Re: [ccp4bb] Refmac5 site?
Yes, I believe York were going to be off-line for a couple of days following some computer problems. The Refmac 5.3 source code is also available from our pre-release page: http://www.ccp4.ac.uk/prerelease_page.php As it happens, I updated it on Monday, so it is up-to-date. Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Paul Paukstelis Sent: Tue 1/30/2007 9:55 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refmac5 site? I'm in need of the source code for Refmac5 (latest version) to recompile with an increased number of atoms. It seems the refmac site is down. Does anyone know another location of the latest source, or the status of the refmac site? --paul -- Paul Paukstelis, Ph.D. Research Associate Institute for Cellular and Molecular Biology The University of Texas at Austin P: 512-471-4778, F: 512-232-3420 [EMAIL PROTECTED]
Re: [ccp4bb] TLSANL: negative mean-sq displacements?
I'd also comment that the absolute values are quite large. Well, I have no knowledge what groups you've chosen, but for domain-sized groups, typical values are 1-10 deg**2. Values can be larger for smaller TLS groups. This is just a rule-of-thumb, but would make me suspicious whether the TLS refinement was really stable in this case. Regards Martyn -Original Message- From: CCP4 bulletin board on behalf of Richard Gillilan Sent: Sun 2/25/2007 1:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] TLSANL: negative mean-sq displacements? After TLS refinement (which seemed to be stable and produced nice R_free values), I have analyzed the rigid body results with TLSANL. I get negative mean-square displacements along the axes of libration WRT to orthogonal axes! Am I misunderstanding something here? The units are (deg^2). I see this with two different structures. Here is the output from TLSANL: AXES OF LIBRATION WRT TOMEAN-SQUARE ANGLE LIBRATION AXES MAKE TO ORTHOGONAL AXES (IN ROWS) DISPLACEMENT ORTHOGONAL AXES (DEG) ABOUT AXES (DEG^2) X Y Z 0.842 0.197 0.502 -53.97532.66 78.63 59.85 -0.494 0.657 0.570 193.421 119.60 48.97 55.24 -0.217 -0.728 0.650 -12.276 102.55 136.73 49.45 MEAN LIBRATION (TRACE/3) 42.390 Anyone seen this happen before? Richard Gillilan MacCHESS
Re: [ccp4bb] search-and-replace
If I understand you correctly, the CCP4 program Chainsaw would do this. It uses an alignment file, which you could hand-craft to select mutate or conserve. Keyword "MODE MIXA" to select the truncate-to-beta option. HTH Martyn -Original Message- From: CCP4 bulletin board on behalf of [EMAIL PROTECTED] Sent: Sun 4/29/2007 3:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] search-and-replace Hello everyone, I have two pdb files for molecule A (A.pdb and A_polyala.pdb) from which I would like to make a hybrid file A_semi.pdb. A_semi.pdb will have some residues with full sidechains (so derived from A.pdb) and some residues with only a C-beta atom for a sidechain (so derived from A_polyala.pdb). The residues I would like mutated are listed in file B.txt (in total about 250 residues to be mutated). I could do this by hand but I figure there must be a fater way to do it. Does anyone have any suggestions on how I might be able to do this? Is there some unix search-and-replace command line I could use to replace all lines of text in A.pdb containing ### (spaced appropriately) with those lines of text in A_polyala.pdb containing the same ###, and then have it repeat this for all ~250 residues listed in the file B.txt? Many thanks in advance, Shekeb
Re: [ccp4bb] CCP4 GUI
That kind of thing has been suggested a few times, and in principle is a better way of doing things. One problem we face, is that we're a collaboration rather than a single project, and it is not always possible to adopt neat solutions across the suite. Which is partly why ccp4i was designed to be totally separate from the underlying programs. I should stress that I'm not offering to do all the ideas raised today ;-) (I'm already behind on enough projects). But we'll try to fix a few things soon within the current ccp4i design. The other suggestions from today will go into the melting pot for longer term development (my plan b from earlier). But we do appreciate the ideas and feedback. Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Peter Adrian Meyer Sent: Thu 5/10/2007 5:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 GUI Hopefully my offhand remark wasn't taken as a criticism of ccp4i (it wasn't meant as such); but seeing as I don't use it, it's not a place where I could tell someone how to find an option. > As developers, we also have to think about long-term maintainability. > Options, in particular little-used options, can soon become out-of-date. This is might be a bad idea*, but I'll throw it out there anyhow: What about the storing program keywords in a grammer file (something along the lines of yacc/lex), reading gui options from the grammer, and generating a parser subroutine from the grammer for the data-processing programs? This would mean changes to the parser library (and to a large number of existing programs which already work), but would eliminate the issue of keeping the gui options in sync with the program options. Pete *specifically, bad idea type #2 - probably more trouble than it's worth Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [ccp4bb] problem with Mr Bump?
