Re: [ccp4bb] shelx HKLF4 to mtz conversion?
You can use f2mtz with the format identifier to convert the file: 8 snip- script start -- #/bin/bash f2mtz hklin yourshelxfile.hkl hklout yourmtzfile.mtz eof cellyou cell dimensions symm your space group format '(3F4.0,2F8.2,F4.0)' ctypout H H H J Q R LABOUT H K L Intensity stddevIntensity freeR end eof ---script end ---snap 8 The important bits are the format line and the ctypout line, and you have to add your cell and symmetry. That can probably even be done through the gui, but a script is simpler (to me, anyway). Hope this helps, Tim On Wednesday 11 July 2007 09:29, Leonard Thomas wrote: I have a Shelx HKLF4 formated reflection file that I would like to convert to a mtz file. The primary reason is to transfer the freeR set. I found a couple of convoluted ways of converting the reflection data, but no real way of getting the freeR set to transfer. Any suggestions? Cheers Leonard M. Thomas Ph.D. Director, Macromolecular Crystallography Laboratory Howard Hughes Medical Institute California Institute of Technology Division of Biology 1200 E. California Blvd. MC 114-96 Pasadena, CA 91125 626-395-2453 [EMAIL PROTECTED] http://www.br.caltech.edu/cmclab -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpuMHpGIBBuY.pgp Description: PGP signature
Re: [ccp4bb] Help with reducing crystal mosaicity
On Tuesday 10 July 2007 09:16, Mary Fitzgerald wrote: If that doesn't work maybe, I'll try seeding at lower MPD concentrations or pressure freezing. Thanks again, Mary With such a high MPD condition I would probably first try micro-seeding at 25-35% MPD before doing anything else. It sounds like a very good candidate. -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpEJuDKsMqme.pgp Description: PGP signature
Re: [ccp4bb] The CCP4 license is ambiguous
To me it seems that clause 2.1.1 of the CCP4 academic license says that one can distribute work derived from or using the CCP4 libraries provided that it complies with clause 2.1.2 The last sentence in clause 2.1.2 says it itself becomes void if the derived work is distributed under the GPL or LGPL. Doesn't that mean that the CCP4 academic license does NOT impose any restrictions at all for work distributed under the LGPL or GPL, because anything that might restrict it is void? Tim On Wednesday 04 July 2007 18:49, Kevin Cowtan wrote: I was speaking imprecisely. I will try again. You cannot create a derived work containing both CCP4 6.* licensed code and GPL'd code, and distribute the resulting program, since the GPL demands that the derived work be distributed without additional restirctions and the CCP4 6.* license imposes additional restrictions on redistribution - in particular (but not limited to) an indemnity clause. Ethan A Merritt wrote: On Tuesday 03 July 2007 06:55, Kevin Cowtan wrote: I'm afraid there is no ambiguity. You can't use the CCP4 version 6.* libraries in GPL software. This sounds strange to me. The question is usually raised in the other direction - whether GPL libraries can be used by a non-GPL program [*]. Here you are saying that a GPL program cannot use non-GPL libraries. I believe this is false. To take an obvious example, consider GPL software running on Windows and calling into the system libraries. Do you think that Cygwin has been in violation of the GPL all these years? Or perhaps I misunderstand. Are you saying that the current CCP4 license does not permit combination with non-CCP4 code? -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpJMJQenaGY9.pgp Description: PGP signature
Re: [ccp4bb] compiling problems ccp4-6.0.2 and gcc-4.1.2
Hi,
according to this page
(http://www.xastir.org/wiki/index.php/HowTo:Ubuntu_6.10) the problem arises
due to a wrong ld option ('ld -shared' rather than 'gcc -shared'). How did
you run configure ? Are you trying to build shared libraries?
ccp4 works fine with Debian lenny, gcc-4.1.2 with just running
FC=g77 F77=g77 ./configure linux
(you should use g77 rather than gfortran. The programs compile but do not work
properly, especially with mosflm in Harry Powell's experience).
