0.0 BFAC 20.0 ATOM5 Ano 0.0772 0.4168 0.5.78 0.0 BFAC 20.0 ATOM6 Ano 0.1139 0.1196 0.00495.10 0.0 BFAC 20.0 The third and fifth are far enough from the origin to represent tranlations. Is the third due to an alternative origin? Could the fifth represent a pseudo-translation? Thanks, Michele
[ccp4bb] Help with MR in P21
Dear all, I am trying to solve a structure at 2.05 A resolution by molecular replacement. The space group seems to be P21, with unit cell dimension 52.63, 29.43, 104.970 and beta = 95.60. Only one copy of the protein should be present in the asymmetric unit, with 58% of solvent content. The search model used for MR is a truncated construct of the same protein, comprising more that 60% of the residues. However, no convincing MR solution is found (I used phaser, molrep, epmr and also mr.bump). No solutions refine to R and Rfree lower than 51-52%. The CCP4 documentation about twinning states that Monoclinic with na + nc ~ a or na + nc ~ c can be twinned. This is not clear to me, but I have c = 2a, and therefore n = 2/3. Nevertheless all the tests run by ctruncate (and sfcheck) exclude twinning. The observed cumulative distribution for |L| almost overlap the expected untwinned, and the observed cumulative intensity distribution is not sigmoidal at all (actually it is growing faster that the theoretical). Also the acentric and centric moments exclude twinning, for example the acentric: E = 0.858 (Expected value = 0.886, Perfect Twin = 0.94) E**3 = 1.442 (Expected value = 1.329, Perfect Twin = 1.175) E**4 = 2.438 (Expected value = 2, Perfect Twin = 1.5) Both ctruncate and sfcheck found a pseudo-translation vector: ctruncate (0.050, 0.000, 0.957), ratio 0.23 sfcheck (0.954, 0.000, 0.040), ratio 0.218 However a second copy cannot be present in the asymmetric unit (there would be 16% of solvent content). Since the protein is expected to form a coiled-coil, I think that the detected pseudo-translation arises from the helices. Alternatively, it is possible that the space group is wrong? And if so, how can I figure out the correct one? Thank you in advance, Michele
[ccp4bb] Bug regarding cell dimensions in autoSHARP / SCALA
I am doing SAD phasing with the latest autoSHARP and CCP4 6.1.1 (SCALA version 3.3.9). The space group is P21 with unit cell dimension 52.67, 28.61 and 105.16. If I give the data as unmerged SHELX file, it happens that the third cell dimension become identical to the first when the data are merged using SCALA. I put the whole log file as attachment. Is this a bug or am I doing something wrong? Michele ### ### ### ### CCP4 6.1: SORTMTZ version 6.1 : 06/09/05## ### User: unknown Run date: 17/11/2009 Run time: 17:01:10 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. Data line--- H K L M/ISYM BATCH Data line--- CONVERT/F2MTZCOMBAT_peak.mtz OPENED INPUT MTZ FILE Logical Name: CONVERT/F2MTZCOMBAT_peak.mtz Filename: CONVERT/F2MTZCOMBAT_peak.mtz * Title: * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 ib18-sad 1 peak 52.6670 28.6140 105.1640 90. 95.9550 90. 0.0 * Number of Columns = 13 * Number of Reflections = 47562 * Missing value set to NaN in input mtz file * Number of Batches = 1 * Column Labels : H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT * Column Types : H H H Y B J Q J Q R R R R * Associated datasets : 0 0 0 1 1 1 1 1 1 1 1 1 1 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 52.6670 28.6140 105.1640 90. 