Re: [ccp4bb] Fd-3m with pdbset - test pdb file
Dear bulletin board, Tim asked me for the pdb file I used for testing (coot version 0.6), which I have attached here. It is a totally artifical pdb file with one random small ligand in it. Using a symmetry radius of 50 Angstrom, one can get an idea of the symmetry in 'F d -3 m'. If in Tim's case with a real protein coot comes to a grinding halt, it looks to me more like a question of memory management than a problem with the symmetry definitions. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of herman.schreu...@sanofi-aventis.com Sent: Monday, September 06, 2010 2:44 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fd-3m with pdbset Hi Tim, The string 'Fd-3m:1' is recognized by pdbset, but still produces 'F d -3 m :'. I did a test with a single small ligand with coot and if you delete the ':' from the CRYST1 card to make 'F d -3 m' coot happily accepts it and seems to produce the correct symmetry mates. I hope that this way you are able to display your molecule. I agree that there must be a bug somewhere. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene Sent: Monday, September 06, 2010 1:38 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fd-3m with pdbset Hello, I tried to assign a cell with space group F d -3 m to a PDB file using pdbset. Since it did not recognize the string 'F d -3 m' (nor 'F d -3 m :1') , I used the space group number 227. This resulted in the space group string 'F d -3 m :' in the PDB-file instead of 'F d -3 m :1' as it is listed in syminfo.lib, and hence coot refused to display the symmetry mates for the molecule. When I add the missing '1' in the resulting PDB-file, coot does display the cell, but when I ask to display the symmetry mates, coot chokes and consumed all my cpu power (for 8 molecules present in the unit cell...) until I killed it. I was wondering if this is a known bug in syminfo.lib (and/or the dependent programs) and if there is a way around it (without using phenix.get_me_out_of_here, I could of course use xp instead of coot for such a small molecule). Kind regards, Tim P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A set.pdb Description: set.pdb
Re: [ccp4bb] Reverse Translatase
Hi Jacob- What an intriguing proposition. I can think of multiple reasons why such a system would not exist, but there is a mechanistic one which is most fundamental, having to do with the nature of the genetic code. Say that there is a cellular machine which would unfold a protein and expose it to some sort of reading system (already a hard problem). There is now the issue of transforming the amino acid information into nucleic acid information. For simplicity let's assume that this system only uses one codon per amino acid, bypassing the degeneracy problem. How would the cell then read off the amino acid sequence? It seems the simplest solution would be analogous to translation, i.e. having adaptor molecules analogues to tRNAs which would guide an enzyme that synthesized the nucleic acid. Otherwise, one would have to invoke the idea of a single enzyme recognizing every amino acid, which seems impossible to me. As we know, the problem of protein-protein recognition is relatively complex. At a minimum, one would need 20 adaptor proteins to recognize the 20 canonical amino acids: however, it seems unlikely that recognition of a single amino acid would be robust enough to select for the correct adaptor molecule. So, let's say instead these adaptors recognize 2 amino acids at a time (still probably not robust enough). Then, one would need 2^20 adaptors, already a far greater number of gene products than that present in any genome than I know of... It might be tempting to draw an analogy between this system and the immune system, where an incredible diversity is generated from a small number of genes. However, diverse immune proteins all take the same input sequence (say antigen recognition) and lead to a single response, whereas this system has a 1 to 1 correspondence between inputs (protein sequence) and outputs (nucleic acid sequences), and thus there is no way that a randomization system could generate the required diversity. Cheers, -Greg Alushin Nogales lab UC Berkeley On Sep 6, 2010, at 7:12 PM, Michael Thompson wrote: Jacob, The idea is enticing, but don't forget that there are multiple degenerate codons for a given amino acid. Once the protein is synthesized, the specific codon information is lost. I think that's a fundamental problem. Keep the ideas coming, Mike Thompson - Original Message - From: "Jacob Keller" To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, September 6, 2010 6:36:14 PM GMT -08:00 US/Canada Pacific Subject: [ccp4bb] Reverse Translatase Dear Crystallographers, does anyone know of any conceptual reason why a reverse translatase enzyme (protein-->nucleic acid) could not exist? I can think of so many things for which such an enzyme would be helpful, both to cells and to scientists...! Unless there is something I am missing, it would seem to me conceptually almost impossible that it *not* exist. Best Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] Reverse Translatase
Jacob, The idea is enticing, but don't forget that there are multiple degenerate codons for a given amino acid. Once the protein is synthesized, the specific codon information is lost. I think that's a fundamental problem. Keep the ideas coming, Mike Thompson - Original Message - From: "Jacob Keller" To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, September 6, 2010 6:36:14 PM GMT -08:00 US/Canada Pacific Subject: [ccp4bb] Reverse Translatase Dear Crystallographers, does anyone know of any conceptual reason why a reverse translatase enzyme (protein-->nucleic acid) could not exist? I can think of so many things for which such an enzyme would be helpful, both to cells and to scientists...! Unless there is something I am missing, it would seem to me conceptually almost impossible that it *not* exist. Best Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
[ccp4bb] Reverse Translatase
Dear Crystallographers, does anyone know of any conceptual reason why a reverse translatase enzyme (protein-->nucleic acid) could not exist? I can think of so many things for which such an enzyme would be helpful, both to cells and to scientists...! Unless there is something I am missing, it would seem to me conceptually almost impossible that it *not* exist. Best Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Can CCP4 calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file?