We sometimes find that a local fasta search against the pdb sequence datafile (for which you need to install fasta package) works better than OCA at EBI, i.e. finds more matches. We have never tracked down why. But not sure what you mean by using local OCA server. How have you specified this server? And how does it fail? Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Harry M. Greenblatt Sent: Tue 8/21/2007 10:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] problem with Mr Bump? BS"D Dear All, While trying to run Mr. Bump, the program fails just after the FASTA step saying it can't find a file, which should contain the search results. This same job got past this point last week, but fails now. In trying to check out what is going wrong, I used the sequence with our local OCA server, and it works, and even finds four matches. Using the EBI's web site for OCA (used by Mr. Bump), it finds only two matches (same last week), but it *does* succeed. Have other people used Mr. Bump today, or this week? Thanks Harry - Harry M. Greenblatt Staff Scientist Dept of Structural Biology [EMAIL PROTECTED] Weizmann Institute of SciencePhone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel
Re: [ccp4bb] Fwd: [ccp4bb] CCP4i and modeller integration
Thanks Ben, Yes, I am acutely aware that our interface has got out-of-date. I can add in these little fixes. If there is sufficient interest, we could talk about updating to the python version. Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Ben Webb Sent: Fri 11/2/2007 10:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] CCP4i and modeller integration Jayashankar wrote: > Dear friends and scientists, > > I want to ask about for an integration of modeller in the ccp4i > interface. The interface in ccp4i is designed for modeller Version 6.2, > we have by now modeller 9.2 , which is a lot different. > Nevertheless I tried to enter the necessary data in ccp4i. I could not > try the integration myself because I got no suitable test data set. > Please can anybody inform me whether it is possible and the way to do that. I am not especially familiar with ccp4i, but I am the lead developer for Modeller, so can hopefully say something useful about that. ;) True, the latest version of Modeller is 9v2, which is very different from 6v2. However, if you are using 'old style' TOP scripts (which ccp4i generates) then 9v2 will quite happily work with the same scripts that work in 6v2. I just tried this out with ccp4i (6.0.2) using the 'simple' modeling example from the Modeller distribution (alignment.ali from examples/automodel/). For the configure window for CCP4i, I just filled in MODINSTALL to the same value as when I installed Modeller, left the install key blank (not needed for 9v2) and filled in the program name as 'bin/mod9v2'. (The bin prefix is needed because CCP4i looks in the MODINSTALL directory for the 9v2 script, not in the bin subdirectory which is where it lives in Modeller 7 and later.) To actually run Modeller, I put alignment.ali and pdb5fd1.ent in my CCP4i project directory, pulled up the 'run Modeller' CCP4i window, selected 'alignment file' for 'input sequence for structure to build as', selected 'define TOP file' (seems not to work properly without that, although I can't tell from the docs what it's supposed to do), put in 'alignment.ali' for 'Align in', left 'Top in' blank, then added two PDB files - one with code name '5fd1' and 'known in' 'pdb5fd1.ent', and another with code name '1fdx' and a blank value for 'known in'. The Run button should then run Modeller normally. This should all be fine for 'no' refinement. For the 'fast' and 'full' settings, you must edit ccp4-6.0.2/ccp4i/templates/modeller.com, and add the line 1 SET PDB_EXT = ' ' immediately after the 1 INCLUDE line. (This is because by default Modeller 7 and later write out files with a .pdb extension, while ccp4i expects them to have no extension.) The CCP4 guys may want to put this into the main CCP4 distribution, since it will also work for Modeller 6 (where it is a no-op). P.S. In at least one place in the CCP4 docs, the user is pointed to the old Modeller page at Rockefeller, which no longer exists. That link should go to http://salilab.org/modeller/ instead. P.P.S. If there is interest from CCP4 users or developers in improving the CCP4i/Modeller integration, I can certainly help out. For example, TOP scripts are deprecated in Modeller 9 in favor of Python scripts, and it would not be especially hard to change the script template to Python (although of course this would then break backwards compatibility with Modeller 4 and 6). Ben -- [EMAIL PROTECTED] http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
Re: [ccp4bb] converting structure factor files to mtz files
You need to update to CCP4 6.0.2, these items are now recognised. We try to keep up with the latest cif definitions, but there is a lag. The documentation for cif2mtz lists the column labels recognised. These are only labels, so if the worst comes to the worst, you can edit these in the cif file to something that cif2mtz recognises (as long as it is the same type of column!!) HTH Martyn -Original Message- From: Björn Kauppi [mailto:[EMAIL PROTECTED] Sent: Tue 11/6/2007 10:16 AM To: Winn, MD (Martyn); CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] converting structure factor files to mtz files Hi, I also have problems running cif2mtz using ccp4i (5.99) interface with several mmCIF files downloaded from the pdb (e.g., 2pip, ) on my linux box. Problems with the _refln.pdbx_F_plus etc cards it seems: Files without anomalous data work. --snip from log file: Line 58:data name "_refln.pdbx_F_plus" not present in dictionary Line 59:data name "_refln.pdbx_F_plus_sigma" not present in dictionary Line 60:data name "_refln.pdbx_F_minus" not present in dictionary Line 61:data name "_refln.pdbx_F_minus_sigma" not present in dictionary Line 62:data name "_refln.pdbx_anom_difference" not present in dictionary Line 63:data name "_refln.pdbx_anom_difference_sigma" not present in dictionary Line 64:data name "_refln.pdbx_I_plus" not present in dictionary Line 65:data name "_refln.pdbx_I_plus_sigma" not present in dictionary Line 66:data name "_refln.pdbx_I_minus" not present in dictionary Line 67:data name "_refln.pdbx_I_minus_sigma" not present in dictionary --- CIF opened read-only for