[ccp4bb] Merging CCP4i projects from two computers
Hi everyone, I've been working on a project using CCP4i on two separate computers in parallel and now unfortunately have jobs spread over the two locations. I would now like to consolidate these. Some of the new jobs on one computer will have the same run number as different ones on the other. Is there any convenient way to merge the projects? I guess the answer is no, or else the question would have been asked and answered already ;-) Thanks Derek -- Derek Logan tel: +46 46 222 1443 Molecular Biophysicsfax: +46 46 222 4692 Lund University mob: +46 76 8585 707 Box 124, Lund, Sweden
Re: [ccp4bb] Merging CCP4i projects from two computers
Hi Derek There's not really any way of doing what you're asking at present. If merging utility would be useful to others then I would be prepared to look into providing one, although there are a bunch of fiddly issues to deal with (e.g. keeping dates consistent, handling file name clashes and so on). Do any other readers of this list want to comment? Best wishes Peter Derek Logan wrote: Hi everyone, I've been working on a project using CCP4i on two separate computers in parallel and now unfortunately have jobs spread over the two locations. I would now like to consolidate these. Some of the new jobs on one computer will have the same run number as different ones on the other. Is there any convenient way to merge the projects? I guess the answer is no, or else the question would have been asked and answered already ;-) Thanks Derek -- Derek Logan tel: +46 46 222 1443 Molecular Biophysicsfax: +46 46 222 4692 Lund University mob: +46 76 8585 707 Box 124, Lund, Sweden -- ___ Peter J Briggs, [EMAIL PROTECTED] Tel: +44 1925 603826 CCP4, [EMAIL PROTECTED] Fax: +44 1925 603825 http://www.ccp4.ac.uk/ Daresbury Laboratory, Daresbury, Warrington WA4 4AD
Re: [ccp4bb] Merging CCP4i projects from two computers
Syncing directories with unison (use the same version of the program on all computers) or rsync can help. Lately I've been using svn, which is I think the best way to deal with this. Setting up a server on linux is probably easiest. You can do this with any type of file, by the way, it doesn't have to be ascii. William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott On Mar 7, 2008, at 3:57 AM, Derek Logan wrote: Hi everyone, I've been working on a project using CCP4i on two separate computers in parallel and now unfortunately have jobs spread over the two locations. I would now like to consolidate these. Some of the new jobs on one computer will have the same run number as different ones on the other. Is there any convenient way to merge the projects? I guess the answer is no, or else the question would have been asked and answered already ;-) Thanks Derek -- Derek Logan tel: +46 46 222 1443 Molecular Biophysicsfax: +46 46 222 4692 Lund University mob: +46 76 8585 707 Box 124, Lund, Sweden
Re: [ccp4bb] Merging CCP4i projects from two computers
Unison is good, as is rsync, but in this particular case will be complicated (if ( understand correctly) by the use of the identical file names for different files on the two computers. I don't see an easy, automatic way around this. I would rename one or some of the directories, put them on the same computer, and then manually go through them and decide which ones are duplicates, and which are unique but identically named files, and rename those. If this is a Unix/Linux system, it might be useful to know that the diff command can work on an entire directory, if you plead with it sincerely enough and use the right parameters. In future, unison or rsync could be used on a regular basis to avoid another situation like this arising. Back in the good old days, we were able to share disks between computers with something called NFS, and even further back, file versioning in VMS might have been relevant and useful. But I am wandering. Cheers, - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Fri, 2008-03-07 at 12:15 +, Johan Turkenburg wrote: Hi, The way I cope with this is by using synchronisation between directories (folders) on the two computers. In my case both are running linux, and the program Unison provides a simple tool to synchronise. If you make sure the projects have the same name on the two computers, the cpp4 database files copy over ok, and the interface copes ok. I am sure this method is easy to break, so be careful trying it out! Johan P.J.Briggs wrote: Hi Derek There's not really any way of doing what you're asking at present. If merging utility would be useful to others then I would be prepared to look into providing one, although there are a bunch of fiddly issues to deal with (e.g. keeping dates consistent, handling file name clashes and so on). Do any other readers of this list want to comment? Best wishes Peter Derek Logan wrote: Hi everyone, I've been working on a project using CCP4i on two separate computers in parallel and now unfortunately have jobs spread over the two locations. I would now like to consolidate these. Some of the new jobs on one computer will have the same run number as different ones on the other. Is there any convenient way to merge the projects? I guess the answer is no, or else the question would have been asked and answered already ;-) Thanks Derek -- Derek Logan tel: +46 46 222 1443 Molecular Biophysicsfax: +46 46 222 4692 Lund University mob: +46 76 8585 707 Box 124, Lund, Sweden
Re: [ccp4bb] Merging CCP4i projects from two computers
NFS is alive and well (even on OS X 10.5), but having separate copies on different computers and/or an svn server has the additional merits of being a backup system and one you can use with computers that don't have static IPs. David J. Schuller wrote: Back in the good old days, we were able to share disks between computers with something called NFS, and even further back, file versioning in VMS might have been relevant and useful. But I am wandering.