Thanks a lot! > Hailiang Zhang wrote: >> Hi, >> >> I want to calculate the R factor based on the given Fo, Fc, and sigFo by >> a >> mtz file. Can some CCP4 tools do this? Thanks! >> >> Best Regards, Hailiang >> > > Yes- rstats > > something like > > rstats hklin sfall.mtz hklout rescaled.mtz < LABIN FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC > TITLE FP column scaled to FC > #RESOLUTION 999.0 2.6! default is 1 to 100 Ang > PRINT LAST! default is LAST > CYCLES 10 ! default is 6 > !LIST 0 > OUTPUT FOFC! default is FOFC > SCALE 1.0 ! 52.5 ! default is 1.0 > !REJECT DELTA 4000 ! default is no rejections > WEIGHTING_SCHEME NONE ! default is NONE > WIDTH_OF_BINS RTHETA=0.005 FBINR=100! defaults are .01 and 1000 > PROCESS FCAL ! default is FCAL > eof-rstats > > > This will rescale Fc to Fo or vice versa, depending on "process". > But if they are already optimally scaled that shouldn't make any > difference. > it prints out R and weighted R in bins and overall. > > OR, scaleit, using > labinFP=FP SIGFP=SIGFP FPH1=Fc > And take R-merge on F as R?? > > OR, use fft to calculate an Fc,Phic map and use sfall to calculate > structure factors > from the map (should precisely replicate the input Fc) giving it the Fobs > for reference > >
Re: [ccp4bb] Can CCP4 calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file?
Hailiang Zhang wrote: Hi, I want to calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file. Can some CCP4 tools do this? Thanks! Best Regards, Hailiang Yes- rstats something like rstats hklin sfall.mtz hklout rescaled.mtz <
[ccp4bb] Can CCP4 calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file?
Hi, I want to calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file. Can some CCP4 tools do this? Thanks! Best Regards, Hailiang
Re: [ccp4bb] Fd-3m with pdbset
I was going to say that we could adopt the convention that the
default setting of a centrosymmetric space group is the one with the
origin on an inversion centre, since this is assumed by all programs
that I am aware of, thus making ':2' for 'second setting' unnecessary
and keeping the name to 11 characters. At first glance this would
solve the problem for Ian's two 'long' space groups ('P 42/n n m :2'
and 'I 41/a m d :2') since only the second of the two settings given
in volume A of International Tables has the origin on an inversion
centre. However as chance would have it, both these space groups have
another alternative non-equivalent setting that also has the origin
on an inversion centre but this third setting is not given in volume
A of the IT!
Perhaps I should mention that with the SHELX method of specifying
the space group symmetry using the symmetry operators, alternative
settings, specified in IT or not, cause no problems. But then we
would not have had this thread (or the H3/R3 and P21221 threads).
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
On Mon, 6 Sep 2010, Ian Tickle wrote:
> It seems that it's the new addition of ':n' which has pushed it over
> the limit of the 11 char field. Has this been thought through? I
> can see that the ':n' qualifier is necessary to disambiguate alternate
> origins. Without the redundant formatting spaces 9 chars would be
> sufficient even for 'P 42/n n m :2' which is indeed the longest one at
> 13 chars (also 'I 41/a m d :2').
