> -----Original Message----- > From: Ethan Merritt [mailto:merr...@u.washington.edu] > Sent: 11 June 2009 00:35 > To: Ian Tickle > Cc: CCP4BB@jiscmail.ac.uk; Phil Evans > Subject: Re: mtz2various is broken [ was: Another pointless question ] > > On Tuesday 09 June 2009 02:45:41 Ian Tickle wrote: > > > > Ethan - that's odd it works for me (CCP4 6.1.0) unless of course it got > > broken recently in 6.1.1: > > I see the same problem in both 6.0.2 and 6.1.1. > I don't have a copy of 6.1.0 around to test.
I just compiled 6.1.1 mtz2various.f with 6.1.1 CCP4 libs & I get identical results (i.e. log & CIF files) with 6.1.0. Differences between the source versions are minor (related only to CIF line length). Also there are minor formatting differences betweeen 6.0.2 & 6.1.x, but symmetry info is identical. So it's not a version issue, but must be what's in the MTZ file header. Have you looked at the file header, does it contain the right symmetry operators? Most programs including mtzdump don't bother to print these out but blithely assume that they are consistent: the mtztona4 program writes out the complete file header in ascii, or you can just open the MTZ file in a text editor (as long as it doesn't mind the non-ascii characters and the long lines!). Here's the relevant bit of mine: CELL 70.3025 68.7834 93.7125 90.0000 94.1913 90.0000 SORT 1 2 3 0 0 SYMINF 4 2 I 4005 'I2 ' 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 END If I change 'I2' to 'I121' to look like yours I still get the same results, so that's not the problem. > > Your version fails to convert space group "4005" to "5". True, but at least it gets the space group name and the symmetry operators right! I think the conversion from '4005' to '5' in your case is not intentional! Cheers -- Ian > > I am running 6.1.1 built from the source tarball. > This version does convert "4005" to "5", but then it makes the > mistake in subroutine wcifhr(mtzin,iun,dbhead) of calling > C--- Change short H-M symbol to full CIF-style symbol: > call MSYMLB3(24,nspgrx,spgrnx_cif,spgrnx_cifs,pgnamx, > & nsympx,nsym,rsym) > > which looks up the space group name and symops based on the converted > number. > Having done that, it now thinks the space group is C2, even though > the cell parameters and reflection indices are not correct for that > setting. > > So both versions are broken, but in different ways. > > I have not been able to track down which routine in which source file > was changed. But since I see the same problem in 6.0.2, I'm not sure > there > _is_ a difference in the source files I have on hand. Is it possible that > this was partially fixed for 6.1.0 but then reverted because of the > problem you > report, leaving it broken again? > > Ethan > > > > First an extract from the mtz2various log file: > > > > * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) > > > > 70.3025 68.7834 93.7125 90.0000 94.1913 90.0000 > > > > * Resolution Range : > > > > 0.00030 0.24999 ( 58.124 - 2.000 A ) > > > > * Sort Order : > > > > 1 2 3 0 0 > > > > * Space group = 'I2' (number 4005) > > > > > > Then the CIF output: > > > > ########## > > # # > > # CELL # > > # # > > ########## > > > > > > _cell.entry_id junk > > _cell.length_a 70.3025 > > _cell.length_b 68.7834 > > _cell.length_c 93.7125 > > _cell.angle_alpha 90.0000 > > _cell.angle_beta 94.1913 > > _cell.angle_gamma 90.0000 > > > > > > ############## > > # # > > # SYMMETRY # > > # # > > ############## > > > > > > _symmetry.entry_id junk > > _symmetry.Int_Tables_number 4005 > > _symmetry.space_group_name_H-M 'I 1 2 1' > > > > > > #################### > > # # > > # SYMMETRY_EQUIV # > > # # > > #################### > > > > > > loop_ > > _symmetry_equiv.id > > _symmetry_equiv.pos_as_xyz > > 1 'X, Y, Z' > > 2 '-X, Y, -Z' > > 3 'X+1/2, Y+1/2, Z+1/2' > > 4 '-X+1/2, Y+1/2, -Z+1/2' > > > > The only thing I see is different is that your space group is shown as > > 'I121' whereas mine is just 'I2' > > > > Hope this helps! > > > > Cheers > > > > -- Ian > > > > > -----Original Message----- > > > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] > > On > > > Behalf Of Ethan Merritt > > > Sent: 08 June 2009 21:56 > > > To: CCP4BB@jiscmail.ac.uk; Phil Evans > > > Subject: mtz2various is broken [ was: Another pointless question ] > > > > > > On Friday 08 May 2009 10:36:28 Phil Evans wrote: > > > > I2 is always an alternative setting to C2, & Pointless (by default) > > > > will choose