input --- The file contains the following data blocks: data_r2piusf (at line 1) >>>> CCIF signal CCIF_CATNOTCOMPLETE (severity: Warning) <<<< (Raised in new_context) Could not open context on category 'refln'; item '_refln.pdbx_F_plus' not defined in dictionary! cif2mtz: Error in ccp4ccif_setup_context: Unexpected context type for category REFLN Times: User: 0.6s System:0.0s Elapsed: 0:00 Björn Kauppi > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Martyn Winn > Sent: den 1 november 2007 10:14 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] converting structure factor files to mtz files > > The first 3 cif columns are not the problem. cif2mtz will happily skip > these along with any other items it doesn't explicitly deal with. > > The problem is simply the extra columns F(+) etc, yes? > > This bug has been seen on Windows. The same job should work fine on > Linux or Macs. Or you should be able to simply delete these spurious > columns with cad, sftools, etc > I'm sure this will be easier than playing with Fortran formatting > > The bug is somewhere in the depths of the cif library, and we don't have > a fix yet. > > HTH > Martyn > > On Wed, 2007-10-31 at 19:49 -0400, Zheng Zhou wrote: > > Hi, > > > > Could anyone give a quick hint for the Fortran format for the > > following structure factor mmCIF file? or Is there any easy program or > > better way to convert it? I think I need to skip first 3 columns. > > > > Thanks in advance. > > > > Joe > > > > loop_ > > _refln.crystal_id > > _refln.wavelength_id > > _refln.scale_group_code > > _refln.index_h > > _refln.index_k > > _refln.index_l > > _refln.F_meas_au > > _refln.F_meas_sigma_au > > _refln.status > > 1 1 1200 617.50 5.41 o > > 1 1 1400 773.50 6.92 o > > 1 1 1600 62.30 3.19 o > > > > I am trying to view the electron density of a published structure. I > > downloaded the file from pdb and used cif2mtz in ccp4. I think the > > following output mtz is wrong. > > > > * Column Labels : > > > > H K L FREE FP SIGFP F(+) SIGF(+) F(-) SIGF(-) DP SIGDP I(+) SIGI(+) > > I(-) SIGI(-) > > > > * Column Types : > > > > H H H I F Q G L G L D Q K M K M > > > > * Associated datasets : > > > > 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 > > > > * Cell Dimensions : (obsolete - refer to dataset cell dimensions > > above) > > > >88.0800 86.3600 80.7700 90. 95.7100 90. > > > > * Resolution Range : > > > > 0.000450.29217 ( 47.298 - 1.850 A ) > > > > * Sort Order : > > > > 1 2 3 0 0 > > > > * Space group = 'C 1 2 1'
Re: [ccp4bb] ncs phased refinement
This is standard gotcha number 17, you are picking up "ncsmask" from XtalView rather than the CCP4 one, see http://www.ccp4.ac.uk/problems/general-probs.php#general_wrong_prog Basically, you need to fix the path in some way so that the CCP4 one comes first. check with "which -a ncsmask" HTH Martyn -Original Message- From: CCP4 bulletin board on behalf of Raja Dey Sent: Sat 12/8/2007 12:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ncs phased refinement Hi All, I was trying to run NCS Phased refinement in the gui of CCP4 (Refmac_5.2.0005) and getting the following error. I just pasted below the last part of the log file. Any help is greatly appreciated. Tarak ROTATION MATRIX -0.567-0.405 0.717 -0.385-0.639-0.665 0.728-0.654 0.206 PATTERSON SPHERICAL POLARS OMEGA PHI CHI OMEGA TO AXIS ZOPHI FROM AXIS XO TO AXIS YO WHEN BETA=0 CAN ONLY DEFINE ALPHA + GAMMA . WHEN BETA = 180 CAN ONLY DEFINE GAMMA - ALPHA. CROWTHER ALPHA BETA GAMMA137.15697 -78.1103841.90139 SPHERICAL POLARS OMEGA PHI CHI 39.04911 -42.37222 179.26884 DIRECTION COSINES OF ROTATION AXIS 0.46554-0.42468 0.77661 Angle between rotation axis and Centroid vector87.88194 * Note: Since this angle between rotation axis and Centroid vector is near to 90.0 this may represent a pure rotation *** LSQKAB: Normal Termination Times: User: 0.0s System:0.0s Elapsed: 0:00 - NCS Mask --- unable to open phase file *** * Information from CCP4Interface script *** The program run with command: ncsmask XYZIN /home/raja/liang/native/p6522/b-sharpen/b-sharpen_1_12_chainI_pdb.tmp MSKOUT /home/raja/liang/native/p6522/b-sharpen/b-sharpen_1_15_msk.tmp has failed with error message child process exited abnormally *** #CCP4I TERMINATION STATUS 0 "child process exited abnormally" #CCP4I TERMINATION TIME 07 Dec 2007 16:13:00 #CCP4I MESSAGE Task failed Raja Dey, Ph.D. Research Associate Molecular and Computational Biology University of Southern California 1050 Childs Way, Los Angeles, CA 90089 - Forgot the famous last words? Access your message archive online. Click here.
Re: [ccp4bb] cannot read .mtz in ccp4i
Yes, it might be the old quotes problem. Later versions of ccp4i add in quotes around the filenames (to deal with WIndows paths with spaces) and later versions of Phaser interpret quoted arguments correctly. But a new gui with an old phaser will cause problems. Martyn -Original Message- From: CCP4 bulletin board on behalf of Tim Gruene Sent: Sat 2/2/2008 3:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] cannot read .mtz in ccp4i Is it possible that you have phenix (or some old version of phenix) installed and that the PATH variable from the CCP4i gui finds that phenix first? Check if ccp4_first_in_path is set to 1 in your $CCP4/include/ccp4.setup script. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 1 Feb 2008, C.Ainsley Davis wrote: > Hello all > > I've recently redone a computer system using Ubuntu Gutsy Gibbon as the OS. > We've had success using Feisty Fawn in the past and using the ccp4i suite > downloaded from wgscott's page (the debian files used in ubuntu). For > whatever reason we cannot use PHASER in the ccp4i suite. The error we > continuously get is "cannot read .mtz file" FAILURE..etc. > > If i use a small script file (for example phaser.sh or phaser.com) with the > following lines > phaser << eof > > MODE MR_AUTO > HKLIN "./p3.mtz" > LABIN F=F_1 SIGF=SIGF_1 > TITLE MR_01 > COMPOSITION PROTEIN MW 13000 NUMBER 1 > SGALTERNATIVE ALL > TOPFILES 5 > ENSEMBLE ensemble1 & > PDBFILE "x.pdb" & > IDENT 40.0 > SEARCH ENSEMBLE ensemble1 & > NUMBER 2 > > RESOLUTION 4.0 30.0 > > > ROOT p3 > > end > > and it works, but the ccp4i GUI cannot read it in PHASER. It works for REFMAC > when doing refinements. > > what the heck! > > thanks all > > Ainsley Davis >
Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