Tim
On Thursday 28 June 2007 20:32, Miguel Ortiz-Lombardía wrote:
Dear all,
Has anyone succeeded at compiling the latest release of CCP4 with gcc-4.1.2
This is the compiler version in Ubuntu 7.04 (Feisty Fawn)
At the very beginning (ccif lib compilation), I get this error:
/usr/bin/ld: final link failed: Nonrepresentable section on output
I looked around and found that:
export CC=gcc -fno-stack-protector
might help. It did help, and the compilation proceeded... to the program
solomon, where I get again:
eval gcc -fno-stack-protector ${pdbhtf_FLAGS--O -DGFORTRAN -DPROTOTYPE
-fPIC} -o pdbhtf pdbhtf.o -Wl,-rpath,/home/miguel/Desktop/ccp4-build/ccp4-
6.0.2/lib -lm rm -f pdbhtf.o
/home/miguel/Desktop/ccp4-build/ccp4-6.0.2/src/solomon_/cmap_io.c: In
function 'WriteMap':
/home/miguel/Desktop/ccp4-build/ccp4-6.0.2/src/solomon_/cmap_io.c:356:
warning: passing arg 3 of 'mat4_to_symop' from incompatible pointer
/usr/bin/ld: solomon: hidden symbol `__stack_chk_fail_local' in
/usr/lib/libc_nonshared.a(stack_chk_fail_local.oS) is referenced by DSO
/usr/bin/ld: final link failed: Nonrepresentable section on output
Any clues anyone?
Thanks a lot!
Miguel
--
Tim Grune
Australian Synchrotron
800 Blackburn Road
Clayton, VIC 3168
Australia
pgpTCIrGsmR9F.pgp
Description: PGP signature
Re: [ccp4bb] mac pro configuration for crystallographic computing
I should apology for my unqualified remark (initiated by a personal note to me). I do appreciate and like grasp. From my experience, though, the appearance of an electrostatic surface representation is so much dependent on the parameters, on the input PDB-file (presence of ligands, waters, several copies), that I suppose many of the calculations could be replaced by a surface with a colour scheme based on acidic or basic residues without loss of information - I have met too many people who use software just as they would use Windows instead of understanding what they are really trying to do, and as soon as they see what they want to see the make a screen shot (not excluding me here). cheers, Tim -Original Message- From: Tim Grune [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Date: Thu, 21 Jun 2007 13:26:54 +1000 Subject: Re: [ccp4bb] mac pro configuration for crystallographic computing On Thursday 21 June 2007 06:50, Juergen Bosch wrote: I don't have one of those beast in my hands unfortunately. But I can verify that all except of HKL2000 (which I don't use, so I don't care/bother to check if there is an OS X version there) of the programs you mentioned run without any troubles. There's one more program I know that has not been ported to OS X and that is Grasp but there are other options to draw nice electrostatics. Grasp2 runs nicely in a Windows XP installation within Virtualbox under Linux. Since Virtualbox is also available for Mac (even though only as beta1-Version) one might get it to run under MacOSX And I think one can run Windows within MacOSX anyhow? (even though in my opinion one might as well use the gimp to paint your protein red-blue and still have about the same information content, but that's only my very personal opinion). Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia
Re: [ccp4bb] mac pro configuration for crystallographic computing
On Thursday 21 June 2007 06:50, Juergen Bosch wrote: I don't have one of those beast in my hands unfortunately. But I can verify that all except of HKL2000 (which I don't use, so I don't care/bother to check if there is an OS X version there) of the programs you mentioned run without any troubles. There's one more program I know that has not been ported to OS X and that is Grasp but there are other options to draw nice electrostatics. Grasp2 runs nicely in a Windows XP installation within Virtualbox under Linux. Since Virtualbox is also available for Mac (even though only as beta1-Version) one might get it to run under MacOSX And I think one can run Windows within MacOSX anyhow? (even though in my opinion one might as well use the gimp to paint your protein red-blue and still have about the same information content, but that's only my very personal opinion). Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpFhY3yeObxL.pgp Description: PGP signature
Re: [ccp4bb] problems with phaser for MR
Hi, this looks very familiar to me. I am pretty certain you have phenix installed, too, and ccp4i does use the phenix version of phaser, which shows this behaviour. You can test this by typing 'which phaser' from the command line. You should make sure that $CBIN comes before the phenix path, e.g. by starting ccp4i with export PATH=$CBIN:$PATH ccp4i Tim -Original Message- From: Ed Wright [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Date: Sat, 9 Jun 2007 19:17:21 -0400 Subject: [ccp4bb] problems with phaser for MR Dear All, I can't seem to read my mtz files with 'PHASER for MR' in version ccp4i 6.0.2 running on either a linux or irix system. I can read the mtz files with virtually every other CCP4 subroutine. Any ideas/suggestions? The error I get in the log file is * *** Phaser Module: READ MR DATA FROM MTZ FILE 1.3.1 *** * FATAL RUNTIME ERROR: Cannot open MTZ file: /home/elias/mergedata/p4/ccp4/sort_p4.mtz EXIT STATUS: FAILURE