Re: [ccp4bb] isopropanol as a precipitant
Shivesh It's often very difficult to harvest crystals from conditions that contain isopropanol because the alcohol is volatile - especially with 50% or over! A solution that has worked several times it so use the Vapor Batch plates. http://www.douglas.co.uk/vb.htm You can cover the drops with oil, and then put isopropanol solution into the moat of the plate. The alcohol diffuses through the oil into the drops, while the oil acts as a buffer, reducing loss of alcohol during harvesting and freezing. For a case study see http://www.douglas.co.uk/winner1.htm Please let me know if anyone wants samples. Patrick -- [EMAIL PROTECTED]Douglas Instruments Ltd. DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK Directors: Peter Baldock, Patrick Shaw Stewart, James Smith http://www.douglas.co.uk/ Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of shivesh kumar Sent: 05 March 2008 07:23 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] isopropanol as a precipitant Dear all Sorry for non-CCP4 query. I have crystallized a 7kDa protein in 50-60% of isopropanol,pH 4.0-4.6.The interesting thing is that the xtal appears within 5 hrs at 16 degree. The protein conc is 5mg/ml and drop size is 3+1 with mother liquor 300 micro lt.Numerous xtals appears and but small is size.Do anyone can share their experience with Isopropanol as a precipitant and to improve the xtal quality with other precipitants.All suggestions are welcome. Thanx in advance. Shivesh
[ccp4bb] MTZ cell troubles after sortmtz reindexing from P321 to C2
Dear all, after much sweat and grief I managed to index my data in P321 but looking at the symmetry I think they might be C2: reindexing from P321 to C2 with the 2h+k, k, l operator in sortmtz produces the right cell (and yes I did tick the Reduce reflexions to the asymmetric unit button so that noreduce is not among the sortmtz keywords): P321 209.3168 209.3168 40.6822 90. 90. 120. C2 362.5473 209.3168 40.6822 90. 90. 90. But: scala then decides that the asymmetric unit is not the right one and it mysteriously changes cell parameters (which I think points to a bug in the sortmtz process of reindexing): Reciprocal space symmetry: Space group: C 1 2 1 Point group: PG2 Laue group: 2/m Reference asymmetric unit: k=0 and (l0 or (l=0 and h=0)) (change of basis may be applied) and I end up with this C2 cell in the mtz output from scala: 285.9320 285.9320 40.6824 90. 90. 90. I have tried OUTPUT ORIGINAL ans some such in scala but to no avail. Now please don't all tell me to go back and reindex-reintegrate these images - although I might have to do it to get the best out of these data once I am convinced they are monoclinic. Rather, I would appreciate suggestions on what program to feed the multirecord mtz to sort its asymmetric unit in C2 so that scala does not play tricks on me; or what keyword to feed scala to keep reflexions in the current asymmetric unit (and use cad or sftools afterwards on the scaled/merged file) Thanks Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
Re: [ccp4bb] Merging CCP4i projects from two computers
David J. Schuller wrote: ... even further back, file versioning in VMS might have been relevant and useful. But I am wandering. [:) Problem is both files are version *.*;1. I keep getting: -RMS-E-FEX, file already exists, not superseded %BACKUP-E-OPENOUT, error opening DISK$USER1:[00.ACRIVOS.JUL99]I0TEST.DIR;1 as output -RMS-E-FEX, file already exists, not superseded %BACKUP-E-OPENOUT, error opening DISK$USER1:[00.BERRY]TEMP.TXT;1 as output -RMS-E-FEX, file already exists, not superseded %BACKUP-E-OPENOUT, error opening DISK$USER1:[00.SAURON]KK9108051.DIR;1 as output ... SYSOPER job terminated at 8-JAN-2008 22:25:07.17 Accounting information: Buffered I/O count: 317527 Peak working set size:1597 Direct I/O count:192669 Peak page file size: 6950 Page faults: 4162 Mounted volumes: 0 Charged CPU time: 0 00:23:26.42 Elapsed time: 0 00:25:07.12 $
Re: [ccp4bb] Thermofluor experiment