95.9550 90. * Resolution Range : 0.000650.18179 ( 39.094 - 2.345 A ) * Sort Order : 0 0 0 0 0 * Space group = 'P 1 21 1' (number 4) Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /home/michele/sharp/database/syminfo.lib WRITTEN OUTPUT MTZ FILE Logical Name: CONVERT/SCALAMERGE_peak.mtz Filename: CONVERT/SCALAMERGE_peak.mtz * Title: * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 ib18-sad 1 peak 52.6670 28.6140 105.1640 90. 95.9550 90. 0.0 * Number of Columns = 13 * Number of Reflections = 47562 * Missing value set to NaN in input mtz file * Number of Batches = 1 * Column Labels : H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT * Column Types : H H H Y B J Q J Q R R R R * Associated datasets : 0 0 0 1 1 1 1 1 1 1 1 1 1 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 52.6670 28.6140 105.1640 90. 95.9550 90. * Resolution Range : 0.000650.18179 ( 39.094 - 2.345 A ) * Sort Order : 1 2 3 4 5 * Space group = 'P 1 21 1' (number 4) SORTMTZ --- Contents Command Input Input File Details Output File Details Header Information for Output MTZ File --- Command Input - ASCEND/DESCEND SORT KEYS --- Input File Details -- 5 sort keys, in columns1 2 3 4 5 --- Output File Details --- 47562 records read from file1 47562 records passed to sort --- Header Information For Output MTZ File -- 47562 records output SORTMTZ: Normal termination Times: User: 0.3s System:0.0s Elapsed: 0:01 ### ### ### ### CCP4 6.1: Scala version 3.3.9 : 20/01/09## ### User: unknown Run date: 17/11/2009 Run time: 17:01:11 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. OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: CONVERT/SCALAMERGE_peak.mtz * Title: * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets =
Re: [ccp4bb] Bug regarding cell dimensions in autoSHARP / SCALA
Clemens Vonrhein wrote: SCALA (as far as I know) gets its cell dimensions from the so-called batch header (since each image could have a different cell it averages those). So the problem isn't yet visible in your output - just do % mtzdmp CONVERT/F2MTZCOMBAT_peak.mtz -b and look at the batch header. Most likely COMBAT (if that is what you used guessing from the name) wrote a wrong batch header - it seems to leave it at some default or undefined state which can be fatal further down the line. f2mtz and combat seem to produce mtz files with the correct cell dimension in the header. Indeed the file read by sortmtz has the correct cell dimension, as reported in the logfile. Also the file opened by scala (CONVERT/SCALAMERGE_peak.mtz in the logfile) seems to have the correct cell dimension. The wrong dimension appears in the output mtz file (CONVERT/SCALAMERGE_peak.mtz1). However I solved the problem by simply merging the reflections when processed by xscale. Thanks anyway for the suggestions! Michele
Re: [ccp4bb] space groups not supported by Refmac5
Dear Arefeh, Arp/warp works with standard space groups, therefore you have to reindex P21221 to P21212. In this message from Anastassis Perrakis you can find some advice: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709L=CCP4BBT=0F=S=P=100954 Michele Arefeh Seyedarabi wrote: Hi, I have a question; recently I have encountered a few space groups which are not supported by Refmac5. Examples include I2 and P21221. Both these space groups have been identified as the best solutions for the two different datasets I am working on using Pointless. However, I am faced with difficulties in Refmac5, and the program fails to complete when I select refinement cycles with Arp-waters...with the message saying 'space group not supported'. Any suggestions on how this problem could be overcome? Regards, Arefeh
Re: [ccp4bb] Problems installing tasks to CCP4i - not yet solved.