Re: [ccp4bb] COOT (version 0.2, Jan 2007) and .FCF file
On Thursday 07 June 2007 15:39, U Sam wrote: /usr/bin/awk Coot uses awk to parse the fcf file, and it assumes the binary is at /usr/bin/awk. Unfortunately on CentOS, awk is at /usr/bin/awk If you have root access to this computer, you can set a link from /bin/awk to /usr/bin/awk, even though this is not a neat nor proper solution. Or wait until Paul tells you from which file awk is called and change the path from /usr/bin/awk to /bin/awk. This is definitely the better solution. Finally chances are that coot uses an environment variable to call coot. Again, wait until Paul tells you its name then set it from /usr/bin/awk to /bin/awk and things should work. Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpTdKrEILway.pgp Description: PGP signature
Re: [ccp4bb] Delphi question
Hello Ibrahim, from the name of the library I would guess it belongs to the IBM compiler. Since you probably don't want to install it only to run Delphi (because it costs quite a bit), you would have to contact the authors of Delphi to recompile their program. Many compilers come with a switch to make the binary independent of the actual compiler libraries, and even though I don't have access to the IBM compilers I guess that this is possible for those, too. Tim On Thursday 31 May 2007 08:22, Ibrahim M. Moustafa wrote: Hi All, I'm trying to install Delphi on the MacOS PPC. The distributed package has a delphiMacOSX. However, when trying to run the program I get the error: dyld: Library not loaded: /opt/ibmcmp/lib/libxlomp_ser.dylib Reasong: Image not found Obviously, I'm missing something here as the directory /opt/ibmcp/lib does not exist!! The makefile does not have any indication for that directory! I have no idea why I see this error and how to remove it! I'd be appreciated if anyone has an experience in installing Delphi on the MacOS would guide me through the installation. P.S. Hope this non-ccp4 question does not bother you guys! thanks, Ibrahim --- --- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., Uinversity Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 --- --- -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgprmQpiu0XOQ.pgp Description: PGP signature
Re: [ccp4bb] Refmac5 restrained refinement could not keep the changes made in Turbo
Hi, at 1.2A resolution, you can probably go higher than 2 with the weighting term, especially at the end of your refinement, when the model is near completeness. You can try 'weight auto' to let refmac5 figure out the correct weight (you have to use 'RunView Com file' to edit the script manually to do this). A large value for the weighting term means that the crystallographic data are weighted more strongly than the geometric restraints, hence you probably want to increase rather than decrease that value. Tim On Friday 18 May 2007 11:13, XJ XJ wrote: Dear all, I am having a problem with refining my structure using refmac5. Basically, I am trying to make some small changes to several places on the backbone. But the thing is that, after restrained refinement, the changes I made would be all gone and the chain stayed exactly where they were before I made those changes. I'm using Turbo for building the model. The resolution I'm working on now is 1.2 A. The refmac was working fine when I was working at a lower resolution (2 A) and I was able to rebuild a whole helix and refine successfully with refmac. Right now, I am still able to change rotamers of single residues and refmac will keep these type of changes for me. It is only when changes are made on the backbones that refmac will refine the structure back to what it was before the changes were made. Other than refining to highest resolution 1.2 A, I'm pretty much using all the default parameters from the restrained refinement, except that, under Geometric parameters, I changed all the overall wt restraints from 1.0 to 2.0. Weighing term has been varied from 0.3 to 0.5 and no difference was made. I guess it's probably some small mistakes I made while running the refmac, but I can't figure out what it is. Can anyone help me out real quick? Thanks! Regards, Xiaofei ___ _Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games. http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpBK9wvWHvLH.pgp Description: PGP signature
Re: [ccp4bb] MolRep with Phaser using a partial existing solution
Hello, you could try to let phaser search for the first fragment, too. That way it should produce a file ending with '.sol' which you can pass to phaser for the second search (bottom at the ccp4-gui, Define search sets...). Otherwise, if you do not want to move the first fragment, both the Euler angles and the translation should be 0 0 0. Tim On Friday 18 May 2007 11:24, Jay Thompson wrote: Hi, I have a question with molecular replacement using Phaser. I'm trying to solve a complex and I have a partial molecular replacement solution solved using another program. This solution is correct and makes up ~50% of the entire complex. I wanted to fix this solution and search for another small fragment of the complex using Phaser. I've been reading the Phaser manual and it seems that I cannot input a pdb with this partial solution and tell the program to fix this molecule. It seems that fixed solutions can be only input by putting in its Euler angles and fractional coordinate translations. Is this correct that I cannot input a pdb and fix it? If I cannot do this, then is there a quick way to identify the euler angles and coordinate translations for Phaser. Thanks a lot!! Jay -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpm9nCMhOS3O.pgp Description: PGP signature