>
> -- Ian
>
> On Mon, Sep 6, 2010 at 2:57 PM, Martyn Winn wrote:
> >> > There seem to be a few CCP4 Fortran files that have character spgnam*10
> >> > from the good old days ...
> >>
> >> What good old days were those? The Cryst1-format for PDB-files in the ccp4
> >> documentation says
> >> 56-66 Space group symbol, left justified (not used)
> >> which is eleven characters. Were there days when this was different?
> >>
> >> Tim
> >
> > I remember when we didn't bother with spacegroup on the
> > CRYST1 line at all, let alone formatting it correctly.
> >
> > And what about 'P 42/n n m :2' which is more than 11 characters?
> >
> > I realise my answer doesn't help with Coot problems, but I will clean up
> > CCP4 Fortran programs at least.
> >
> > m
> >
> > --
> > ***
> > * *
> > * Dr. Martyn Winn *
> > * *
> > * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
> > * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk *
> > * Fax: +44 1925 603634 Skype name: martyn.winn *
> > * URL: http://www.ccp4.ac.uk/martyn/ *
> > ***
> >
>
>
Re: [ccp4bb] Refmac bref MIXED failed
Hi Garib, I tried with refmac 5.6 and the same inputs; it worked fine. Thanks, Lionel 2010/9/6 Garib N Murshudov > Could you please try refmac 5.6. I think we have fixed this problem. It is > available from: > > www.ysbl.york.ac.uk/refmac/latest_refmac.html > > You need to take experimental version (it is now fairly stable) > > Regards > Garib > > On 6 Sep 2010, at 15:01, Lionel Costenaro wrote: > > > Hello, > > > > When I run Refmac with the mixed iso/anisotripic B-value option (refi > bref MIXED), refmac failed with the error message below. > > My pdb comes from previous refmac runs with anisotropic B values for all > atoms (H generated but not written). > > I just removed from the pdb the ANISOU lines for all water molecules. > > > > Refmac with "refi bref ANIS" (all anisotropic B) works fine (normal > termination) with the same input data and pdb - with all ANISOU lines. > > CCP4Interface 2.0.5 > > Refmac_5.5.0102 > > > > Any comments, help, fix are welcome. > > > > Best regards, > > Lionel > > > > ** > > CGMAT cycle number = 1 > > > > . > > Trying gamma equal0.00 > > Not converging with gamma equal0.00 > > Trying gamma equal 5.503E-02 > > Not converging with gamma equal 5.503E-02 > > Trying gamma equal 0.1155000 > > . > > Not converging with gamma equal2655.967 > > Trying gamma equal2921.619 > > Not converging with gamma equal2921.619 > > Trying gamma equal3213.836 > > Gamma decreased to3155.393 > > > *** > > * Information from CCP4Interface script > > > *** > > The program run with command: /all/programas/ccp4-6.1.2/bin/refmac5 XYZIN > "/data/refmac8-coot-0Wiso.pdb" XYZOUT "/tmp/lcocri/21_2_pdb_1.tmp" HKLIN > "/data/4_unique1.mtz" HKLOUT "/tmp/lcocri/21_3_mtz_1.tmp" LIBIN > "/data/ligand.cif" LIBOUT "/data/21_lib.cif" > > has failed with error message > > child killed: SIGABRT > > > *** > > > > > > #CCP4I TERMINATION STATUS 0 child killed: SIGABRT > > #CCP4I TERMINATION TIME 06 sep 2010 15:28:12 > > #CCP4I MESSAGE Task failed > > > > > > > > > > > > -- ___ Interactions faibles entre protéines en solution Costenaro L. (2010) Editions Universitaires Européennes, ISBN 9786131506048 Livre disponible en francais sur amazon: http://www.amazon.com/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=ISBN+9786131506048&x=0&y=0 ___ Dr. Lionel Costenaro Institut de Biologia Molecular de Barcelona - CSIC and Institute for Research in Biomedicine Parc Cientific de Barcelona C/ Baldiri i Reixac 10-12 E-08028 Barcelona, Spain Phone +34 93 403 49 57 Fax +34 93 403 49 79 Emaillionel.costen...@ibmb.csic.es , lionel.costen...@irbbarcelona.org URL www.ibmb.csic.es , www.irbbarcelona.org
Re: [ccp4bb] Fd-3m with pdbset