Clearly a few interesting entries . 2) in the context of PX, only the total "B factor" contribution to Fcalc needs to be positive definite, the TLS component might not be (though it is satisfying if it is) 3) how do you calculate the "TLS origin" ? The PDB entries should contain the origin of the coordinate system to which the TLS parameters refer, and thus it is something you choose not something you calculate. You are perhaps comparing the origin used by refmac with the centre of reaction ?? Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Pavel Afonine Sent: Wed 3/12/2008 10:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB Hi Dale, a few of my observations regarding this issue: 1) A quick run over all TLS containing models in PDB results in this list of models with incorrect TLS selections or other artifacts (see "errors1" file, attached). 2) A lot of reported TLS matrices in PDB are not positive definite. You can easily verify it (I did). 3) Reported TLS origins are not always the same if you compute them yourself (see "errors2" file, attached). This file shows the distance between reported and re-computed TLS origin for each group. 4) Some files contain residual B-factors (Btotal-Btls), and some files contain total B-factors (Bresidual + Btls). ... I have a *very* long list. I re-refine all PDB models (for which data are available) from time to time -:). Let me know if interested. And finally, how you like the anisotropic B-factors in this file -:) http://www.rcsb.org/pdb/files/2atb.pdb Without some prior re-refinement you have almost no chances to reproduce the R-factors for most of these structures. Cheers, Pavel. --- Pavel V. Afonine, Ph.D. Lawrence Berkeley National Lab, Berkeley CA, USA (http://www.lbl.gov/) CCI: Computational Crystallography Initiative (http://cci.lbl.gov/) PHENIX (http://phenix-online.org/) On 3/12/2008 2:20 PM, Dale Tronrud wrote: > Hi, > >I am looking over a number of models from the PDB but have been > unable to reproduce the R-factors for any model that was refined > with Refmac and contains TLS parameters. I usually can't get within > 5% of the reported value. On the other hand, I usually do pretty > well for models w/o TLS. > >An example is the model 1nkz. The PDB header gives an R value > of 17% but even when I use tlsanal in CCP4i to generate a PDB with > anisotropic B's that mimic the TLS parameters I get an R value of > 22.4% using SFCheck. (I'm not implying that I suspect any problem > with 1nkz, in fact I have every reason to believe this is the great > model its published stats indicate.) > >I've found a CCP4 BB letter that stated that SFCheck does not > pay attention to anisotropic B's but that letter was dated 2002. > I hope this limitation has been removed, or at least the output > would mention this limitation. > >Setting up a refinement in Refmac involves a large overhead, > since even for zero cycles of refinement the program insists on > a complete stereochemical definition for the strange and wondrous > groups in this model. I would just like to verify the R factor > and calculate a proper map for inspection in Coot. Since I have > many models I would like to look at, I would like a simple procedure. > >I did set up a Refmac run for another model, for which I do > have all the .cif's required, but even after refinement I was not > close to the reported R. > >I see that the models I'm interested in are not present in the > Electron Density Server, so I suspect I'm not alone in fighting > this battle. > > Any advice would be appreciated, > Dale Tronrud
Re: [ccp4bb] Summary: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
Refmac (at least 5.2) and TLSANL write a line into the PDB header specifying what is in the B column: REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY Looking at 2qua which used Refmac 5.3, that line isn't there. I don't know at what stage it has been lost. Of course, it would be nice if all the TLS stuff was in dedicated header records. Note that you can use TLSANL to recover residual B from combined B (given TLS parameters), see keywords BRESID and ISOOUT. Note also you would need ANISOU records to reproduce R factors - combined B would not be enough. Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Pavel Afonine Sent: Tue 3/18/2008 1:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Summary: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB >> 2) Some files list in the ATOM "B" column the residual B after TLS >>has been accounted for while others list the total B (TLS and >>residual). There is no clear indication in the PDB file which >>interpretation is being used. >> > > That is a fundamental deficiency in the existing PDB standard. It simply > doesn't specify how to present this critical information. A draft change > covering this was circulated at the PDB get-together of last summer's ACA > meeting, and I discussed with Garib and Eleanor that we should as a community > decide how we would like it handled. The consensus as I understand it is > that people would prefer that the B field of individual ATOM records contain > the *net* B rather than the residual B, so that old programs will continue > to work as expected. However, this puts even more importance on the TLS > description in the header being correct, since the information is otherwise > not recoverable. We were going to circulate a letter, but I plead guilty > to letting the matter slide. > This is exactly what phenix.refine does (since 2005, I guess): it always prints out the total B-factor for each atom (Bindividual+Btls+Boverall). The TLS information (TLS matrices, origin coordinates and TLS group selections) are reported as well in PDB file header, so if necessary one can always extract the information about individual contributions. This makes it more straightforward to reproduce the R-factor statistics without any prior manipulations with the model. > Another notable omission is > the lack of scattering factors. If you have refined a SAS data set, > e.g. a Se-edge dataset of a SeMet metallo-protein, then the R factors may > vary by >1% just because of incorrectly reproduced f' terms for the > Se and metal atoms. > > Ethan Merritt > phenix.refine also always reports f' and f'' in output PDB file if they were used in refinement. I hope they don't get stripped off when deposited with PDB. Pavel.
Re: [ccp4bb] PRODRG?