this (since 1.2.12 I think) if it gives a smaller beta > > > > angle than the C2 setting > > > > > > > > I am assured that this is the IUCr approved "standard", along with > > > > always setting primitive orthorhombic space groups with a < b < c > > even > > > > if this makes eg space group 18 P 2 21 21. However, there are some > > > > "old-fashioned" programs :-) which don't like this (arp/warp at > > > > present for example, though I believe this will change in future), > > so > > > > Pointless does offer the option SETTING SYMMETRY-BASED, also an > > option > > > > in the ccp4i GUI, to choose the "reference" setting and C2 > > > > > > A follow-up to this discussion. > > > > > > I finished refinement, and I am ready to deposit with the PDB. > > > However, when I went to produce a *.cif file for deposition, I found > > > that mtz2various is confused by the I2 setting. It kept the cell > > > edges and angles from I2, but created a *.cif output file that claims > > > the cell is C2 and it lists the symmetry operators for C2. > > > > > > I manually corrected the header records in the *.cif file, but the > > > program itself should be fixed as well. > > > > > > I ran: > > > > > > ### CCP4 6.1: MTZ2VARIOUS version 6.1 : 12/11/08## > > > > > > The mtz2various log file contains the line: > > > > > > * Space group = 'I121' (number 5) > > > > > > By contrast, running mtzdmp on the input file it is converting reports > > > > > > * Space group = 'I 1 2 1' (number 4005) > > > > > > > > > cheers, > > > > > > Ethan > > > > > > > > > > Keeping the obliquity of the cell small has some advantages: it may > > > > make map viewing easier, and improve the accuracy of map > > interpolation > > > > in programs which are a bit casual about doing this properly > > > > > > > > Phil > > > > > > > > > > > > On 8 May 2009, at 17:45, Ethan Merritt wrote: > > > > > > > > > I was very surprised recently when a run of pointless chose to > > > > > transform my data into spacegroup I2 [*]. Here are excerpts from > > the > > > > > output log: > > > > > > > > > > %%%%%%%%%%%% > > > > > Selecting space group I 1 2 1 as there is a single space group > > with > > > > > the highest score > > > > > Space group confidence (= Sqrt(Score * (Score - NextBestScore))) > > > > > = 0.37 > > > > > %%%%%%%%%%%% > > > > > The input crystal system is C-centred monoclinic > > > > > (Cell: 291.8 98.38 148.6 90 120.3 90) > > > > > The crystal system chosen for output is body-centred monoclinic > > > > > (Cell: 148.6 98.38 252 90 90.33 90) > > > > > %%%%%%%%%%%% > > > > > > > > > > Notice that the log file output doesn't say, for instance, > > > > > "you might want to consider the non-standard setting I2". > > > > > It says "there is a single space group with the highest score", > > > > > and proceeds to convert away from the standard setting C2. > > > > > > > > > > I am not complaining, as in fact this solved a bit of a mystery > > for > > > > > me. > > > > > The diffraction images had originally been indexed as I222. > > > > > Integration > > > > > proceeded without a hitch, but the data failed miserably to scale > > > > > acceptably. > > > > > Running pointless immediately made clear what the problem had > > been. > > > > > > > > > > Instead I am merely curious. > > > > > What are the criteria that pointless uses to decide such a thing? > > > > > In this case the beta angle is _very_ near to 90. I have fed > > other > > > > > C2 data sets to pointless and not seen even a mention of I2 in the > > > > > output. Is the "score" mentioned in the log file some weighted > > > > > function that > > > > > says the closer beta approaches 90 after re-indexing, the more > > that > > > > > re-indexing is preferred? > > > > > > > > > > Ethan > > > > > > > > > > > > > > > [*] Not least because I had never previously encountered "I2" as > > the > > > > > name of a spacegroup. Live and learn. > > > > > > > > > -- > > > Ethan A Merritt > > > Biomolecular Structure Center > > > University of Washington, Seattle 98195-7742 > > > > > > > > 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 i.tic...@astex-therapeutics.com 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 > > > > > > > > > > -- > Ethan A Merritt > Biomolecular Structure Center > University of Washington, Seattle 98195-7742 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 i.tic...@astex-therapeutics.com 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