Re: [ccp4bb] MolRep with Phaser using a partial existing solution
Hi, what resolution range do you use? You can try reducing it a little. How big is your cell? Tim On Friday 18 May 2007 13:46, Jay Thompson wrote: Hi, Thanks for the suggestions and quick reply. Suggestions work great! But I have another problem and looking back at the ccp4bb, I see that Elenor had a similar problem late last year. The error message is as follows: BFONT COLOR=#FF8800 -- OUT OF MEMORY ERROR: St9bad_alloc -- /FONT/B !--SUMMARY_END-- EXIT STATUS: FAILURE CPU Time: 0 days 0 hrs 19 mins 53.80 secs (1193.80 secs) Finished: Thu May 17 20:28:14 2007 /pre /html The only suggestion from the ccp4bb threads that I could see was to try running it on a different computer with more memory. I've tried running the job on two different Mac G5 and I get the same error message. The computers that I have are pretty new and have 2 GB of SDRAM. I'm surprised that I have a memory problem. I'm also using the Phaser 1.3.3 (I'm assuming this is the latest version). Thanks for all your help, in advance. Jay On 5/17/07, Jay Thompson [EMAIL PROTECTED] wrote: Hi, I have a question with molecular replacement using Phaser. I'm trying to solve a complex and I have a partial molecular replacement solution solved using another program. This solution is correct and makes up ~50% of the entire complex. I wanted to fix this solution and search for another small fragment of the complex using Phaser. I've been reading the Phaser manual and it seems that I cannot input a pdb with this partial solution and tell the program to fix this molecule. It seems that fixed solutions can be only input by putting in its Euler angles and fractional coordinate translations. Is this correct that I cannot input a pdb and fix it? If I cannot do this, then is there a quick way to identify the euler angles and coordinate translations for Phaser. Thanks a lot!! Jay -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgp5jlv8p2U4l.pgp Description: PGP signature
Re: [ccp4bb] ccp4mg can't start
Hi Yanming, it looks like ccp4mg looks for python in a specific path within the ccp4mg. Edit the script ccp4mg (you find out where it is with 'which ccp4mg'). Look at the very end of that file for where python is called (probably with some arguments). Make sure it says only 'python', not anything like '/usr/local/ccp4/ccp4mg-0.12.1/bin/..//pythondist/bin/python'. Then ccp4mg will use the python of your system. This works for me and ccp4mg does not need its own python installation. Maybe the ccp4mg-developers may want to comment on whether this is a bad idea and may have a negative influence on ccp4mg's performance? Tim -Original Message- From: Yanming Zhang [EMAIL PROTECTED] To: Tim Grune [EMAIL PROTECTED] Date: Wed, 16 May 2007 01:47:08 -0400 (EDT) Subject: Re: [ccp4bb] ccp4mg can't start Dear Tim, Thanks for your help. python 2.4.2 is the version. Following is the output of ccp4mg -dbx: GNU gdb Red Hat Linux (6.3.0.0-1.132.EL4rh) Copyright 2004 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type show copying to see the conditions. There is absolutely no warranty for GDB. Type show warranty for details. This GDB was configured as i386-redhat-linux-gnu.../usr/local/ccp4/ccp4mg-0.12.1/bin/..//pythondist/bin/python: No such file or directory. (gdb) Starting program: /usr/local/ccp4/ccp4mg-0.12.1/bin/..//python/ui/ui.py -debug opengl command No executable file specified. Use the file or exec-file command. (gdb) No stack. (gdb) No symbol table is loaded. Use the file command Any suggestion? Thanks On Wed, 16 May 2007, Tim Grune wrote: Hi Yanming, which version of python is running on your system(python -V)? Maybe it is too old? Otherwise, does 'ccp4mg -dbx' produce any more output? On Wednesday 16 May 2007 11:20, you wrote: Dear Tim, I checked the two files, Both are empty. Linux distribution: 2.6.9-42.ELsm Thanks Yanming On Wed, 16 May 2007, Tim Grune wrote: Could you send the contents of the files /home/yzhang/.CCP4MG/ccp4mg_stdout.txt and /home/yzhang/.CCP4MG/ccp4mg_stderr.txt What Linux distribution are you using? Tim On Wednesday 16 May 2007 10:31, Yanming Zhang wrote: Dear All, lately I have a fantacy toward ccp4mg. But either from ccp4i or typing 'ccp4mg' directly from the prompt(Linux), I got the following error message: Loading fonts.. ...DONE Starting graphics thread.. ...DONE Parsing command line.. ...DONE Redirecting output to /home/yzhang/.CCP4MG/ccp4mg_stdout.txt Redirecting errors to /home/yzhang/.CCP4MG/ccp4mg_stderr.txt Started at Fri May 16 09:16:59 2003 /usr/local/ccp4/ccp4mg-0.12.1/bin/ccp4mg: line 281: 10773 Killed python $CCP4_MG/python/ui/ui.py $* Any quick remedy? Thanks Yanming -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia
Re: [ccp4bb] crystallographic magic
The 'magic' file is the database the unix command 'file' uses to determine different fileformats. It is plain text and jsut describes the first couple of bytes of each file which are supposed to be enough to determine what type of file it is (e.g., a PNG-image, or an MTZ-file, or a CNS-map). ;-) On Tuesday 15 May 2007 15:36, you wrote: uhhh? 2007/5/14, Tim Grune [EMAIL PROTECTED]: Hi, I just found out that my magic file contains a large section with respect to crystallographic file formats. I was pretty impressed. According to the header it is attributed to Joe Krahn. Full ACK to him! Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpAGQB4ZyCjX.pgp Description: PGP signature
[ccp4bb] crystallographic magic
Hi, I just found out that my magic file contains a large section with respect to crystallographic file formats. I was pretty impressed. According to the header it is attributed to Joe Krahn. Full ACK to him! Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgp1D27STaMEd.pgp Description: PGP signature
Re: [ccp4bb] CCP4 GUI
As long as I have been using the ccp4i (which has been a couple of years now), this magic button has been there, and it has even been in the 'lower left corner': When you hold your mouse button on the Run button, a submenu appears, the second item of which is saying RunView com file. This opens an editable window with the script used to run the ccp4-program. This, by the way, is very handy for setting the matrix weight in Refmac5 to 'auto', as recommended by the authors of ARP/wARP. Tim -Original Message- From: Roger Rowlett [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Date: Thu, 10 May 2007 10:44:13 -0400 Subject: Re: [ccp4bb] CCP4 GUI I think a tweak script button or option (before running) would be an excellent idea. Cheers, ___ Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Juergen Bosch Sent: Thursday, May 10, 2007 10:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 GUI Hi Martyn, how about option c: in each gui window at the lower left corner have a button called Display script, or call it Expert Mode if people feel better as Experts :-) , before running of course. Then people who would like to edit their stuff could do so before running the script. I think it would be scary to many if the Expert Mode actually would display all other options available for that particular program - for this you have the RTFM* I tend to use the GUI only for standard stuff and keep migrating my scripts from directories to directories, which if you run a search on say e.g. refmac. spits out a ton of handcrafted scripts for each project - maybe also not the best thing to do, but that's how it is. Juergen * Fine of course, what else ! Martyn Winn wrote: This is timely. We're in the process of a) trying to organise a major effort to tidy up the existing ccp4i classic (rather than fire-fighting problems), and b) thinking about designing the next generation. Not sure which this is. Option b) would be a project over several years. Can you elucidate further. As an expert user, would you want a less scary free text box (which is essentially what RunView Com File is), or actual widgets for every option. The latter could be done as a hidden folder, made visible according to an Expert switch in Preferences. As developers, we also have to think about long-term maintainability. Options, in particular little-used options, can soon become out-of-date. m On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I'm a well-known luddite as Eleanor says. However, I shamelessly confess that the CCP4 GUI is great. Not that I think this is necessary here, I'm sure most people agree with that. If I write now is because Martynn's e-mail have reminded me of something I thought once, but forgot to ask for to the ccp4i developpers: perhaps the GUI could have two faces/modes, a basic one and an expert/advanced one. I understand that they already exist, but the expert one is hidden under the RunView Com File, while I'm thinking on a real expert GUI-mode. Users should be able to choose one or the other in their defaults, or switch from one to the other on-the-fly. I don't have a particular problem in editing the scripts as it is done now, but I have found that students tend to get a bit nervous about doing it themselves ;-) Cheers, Miguel Martyn Winn escribió: The level of detail in the GUI is a matter of constant debate. The underlying programs are far far richer, so the question is how much to expose in the GUI. We try to get a balance between ease-of-use and coverage, but it won't always work. BTW I don't think we ever claimed that ccp4i (or anything else in ccp4) is finished ;-) Having said that, we're always happy to hear about specific defects in the GUI. When reporting these to [EMAIL PROTECTED] please give as much information as possible, in particular knowing the context is always helpful. Cheers Martyn -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX:+1-206-685-7002
Re: [ccp4bb] can truncate import Rfree?