Yes, it is down at the moment, due to a hacking event apparently. Don't know any more. Martyn -Original Message- From: CCP4 bulletin board on behalf of Harry M. Greenblatt Sent: Wed 3/19/2008 1:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PRODRG? BS"D Hi all, Does anybody know what happened to the PRODRG server web site? Thanks Harry - Harry M. Greenblatt Staff Scientist Dept of Structural Biology [EMAIL PROTECTED] Weizmann Institute of SciencePhone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel
Re: [ccp4bb] [phenixbb] Rant: B vs TLS, anisou, and PDB headers
> 2) All you need to reproduce the R-factors are the ATOM records and > structure factor formula (and not ATOM records, PDB header with TLS > records that sometimes may be lost or manipulated and specific > converting programs to add TLS contribution). Also note, that not all > programs extract TLS information from PDB header to compute R-factors, > but ALL programs can read ATOM records. As you have stated this, it is not true. The big plus with TLS is that it models anisotropic displacements, which are not described in ATOM lines. You would need to include the (derived) ANISOU lines to reproduce R-factors. I bring this up again, because I feel undue respect is given to the total B factor (I have heard it called the "true" B factor - I have no idea what kind of truth that is!). Anyway, these are all different representations of the same thing, and should work equally well so long as you know which you are using. The scariest thing from the last thread was that our attempt to document it with a REMARK 3 line is being stripped by the RCSB. Cheers Martyn
Re: [ccp4bb] 3D structure based alignment
Just to point out that the CCP4 wrapper to SSM "superpose" allows you to specify residue ranges to consider - very useful for multi-domain proteins. See the -s switches in http://www.ccp4.ac.uk/dist/html/superpose.html I'm not clear if this was your issue. Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Tânia Oliveira Sent: Fri 3/28/2008 5:20 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 3D structure based alignment 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] Rant: B vs TLS, anisou, and PDB headers
Yep, agree completely! My point was that if you try to bypass the TLS parameters, then you still need to retain the anisotropic component somehow. But I wasn't advocating it. I believe the simplest and most honest thing to deposit are the parameters of your model, viz the TLS parameters and the residual B factors. Derived quantities should be calculated as and when you need them. But I recognise there are genuine concerns about the lack of software support for new (?) model parameterisations. There is software for inter-converting but it is not always used, and you don't always know what you are starting with. m -Original Message- From: CCP4 bulletin board on behalf of Robbie Joosten Sent: Sat 3/29/2008 8:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rant: B vs TLS, anisou, and PDB headers ANISOU records imply that individual anisotropic B-factors were refined. This will cause problems when you try to redo the final refinement: you add loads of parameters all of a sudden. Using ANISOU records may give you more reliable information about the B-factors, but not about the refinement. Cheers, Robbie Joosten From: "Winn, MD (Martyn)" <[EMAIL PROTECTED]> Sent: Saturday, March 29, 2008 20:57 To: Subject: Re: [ccp4bb] [phenixbb] Rant: B vs TLS, anisou, and PDB headers >> 2) All you need to reproduce the R-factors are the ATOM records and >> structure factor formula (and not ATOM records, PDB header with TLS >> records that sometimes may be lost or manipulated and specific >> converting programs to add TLS contribution). Also note, that not all >> programs extract TLS information from PDB header to compute R-factors, >> but ALL programs can read ATOM records. > > As you have stated this, it is not true. The big plus with TLS is that it > models anisotropic displacements, which are not described in ATOM lines. > You would need to include the (derived) ANISOU lines to reproduce > R-factors. I bring this up again, because I feel undue respect is given to > the total B factor (I have heard it called the "true" B factor - I have no > idea what kind of truth that is!). > > Anyway, these are all different representations of the same thing, and > should work equally well so long as you know which you are using. The > scariest thing from the last thread was that our attempt to document it > with a REMARK 3 line is being stripped by the RCSB. > > Cheers > Martyn >
Re: [ccp4bb] Scala summary and log file- sometimes shortened
Note the appearance of "Normal Termination" in the middle of the table. So I think it is this problem: http://www.ccp4.ac.uk/problems.php#6.0.0-gfortran-unbuffered-22May2006 i.e. the GFORTRAN_UNBUFFERED_ALL one. Martyn -Original Message- From: CCP4 bulletin board on behalf of hari jayaram Sent: Thu 4/24/2008 9:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Scala summary and log file- sometimes shortened Hello everyone, It seems that the reason I get "short summaries" in scala is because the "Show Summary button" is affected by a possible intermitently appearing change in scala log file formatting. When I looked for the text "Summary" in the log file I did find the entire table -intact. SO just for completeness - here is what the "Show summary" gave . And below this I have the intact summary in the log file. It seems like ccp4i "Show summary" button for scala log file viewing does not include the entire table in the window everytime. Summary data for Project: cy Crystal: P10_2 Dataset: P10_2 Overall InnerShell OuterShell Low resolution limit 102.06102.06 2.11 High resolution limit 2.00 6.34 2.00 Rmerge 0.252 0.112 5.247 Rmeas (within I+/I-) 0.269 0.118 6.982 Scala: ** Normal termination ** Times: User: 403.8s System:7.8s Elapsed: 6:52 ### INTACT summary: When I do Full log file view : I get the entire summary Summary data for Project: cy Crystal: P10_2 Dataset: P10_2 Overall InnerShell OuterShell Low resolution limit 102.06102.06 2.11 High resolution limit 2.00 6.34 2.00 Rmerge 0.252 0.112 5.247 Rmeas (within I+/I-) 0.269 0.118 6.982 Scala: ** Normal termination ** Times: User: 403.8s System:7.8s Elapsed: 6:52 Rmeas (all I+ & I-)0.269 0.118 6.982 Rpim (within I+/I-)0.091 0.036 4.552 Rpim (all I+ & I-) 0.091 0.036 4.552 Fractional partial bias -0.113-0.122-1.163 Total number of observations 1458009111004 8307 Total number unique 212719 9864 4327 Mean((I)/sd(I)) 6.4 16.6 0.3 Completeness67.9 99.6 9.4 Multiplicity 6.9 11.3 1.9 ### User: hari Run date: 22/ 4/2008 Run time: 16:39:47 On Tue, Apr 22, 2008 at 4:14 PM, hari jayaram <[EMAIL PROTECTED]> wrote: > For some reason scala does not output the same log file for me everytime. I > got used to looking at the summary for my scala run, using the Show summary > button in ccp4i after picking view log file. > In most cases I get a detailed summary. For this particular dataset , > despite not changing any parameters in the GUI I get a very shortened > summary. > Is it that I clicked some button by mistake, that shortens the log-summary. > > I am using the latest version of ccp4 6.2.2 and fink installed ccp4 on OSX > Leopard. > I am reproducing the short and long summary here. > > Thanks for your help > Hari Jayaram > > > BAD Case: > > Summary data for Project: cy Crystal: P10_2 Dataset: P10_2 > >Overall InnerShell OuterShell > > Low resolution limit 102.06102.06 2.11 > High resolution limit 2.00 6.34 2.00 > > Rmerge 0.252 0.112 5.247 > Rmeas (within I+/I-) 0.269 0.118 6.982 > Scala: ** Normal termination ** > Times: User: 404.5s System:8.0s Elapsed: 6:53 > > > > GOOD case: > > Summary data for Project: cy Crystal: p10_1 Dataset: p10_1 > >Overall InnerShell OuterShell > > Low resolution limit 102.60102.60 2.12 > High resolution limit 2.01 6.35 2.01 > > Rmerge 0.164 0.053 3.283 > Rmeas (within I+/I-) 0.183 0.058 4.363 > Rmeas (all I+ & I-)0.183 0.058 4.363 > Rpim (within I+/I-)0.080 0.021 2.835 >
Re: [ccp4bb] [Re: [ccp4bb] warp/arp 7.0.1 to really use the Free R flag] - Summary
Yes, the Rfreeflag column should be of type I, see e.g. "Output:" section of
http://www.ccp4.ac.uk/dist/html/freerflag.html
And this is what ccp4i expects, see $CCP4/etc/types.def
But not all programs will check it.