Hi, I am interested in using the thermofluor to assess the stability of my protein in different buffers. Can anyone recommend a vendor that supplies buffer screens, possibly in 96 well format? Not crystallization buffers, just ordinary storage buffers. Thanks brenda Quoting Andreas Förster [EMAIL PROTECTED]: Dear Kornelius, I found the idea of doing Thermofluor on membrane proteins really intriguing - for identifying the best buffer and detergent, secondary detergents, even for checking crystallization drops that stayed clear. (This latter experiment should theoretically be possible with large drops, even though you'd be working very near the limits claimed in the publications.) In the end, I didn't find the method too useful because of noise issues due to detergent and exposed hydrophobic portions of the protein. I always felt that, in order to get reasonable signal, I'd have to use protein at unreasonable concentrations. The method works much better for soluble protein, though I can't tell you a success story where it led to crystallization that seemed impossible before. Andreas Kornelius Zeth wrote: Dear all, a question very related to the discussion before. I have been reading the papers about the thermofluor experiment with great interest. I wonder what people think about the underlying principles/ideas and the success that the method yielded in their own labs for crystallization or related purposes? Has anybody used this method with membrane proteins in order to find out the stability of the protein in the presence of a second detergent? Is the method limited to this certain dye (sypro orange)? Have a nice day Kornelius P.S.: I will make a summary of all opinions. -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany [EMAIL PROTECTED] Tel -49 7071 601 323 Fax -49 7071 601 349
Re: [ccp4bb] MTZ cell troubles after sortmtz reindexing from P321 to C2
Hi Pietro, I would use pointless for this - it will correctly reindex the reflections and sort them to boot. You can specify the correct pointgroup and reindex operator to reindex the reflections, and (I am 99% sure) pointless will compute the correct unit cell... You can find recent versions of pointless which do this, and documentation on how to do this, on the ccp4 prerelease pages. Cheers, Graeme -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Pietro Roversi Sent: 07 March 2008 18:18 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] MTZ cell troubles after sortmtz reindexing from P321 to C2 Dear all, after much sweat and grief I managed to index my data in P321 but looking at the symmetry I think they might be C2: reindexing from P321 to C2 with the 2h+k, k, l operator in sortmtz produces the right cell (and yes I did tick the Reduce reflexions to the asymmetric unit button so that noreduce is not among the sortmtz keywords): P321 209.3168 209.3168 40.6822 90. 90. 120. C2 362.5473 209.3168 40.6822 90. 90. 90. But: scala then decides that the asymmetric unit is not the right one and it mysteriously changes cell parameters (which I think points to a bug in the sortmtz process of reindexing): Reciprocal space symmetry: Space group: C 1 2 1 Point group: PG2 Laue group: 2/m Reference asymmetric unit: k=0 and (l0 or (l=0 and h=0)) (change of basis may be applied) and I end up with this C2 cell in the mtz output from scala: 285.9320 285.9320 40.6824 90. 90. 90. I have tried OUTPUT ORIGINAL ans some such in scala but to no avail. Now please don't all tell me to go back and reindex-reintegrate these images - although I might have to do it to get the best out of these data once I am convinced they are monoclinic. Rather, I would appreciate suggestions on what program to feed the multirecord mtz to sort its asymmetric unit in C2 so that scala does not play tricks on me; or what keyword to feed scala to keep reflexions in the current asymmetric unit (and use cad or sftools afterwards on the scaled/merged file) Thanks Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
Re: [ccp4bb] MTZ cell troubles after sortmtz reindexing from P321 to C2
As Graeme says, Pointless should sort this out for you, either from CCP4 pre-release, or from ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre Phil On 7 Mar 2008, at 20:25, Winter, G (Graeme) wrote: Hi Pietro, I would use pointless for this - it will correctly reindex the reflections and sort them to boot. You can specify the correct pointgroup and reindex operator to reindex the reflections, and (I am 99% sure) pointless will compute the correct unit cell... You can find recent versions of pointless which do this, and documentation on how to do this, on the ccp4 prerelease pages. Cheers, Graeme -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Pietro Roversi Sent: 07 March 2008 18:18 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] MTZ cell troubles after sortmtz reindexing from P321 to C2 Dear all, after much sweat and grief I managed to index my data in P321 but looking at the symmetry I think they might be C2: reindexing from P321 to C2 with the 2h+k, k, l operator in sortmtz produces the right cell (and yes I did tick the Reduce reflexions to the asymmetric unit button so that noreduce is not among the sortmtz keywords): P321 209.3168 209.3168 40.6822 90. 