Hello Ian, that feature also does not seem to having it made into the GUI either. From the truncate code it looks like the corresponding LABIN flag is ''FreeR_flag'. Is this correct? To the others: Thank you for the comments. It's good to know that 'cad' is the program to use, I think, though, that this method is very error prone and unexperienced users might easily screw up their Rfree-flags. Cheers, Tim -Original Message- From: Ian Tickle [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Date: Thu, 3 May 2007 09:47:36 +0100 Subject: Re: [ccp4bb] can truncate import Rfree? Hi, the distributed version of truncate (from v 6.0 I think) has an option to assign label FreeR_flag on input copy to output, this is an option I added because we needed it here. Unfortunately the relevant info doesn't seem to have made it to the man page, sorry about that. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tim Grune Sent: 03 May 2007 00:16 To: CCP4BB@jiscmail.ac.uk Subject: can truncate import Rfree? Hello, is it possible to make truncate preserve an rfree flag possibly present in an mtz-file? Looking at its man-page it does not seem to accept RFREE labels neither for LABIN nor for LABOUT. How do I preserve my Rfree-flags if when using truncate? I noticed the option to Copy FreeR from another MTZ if I select the Ensure unique data add FreeR column in the truncate GUI. Is this the correct way to go by selecting the file itself for the reference mtz file? This seems extremely error prone to me. Cheers, Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia 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
[ccp4bb] can truncate import Rfree?
Hello, is it possible to make truncate preserve an rfree flag possibly present in an mtz-file? Looking at its man-page it does not seem to accept RFREE labels neither for LABIN nor for LABOUT. How do I preserve my Rfree-flags if when using truncate? I noticed the option to Copy FreeR from another MTZ if I select the Ensure unique data add FreeR column in the truncate GUI. Is this the correct way to go by selecting the file itself for the reference mtz file? This seems extremely error prone to me. Cheers, Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpKqLncut0OY.pgp Description: PGP signature
Re: [ccp4bb] further inconsistencies (was: tcltkblt and python distributions)
Hello Oliver, if by 'conventional' you mean - download the source code - ./configure OS make make install I did not share your experience a couple of days ago when I did that. I used both the ftp and the download interface and nothing was missing. However from from your mentioning of 'BINARY.setup' you may have meant installation of the binary version. I never payed attention to that file, though, even though I also installed a binary set on a PC running CentOS 4.4. All I did was change a few variable in $CCP4/include/ccp4.setup-bash: CCP4_MASTER to the correct root of the installation CCP4I_TCLTK to /usr/bin to use the system wish and remove the MANPATH entries since with an unset MANPATH bash (or man itself, not sure) figures out the correct path from PATH - which makes maintenance a lot easier. For CentOS and Debian I also have to change bltwish to wish in the tcl-scripts under $CCP4/ccp4i/bin since in both systems blt comes as a library. Finally I used good old g77 instead of gfortran since the latter made mosflm crash with a segmentation fault as soon as it tried to display an image. Maybe you can just try to re-download it? Unless this was all for a different platform in which case my advise may not be applicable - sorry. Cheers, Tim -Original Message- From: [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Date: Fri, 20 Apr 2007 10:44:37 +0200 Subject: [ccp4bb] further inconsistencies (was: tcltkblt and python distributions) Dear ccp4 developers, when trying to do a conventional install of ccp4 (i.e. avoiding the install.sh script), I ran across additional problems/inconsistencies with the package: 1. In the tarball I freshly downloaded this morning, the cctbx tree under ccp4-6.0.2/lib was completely missing!!! 2. The BINARY.setup script checks for src/phaser, which does not exist (instead there are phaser-ucs and phaser-utf directories). Simply creating the phaser directory may resolve this, but of course the phaser installation is corrupted due to the missing cctbx files. It would be nice if the responsible persons could comment on this. Is the conventional install no longer supported or not even checked? Greetings Oliver --- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ---