In fact, the type changed from W to I in 1995, back in the days when free R was
still new and exciting.
Cheers
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of iulek
Sent: Sun 5/18/2008 12:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] [Re: [ccp4bb] warp/arp 7.0.1 to really use the Free R flag] -
Summary
Hi,
Concerning this point, it turned out that some scripts of mine (for
some historical good reasons) attribute "R" as column type for my
r-free-flag column. Changing it to "I" (which I think is more ccp4
standard) solved the problem. According to what I talked to Anastassis,
that must be a requirement from ccp4i. For several other programs there
was no problem (although I must recognize that I make a very limited use
of the ccp4 interface, ccp4i). Anyway, I will attach more to the
conventions, now.
Jorge
Original Message
Subject:{Spam?} Re: [ccp4bb] warp/arp 7.0.1 to really use the Free R
flag
Date: Tue, 29 Apr 2008 11:01:41 +0200
From: Anastassis Perrakis <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
CC: CCP4BB@JISCMAIL.AC.UK
References: <[EMAIL PROTECTED]>
Dear Jorge,
I was unable to reproduce the error you report with 7.0.1.
I selected an MTZ file, then chose 'use' FreeR flag and I run the job.
I get:
#CCP4I VERSION CCP4Interface 1.4.4.2
#CCP4I SCRIPT LOG arp_solvent
#CCP4I DATE 29 Apr 2008 10:56:28
#CCP4I USER Tassos
...
mtz labels taken: FP SIGFP FreeR_flag
...
FreeR will be used for monitoring and sigmaa calculations
...
Starting model: After refmac, R = 0.162 (Rfree = 0.170)
Could you please try to do the same with first building the standard
example (psp) and then adding waters?
It might be a problem with your mtz file.
Tassos
On Apr 28, 2008, at 15:22, [EMAIL PROTECTED] wrote:
> Hi all,
>
>We recently installed arp/warp 7.0.1 under ccp4i (CCP4_6.0.2).
> The installation went fine. We just wanted to add water molecules to
> the current model. We toggle to "use" in the box
>
> "For refmac5 refinement do -use- the Free R flag"
>
>Also, we choose the due flag in the box
>
> Determine the free R label for reflections to be escluded from
> refinement -FreeR_flag-"
>
>When we ask the program to run, it does, but without using the
> Free R-flag; it says "FreeR will not be used" in the log file and
> the R-free is reported as 0.000. Curiously, the box where the free R
> label is becomes blank.
>We googled and searched archive lists (both warp and CCP4).
>What the problem might be ?
>
> Jorge
Re: [ccp4bb] Rotation axis
ROTMAT will also do this. But I am not sure that this is what Phil wants? The superposition transformation includes a translation, so there is no locus of points that are left unchanged. You can generate an axis of rotation for polar angles from the R which will be quite different from t. You should be able to translate the rotation axis (change the origin of the coordinate system) to get a new transformation x' = R'x + t' which might be better for visualisation. If Phil's last sentence is right, you should be able to arrange it so that t' is parallel to the rotation axis of R' No, I don't know how to do this off the top of my head, but it sounds very similar to the transformations done in the Schomaker and Trueblood TLS paper. Or maybe this is over-complicating things ;-) Martyn -Original Message- From: CCP4 bulletin board on behalf of [EMAIL PROTECTED] Sent: Tue 7/29/2008 1:32 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rotation axis Dear Phil, Because question keep popping up in the bullitin board about conversion from a rotation matrix into rotation angles, I decided to take the relevant subroutines from an old program from Groningen and make a jiffy to do these conversions. It is a small fortran program and does not need any additional libraries or subroutines. The program will take a rotation matrix and translation vector and print all kind of rotation angles and also the component of the translation vector parallel to the rotation axis, which is the number you want. All other components of the translation vector can be made zero by choosing the right position of the rotation axis. Best regards, Herman Schreuder -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans Sent: Tuesday, July 29, 2008 10:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rotation axis If I've go a superposition transformation (x' = Rx + t), as it happens from a superposition in ccp4mg, how do I get the position & direction of the rotation axis (to draw in a picture)? I know that any (orthonormal) transformation can be represented as a rotation about an axis + a screw translation along that axis I'm sure I've done this before ... thanks Phil
Re: [ccp4bb] installing Phaser EP
Well, in case of installation difficulties, you can always contact the friendly and helpful staff at [EMAIL PROTECTED] . ;-) Unfortunately, our friendly and helpful Mac expert is away at the moment, but I can try to help. If you follow through to the Mac download page, you have a few choices. Which ones did you try? The ftp site also has a few combinations which are not linked on the downloads page. If you do have the right package, it may be that the update of ccp4i went wrong for some reason. You may need to do a manual System Administration -> Install/uninstall Tasks HTH Martyn -Original Message- From: CCP4 bulletin board on behalf of James Whittle Sent: Sun 10/26/2008 4:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] installing Phaser EP Hi all- I'm trying to get Phaser EP working through ccp4i on an intel Mac. I've tried re-installing both ccp4 and phaser from the automatic downloads section of the website, but Phaser EP still does not appear in the program list. Can anyone suggest how to fix this? --James
Re: [ccp4bb] 6.1 release date
At a recent developers' meeting we predicted a release date 2 weeks from now.* Meanwhile, the previously announced test release series is pretty stable, and much better than 6.0.2, so it is worth a try. HTH Martyn * Calculation done assuming: 1) testing reveals 0 problems, 2) none of our collaborators talk to us, 3) we get invited to no meetings. For more details of the reliability, see Supplementary Information. -Original Message- From: CCP4 bulletin board on behalf of Bernhard Rupp Sent: Mon 11/10/2008 6:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 6.1 release date Dear Developers, is there a more or less reliable release date/target for 6.1? Thx, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
Re: [ccp4bb] Restrictions in ccp4-6.1 ?