90. 120. C2 362.5473 209.3168 40.6822 90. 90. 90. But: scala then decides that the asymmetric unit is not the right one and it mysteriously changes cell parameters (which I think points to a bug in the sortmtz process of reindexing): Reciprocal space symmetry: Space group: C 1 2 1 Point group: PG2 Laue group: 2/m Reference asymmetric unit: k=0 and (l0 or (l=0 and h=0)) (change of basis may be applied) and I end up with this C2 cell in the mtz output from scala: 285.9320 285.9320 40.6824 90. 90. 90. I have tried OUTPUT ORIGINAL ans some such in scala but to no avail. Now please don't all tell me to go back and reindex-reintegrate these images - although I might have to do it to get the best out of these data once I am convinced they are monoclinic. Rather, I would appreciate suggestions on what program to feed the multirecord mtz to sort its asymmetric unit in C2 so that scala does not play tricks on me; or what keyword to feed scala to keep reflexions in the current asymmetric unit (and use cad or sftools afterwards on the scaled/merged file) Thanks Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
Re: [ccp4bb] MTZ cell troubles after sortmtz reindexing from P321 to C2
Just for the record, if you feed the data into XPREP (using Tim Gruene's mtz2sca if necessary) it will almost certainly give you the choice of space groups - with an indication of which is the most likely - and do the necessary cell and index transformations automatically. I recommend inputting unmerged data in such cases! 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 Fri, 7 Mar 2008, Pietro Roversi wrote: Dear all, after much sweat and grief I managed to index my data in P321 but looking at the symmetry I think they might be C2: reindexing from P321 to C2 with the 2h+k, k, l operator in sortmtz produces the right cell (and yes I did tick the Reduce reflexions to the asymmetric unit button so that noreduce is not among the sortmtz keywords): P321 209.3168 209.3168 40.6822 90. 90. 120. C2 362.5473 209.3168 40.6822 90. 90. 90. But: scala then decides that the asymmetric unit is not the right one and it mysteriously changes cell parameters (which I think points to a bug in the sortmtz process of reindexing): Reciprocal space symmetry: Space group: C 1 2 1 Point group: PG2 Laue group: 2/m Reference asymmetric unit: k=0 and (l0 or (l=0 and h=0)) (change of basis may be applied) and I end up with this C2 cell in the mtz output from scala: 285.9320 285.9320 40.6824 90. 90. 90. I have tried OUTPUT ORIGINAL ans some such in scala but to no avail. Now please don't all tell me to go back and reindex-reintegrate these images - although I might have to do it to get the best out of these data once I am convinced they are monoclinic. Rather, I would appreciate suggestions on what program to feed the multirecord mtz to sort its asymmetric unit in C2 so that scala does not play tricks on me; or what keyword to feed scala to keep reflexions in the current asymmetric unit (and use cad or sftools afterwards on the scaled/merged file) Thanks Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
Re: [ccp4bb] Molecular replacement of a multidomain protein
I've had a very good experience with MrBump: http://www.ccp4.ac.uk/MrBUMP/ Not only because of the program itself, which was able to find an unexpected template for the problematic chain (the first one was straightforward in Phaser), but also because of great support from Martyn Ron. It's definitely worth a try. Lucas --- Anjali Mehta [EMAIL PROTECTED] escreveu: Dear All, I am working with a Bifunctional protein of molecular weight ~60 kDa. I have a 3.3 angstrom native dataset. The matthews number show there are 6 molecules in the asymmetric unit. The structures of the individual domains are already known from prokaryotes. The sequence identity with the known structures are about 30%. I have tried molecular replacement using the two parts as models respectively with CNS, MOLREP, PHASER etc. However I always get the solution for one domain. I have also tried to fix that domain and find the other one. But none of the programs can find a solution. I am trying to model build the correct sequence of one domain using a density modified (using CNS), NCS averaged (using RAVE) map but the map does not look very good. The side chains are not clear. That might be due to the fact that I am only having a partial model. Any suggestion will be appreciated. Thanks. Ms. Anjali Mehta Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/