Hi Klaas, I had exactly the same problem with opensuse 11.1. I installed the precompiled version of ccp4 6.1.1, so I don't think the problem is related to the compiler. I resolved the problem in a dirty way, simply copying the ccp4i configuration files for arp/warp from another installation of ccp4 on a machine running suse 9.1. Indeed, with suse 9.1 the installation of the arp/warp ccp4i interface is successful. I suspect that the problem is related to the new versions of tcl/tk. Try to use the one distributed on the ccp4 server ftp://ftp.ccp4.ac.uk/tcltk/TclTk-8.4 -- install it locally on your user account and set accordingly the variable CCP4I_TCLTK in the ccp4.setup-dist file. Hope it helps, Michele Max, Klaas wrote: Hi Tim, thankyou very much for the fast reply. Dear colleagues, Tim suggested: Hi Klaas ... Actually, you don't need to install arpwarp through the ccp4i interface. Once you setup your ccp4 environment, you can just run the install.sh (or install.csh in your case) which is in the arp-warp directory and everything should be set up for you. Tim Been there, done that. Ain't working. To be more specific, the installer is required to set up ARP/wARP, appears to run flawlessly and ends with lots of ok messages. Finally the script terminates with the remark: Installing GUI for ARP/wARP 7.0.1 CCP4 interface version detected is : 2.0.3 Using tarball ARP_wARP_CCP4I6.tar.gz (for ccp4 version 6 and newer). *** INSTALLATION OF ARP/wARP 7.0.1 GUI HAS BEEN SUCCESSFUL *** When I now try to run a ARP/wARP task in CCP4i after sourcing the arpwarp_setup.csh, I get the message: An interface to ARP/wARP is not available. The ARP/wARP interface doesn't appear to have been installed. Any further suggestions are most welcome. Cheers, Klaas --- Dr. Klaas Max MDC Berlin Buch Macromolecular Structures and Interactions Robert-Roessle-Strasse 10 13125 Berlin phone +49 30 9406 2265 fax +49 30 9406 2548 --- -- Dr. Michele Lunelli Department of Cellular Microbiology Max Planck Institute for Infection Biology Campus Charité Mitte Charitéplatz 1 D-10117 Berlin
[ccp4bb] Question about strange MR solution
Dear all, I refined a protein structure in the space group P6(1)22, with one copy in the asymmetric unit, resolution ~1.8 A, Rwork=0.20, Rfree=0.22. Then I tried to feed Phaser (version 1.3.3) with this structure. It found quickly a very prominent solution, but the first euler angle is 180 instead of 0 degrees (the others are 0, as well as the fractional coordinates). This solution is not symmetry-related with the structure that I used as search model: indeed, there are a lot of clashes. However, when I refine this solution, I obtain immediately R factors as good as the search model, and also the electron density map looks perfect. Of course, I used the same reflections file to refine the initial structure and the MR solution rotated of 180 degrees. How can I explain this? The analysis with Truncate (moments and cumulative intensity distribution) don't suggest any twinning, as well as the Padilla-Yeates test. Is it possible, that I refined the structure in the wrong space group? Thank you in advance, Michele Lunelli
Re: [ccp4bb] CCP4 mailing list
Maybe some post is rejected because (incorrectly) marked as spam, it happens the same to me with yahoo.. Michele Thomas Stout wrote: Has anyone else noticed that they're only getting some of the postings on the CCP4 mailing list?
[ccp4bb] I/sigma in XDS output
Dear all, I'm a bit confused from the output of the CORRECT step in XDS. In one of the first tables I can read the mean I/sigma for each resolution shell, but these values are much different from the I/sigma reported in the table at the end of the output files, titled completeness and quality of data set for the full data range with signal/noise -3.0. For example, from the first table I have I/sigma = 2 at 3.6 A, while from the second table I have I/sigma = 2 at 2.8 A! What is exactly the difference between the two values? And which one is reliable to decide the resolution cutoff? Thank you in advance, Michele Lunelli MPI for Infection Biology Berlin - Germany
[ccp4bb] Duration of a phaser job
Dear all, I am running a very long phaser job (using the keyword FINAL SELECT ALL). It found and refined 30370 solutions, and now it is in the very last stage (PRUNE DUPLICATES). How long could take this step on a machine with a xeon 3.2GHz cpu? Days, weeks, or months? I have no clue from the log file. The search model consists of a polyala of 42 residues. Thank you, Michele Lunelli Department of Cellular Microbiology Max Planck Institute for Infection Biology Campus Charité Mitte Charitéplatz 1 D-10117 Berlin Chiacchiera con i tuoi amici in tempo reale! http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com