The current value of maxbat in scala_/parameters.fh is 5000 Mind you, according to CVS this was increased from 1000 to 5000 in 1999! sortmtz and reindex also have MBATCH=5000. There's no restriction in the library itself. Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Mueller, Juergen-Joachim Sent: Tue 12/9/2008 7:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Restrictions in ccp4-6.1 ? Dear developers, I wonder if the restrictions for MBATCH=1000 in CCP4-v6.0.2 and for scala (maxbat=1000,maxpmr=2000,maxmat=1000, maxrun=3) hold also in V6.1? Otherwise I cannot use the precompiled versions and have to recompile!? Thank you, Jürgen
Re: [ccp4bb] NCS restraints of domains
Sounds like a good candidate for (domain-level) TLS to me. Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Nicholas Keep Sent: Thu 1/8/2009 10:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] NCS restraints of domains I am refining a low (3A) resolution structure of a 3 domain protein. There are 4 copies in the ASU. I have been applying tight NCS restraints by domain in refmac and have pulled the weak MR solution down to Rfree below 30 (just). However my question is that in 2 of the 4 copies one of the domains is very poorly resolved. I can lower Rfree by around 0.5% by omitting the domains from the PDB entirely or not applying the NCS restraints to these copies of the domain. Clearly they are there and should resemble the moderately well resolved copies by coordinates but the way Bfactor restraints are applied between NCS copies seems to be the issue. If tight restraints are included the B factors are much lower (30-40) rather than 60-80 for the poor domains. I was wondering if there is a theoretically correct way to treat this? Would applying TLS scaling to each domain lead to the residual B factors being more balanced? Can a B factor offset be applied to the NCS restraints or could I only apply a coordinate restraint not a B factor restraint between certain copies? Comments welcomed especially from Garib. Happy New Year Nick -- Dr Nicholas H. Keep Dean of Faculty of Science Reader in Structural Biology School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G57 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] Replacement for arp_waters?
Part of the reasoning was that arp_waters corresponded to a very old version of arp/warp It was felt that up-to-date arp/warp and/or findwaters covered the functionality. Of course, every implementation does things in a slightly different way, and each has their fans. Which means it is hard to deprecate anything. Which means the suite bloats ... Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Roger Rowlett Sent: Tue 1/20/2009 7:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Replacement for arp_waters? I will second noting the loss of arp_waters in CCP4 6.1. I know there is a "find waters" option in Coot 0.5.2 under "Calculate...Other modeling tools", and perhaps this is adequate, but it doesn't seem to have as many options for fine-tuning as arp_waters did. Coot allows for finding waters above a certain sigma value; arp_waters allowed this option plus setting minimum and maximum hydrogen bonding distances between heavy atoms. At any rate, it was very handy to have this option for refmac for both Windows and Linux platforms, especially for teaching new users or undergraduates working in the CCP4i environment. I suppose I can always add ARP/WARP to CCP4i in the Linux environment, but that leave Windows users out in the cold. Just my 2 cents. 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: rrowl...@mail.colgate.edu David J. Schuller wrote: I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] TLS Create/Edit module error erases project folder
Well, I am sure this is not meant to happen. It doesn't seem to happen with my 6.1 version First question: are you sure that the project directory really has gone? Rather than it no longer showing in ccp4i. Check for the directory in a terminal window. If it has really gone, then you have to rely on your disk backup. If it is still there, then you should be able to reload it via Directories&ProjectDir Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Michael Jackson Sent: Fri 2/6/2009 3:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] TLS Create/Edit module error erases project folder Hello, I was using the TLS Create/Edit module to create a TLS file from scratch. In the module I ran it once but wanted to change some parameters. While I had the module interface still open, I selected to delete the TLS project entry just made in the list of jobs. When I did this I did not realize it was going to erase the entire project directory I was currently in. There was a warning that it was going to erase a directory but I thought it was some created subdirectory in the project folder when I had ran the TLS module intially. I did not have any trace back or log file to recover to send with this message. I am using the ccp4 6.0.2 with the interface 1.4.4.2 versions on a linux intel dual core PC using Fedora 9 OS.
Re: [ccp4bb] Low-level disable ccp4i database...?
Well, the guys may have distributed a phx-specific configure file, but
otherwise, I think it is USE_DBCCP4I_ON_STARTUP in ~/.CCP4/unix/configure.def
At least it worked for me after the briefest of tests of the Windows equivalent.
Cheers
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Frank Von Delft
Sent: Mon 4/20/2009 11:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Low-level disable ccp4i database...?
Panic, I'm trying to configure ccp4i for a tutorial (i.e. multiple clueless
students about to descend on the same user account), but the DB handler is
somehow not responding, nor will it let me get to System Administration to turn
it off. ("I'm sorry Dave, I'm afraid I can't do that.")