Re: [ccp4bb] Molecular replacement of a multidomain protein
EPMR (now Open-EPMR, http://www.epmr.info) is an excellent alternative for finding difficult, high-dimensional MR solutions. Experiment with various resolution limits. We solved an asymmetric unit with 3 difficult-to-place dimers of low sequence homology by gradually increasing the high-resolution limit of the structure factor data used. If you have a partial static solution, it can look for additional protein chain placements. It is strongly recommended for your type of problem that you set the correlation coefficient threshold for a good solution to 1.00 and not use the defaults. This will force EPMR to do an exhaustive search. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] Lucas Bleicher wrote: I've had a very good experience with MrBump: http://www.ccp4.ac.uk/MrBUMP/ Not only because of the program itself, which was able to find an unexpected template for the problematic chain (the first one was straightforward in Phaser), but also because of great support from Martyn Ron. It's definitely worth a try. Lucas --- Anjali Mehta [EMAIL PROTECTED] escreveu: Dear All, I am working with a Bifunctional protein of molecular weight ~60 kDa. I have a 3.3 angstrom native dataset. The matthews number show there are 6 molecules in the asymmetric unit. The structures of the individual domains are already known from prokaryotes. The sequence identity with the known structures are about 30%. I have tried molecular replacement using the two parts as models respectively with CNS, MOLREP, PHASER etc. However I always get the solution for one domain. I have also tried to fix that domain and find the other one. But none of the programs can find a solution. I am trying to model build the correct sequence of one domain using a density modified (using CNS), NCS averaged (using RAVE) map but the map does not look very good. The side chains are not clear. That might be due to the fact that I am only having a partial model. Any suggestion will be appreciated. Thanks. Ms. Anjali Mehta Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/ -
Re: [ccp4bb] Molecular replacement of a multidomain protein
Hi, A few things you might try (or that you may have tried, but didn't mention): 1. Run the search models through chainsaw with their sequence alignments before searching (or just use poly-alanine versions of the search models), and reset the B-factor of the search models to the B-factor of the dataset (or your favorite number, the important part is that it's constant). 2. You mentioned that you get a solution for one domain. Is this a single Rotational/Translational solution set for 6 copies of this one search model, or something else? Assuming it is, you could try with fewer copies of your search model. If there are in fact 6 copies, and you search for 4, there should be density for all 6 in the maps phased from from the 4-model solution (assuming the MR solution is correct); but if it's the other way around there may be problems finding a solution. You may also want to try a range of combinations for searching (1 domain A + 1 domain B, 2 domain A + 1 domain B, 1 domain A + 2 domain B, etc). 3. It might be better not to bother with density modification for a 3.3 Angstrom model-phased dataset, especially if you have the possibility of using NCS. Good luck, Pete -Original Message- From: CCP4 bulletin board on behalf of Anjali Mehta Sent: Thu 3/6/2008 7:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Molecular replacement of a multidomain protein Dear All, I am working with a Bifunctional protein of molecular weight ~60 kDa. I have a 3.3 angstrom native dataset. The matthews number show there are 6 molecules in the asymmetric unit. The structures of the individual domains are already known from prokaryotes. The sequence identity with the known structures are about 30%. I have tried molecular replacement using the two parts as models respectively with CNS, MOLREP, PHASER etc. However I always get the solution for one domain. I have also tried to fix that domain and find the other one. But none of the programs can find a solution. I am trying to model build the correct sequence of one domain using a density modified (using CNS), NCS averaged (using RAVE) map but the map does not look very good. The side chains are not clear. That might be due to the fact that I am only having a partial model. Any suggestion will be appreciated. Thanks. Ms. Anjali Mehta