(Ref Ronan Keegan's reply on 18 March 09 on the BB.)
What is the low-level way to turn it off? It must be either in the
installation directory, or in ~/.CCP4 somewhere, but I couldn't find it.
Hope someone's solved this before...
phx
Re: [ccp4bb] TLSANL gives zero off-diagonal ANISOU matrix in CCP4 6.1
Apologies, this was a bug introduced by a recent change. It is fixed and will be in 6.1.2 Martyn -Original Message- From: CCP4 bulletin board on behalf of Alejandro Buschiazzo Sent: Thu 5/21/2009 6:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] TLSANL gives zero off-diagonal ANISOU matrix in CCP4 6.1 Dear all, I have observed a strange behavior when using TLSANL (v. 3.8) under CCP4 6.1.0 : using identical input (only coordinates have changed a bit after some TLS+restrained refinement) what used to work perfectly well before (under CCP4 6.0), now gives an evidently wrong calculation, resulting in writing final ANISOU matrices with U(1,2), U(2,3) and U(1,3) equal to zero. Otherwise the program does run and finishes properly without explicit errors or warnings. the input is simple : ANISO BINPUT t BRESID t ISOOUT FULL END (seeking to end up with a B-factor column ont the ATOM cards containing the isotropic equivalent of the TOTAL ADP (including TLS); this generates ANISOU cards describing the TLS modelization for each atom included in TLS domains; although I am aware that this is still matter of debate, this 'seems' to be the most correct way to communicate what has been done, otherwise REFMAC5 will just leave the residual B fac on the ATOM card, giving somewhat 'misleading', frequently extremely low values) Any help on this TLSANL problem will be very much appreciated! Best, -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185
Re: [ccp4bb] mtz2various is broken [ was: Another pointless question ]
I didn't mean to commit to a particular solution. That wouldn't be wise on a Friday night with jet lag ;) As an internal call in mtz2various, it should use symops ... but I need to check that this works. Spacegroup number vs name is an issue for the user interface (graphical or otherwise). We always try to support as many "standards" as possible, but there will always be ambiguities. m -Original Message- From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com] Sent: Fri 6/12/2009 10:45 PM To: Winn, MD (Martyn) Cc: CCP4BB@JISCMAIL.AC.UK; Kevin Cowtan; Phil Evans; Ethan Merritt; Eleanor Dodson Subject: RE: [ccp4bb] mtz2various is broken [ was: Another pointless question ] Hi Martyn Since seeing Ethan's last posting I guessed immediately, following on from what Kevin had said earlier, that the program in Ethan's sequence which made the change from SG #4005 to #5 in the MTZ header (and my tests confirm this) is ctruncate; this behaviour presumably is a feature of the Clipper library, so I guess is common to all programs using Clipper (though pointless appears to be an exception - presumably because it specifically creates the 4005 code rather than simply transferring it from input to output). All the other programs in his sequence copy the SG #4005 unchanged. So essentially the problem is an incompatibility between the old (c)symlib and the Clipper library; the former still uses the old conventions that 1) the SG number uniquely identifies alternative settings corresponding to a given standard setting, and 2) the SG number takes precedence over the SG name and/or symm ops to determine the space group, whereas the latter doesn't use unique numbers to identify alternative settings, and assumes the reverse precedence. You suggest changing MSYMLB3 to fix this, i.e. essentially changing it to conform to the symlib documentation (!), so that the SG name takes precedence over the number - I agree this ought to work. The only issue I see is that many programs (e.g. see several examples of this usage in SFALL documentation) allow user input of either the SG name or number, e.g. in SFALL, PDBSET etc: SYMM I2 and SYMM 4005 are equivalent. If we are going to move to the new Clipper-style convention I wonder how this would be handled, if the SG numbers no longer uniquely identify the setting. I guess we would lose this rather useful (IMO at least) feature! I assume you would at least continue to allow use of CCP4-style SG numbers via MSYMLB3 - all our internal scripts rely on this feature. Cheers -- Ian > -Original Message- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of Martyn Winn > Sent: 12 June 2009 20:46 > To: Ethan Merritt > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] mtz2various is broken [ was: Another pointless > question ] > > Apologies, have been away. I hope I have extracted the relevant points > from this thread. > > For the record, the CCP4 library also uses the symops to determine the > spacegroup, when it can. Hence the observation below that mtzdmp and > refmac find the right spacegroup. > > However there are plenty of cases where the symops are not available, > PDB files with CRYST1 card only, user keywords, etc. And there is plenty > of independently developed application code which may not follow the > library (bearing in mind that we are an anarcho-syndicalist commune etc > etc). > > Ian is right that the surest way of checking the MTZ file is to open in > a text editor. You can also edit the SYMINF line this way, though this > is probably classed as advanced ccp4 usage... So in my tests > > SYMINF 4 2 I 4005 'I 1 2 1' PG2 > > works fine, while > > SYMINF 4 2 I 5 'I 1 2 1' PG2 > > shows the problem. And yes, the problem is then MSYMLB3 using the 5 > rather than the spacegroup name or the operators. We should be able to > fix that. > > 4005 is for internal usage, converting to 5 on export from the suite. > Probably the generating program should have used 4005. > > Cheers > Martyn > > > My mtz file contains > > CELL 148.6099 98.3798 251.9687 90. 90.3258 90. > > SORT1 2 3 0 0 > > SYMINF 4 2 I 5 'I121' PG2 > > SYMM X, Y, Z > > SYMM -X, Y, -Z > > SYMM X+1/2, Y+1/2, Z+1/2 > > SYMM -X+1/2, Y+1/2, -Z+1/2 > > RESO 0.607290094194 0.1371708661317825 > > > > So there is a difference, but not the expected one. > > My mtz file has exactly the info that should go into the cif headers, > > including the space group number of the standard setting: 5. > > But mtzdmp and refmac, etc, do manage to find and report the spacegroup > > as 4005 f