It seems that it's the new addition of ':n' which has pushed it over the limit of the 11 char field. Has this been thought through? I can see that the ':n' qualifier is necessary to disambiguate alternate origins. Without the redundant formatting spaces 9 chars would be sufficient even for 'P 42/n n m :2' which is indeed the longest one at 13 chars (also 'I 41/a m d :2'). -- Ian On Mon, Sep 6, 2010 at 2:57 PM, Martyn Winn wrote: >> > There seem to be a few CCP4 Fortran files that have character spgnam*10 >> > from the good old days ... >> >> What good old days were those? The Cryst1-format for PDB-files in the ccp4 >> documentation says >> 56-66 Space group symbol, left justified (not used) >> which is eleven characters. Were there days when this was different? >> >> Tim > > I remember when we didn't bother with spacegroup on the > CRYST1 line at all, let alone formatting it correctly. > > And what about 'P 42/n n m :2' which is more than 11 characters? > > I realise my answer doesn't help with Coot problems, but I will clean up > CCP4 Fortran programs at least. > > m > > -- > *** > * * > * Dr. Martyn Winn * > * * > * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * > * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk * > * Fax: +44 1925 603634 Skype name: martyn.winn * > * URL: http://www.ccp4.ac.uk/martyn/ * > *** >
Re: [ccp4bb] Problem with NCS detection in Parrot
Hi Florian, I have found that, in some cases, playing with -ncs-mask-filter-radius can help parrot to successfully detect and apply ncs averaging. In one recent case, with 8 molecules where NCS was not found without this option, values from 14 to 30 angstroms worked (but gave maps of variable quality). I don't know what's the default value for this. Best regards, Pierre Legrand, PROXIMA-1 Phone-office +33 1 69 35 96 60 Phone-beamline +33 1 69 35 97 38 http://www.synchrotron-soleil.fr/Recherche/LignesLumiere/PROXIMA1 -Original Message- From: CCP4 bulletin board on behalf of Florian Schmitzberger Sent: Fri 9/3/2010 9:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Problem with NCS detection in Parrot Dear All, I am encountering a problem when using Parrot (for combined density modification and non crystallographic symmetry (NCS) averaging) in ccp4 6.1.13, run via ccp4i. Parrot does not detect the (2-fold) NCS present among my heavy atom substructure with 20 seleniums (the pdb was output by Phaser-EP, single chain ID, and is read by Parrot from what I can tell). I have tried a to split the NCS related heavy atoms into separate chains, but Parrot does still not appear to detect any NCS (error message: WARNING: No NCS found from heavy atoms). The Professs program seems to detect the NCS readily. Unfortunately, I don't think it is possible to input externally determined NCS operators into Parrot. Regards, Florian --- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602
Re: [ccp4bb] Refmac bref MIXED failed
Hi, I'm not sure whether it's related to the error you're seeing but as far as I know, in order for refmac to do mixed B-refinement (that is Biso and Baniso) you have to set yourself by editing (!!) the incoming pdb such that whichever atoms you'd like to have Biso refined should have only Biso in the input file. I suggested a while ago that this be fixed to become more elegant (say by specifying range of residues in the gui) but apparently it still works only the old way. Cheers, Boaz - Original Message - From: Lionel Costenaro Date: Monday, September 6, 2010 17:09 Subject: [ccp4bb] Refmac bref MIXED failed To: CCP4BB@JISCMAIL.AC.UK > Hello, > > When I run Refmac with the mixed iso/anisotripic B-value option > (refi bref > MIXED), refmac failed with the error message below. > My pdb comes from previous refmac runs with anisotropic B values > for all > atoms (H generated but not written). > I just removed from the pdb the ANISOU lines for all water molecules. > > Refmac with "refi bref ANIS" (all anisotropic B) works fine (normal > termination) with the same input data and pdb - with all ANISOU lines. > CCP4Interface 2.0.5 > Refmac_5.5.0102 > > Any comments, help, fix are welcome. > > Best regards, > Lionel > > ** > CGMAT cycle number > = 1 > > . > Trying gamma equal 0.00 > Not converging with gamma equal 0.00 > Trying gamma equal 5.503E-02 > Not converging with gamma equal 5.503E-02 > Trying gamma equal 0.1155000 > . > Not converging with gamma equal 2655.967 > Trying gamma equal 2921.619 > Not converging with gamma equal 2921.619 > Trying gamma equal 3213.836 > Gamma decreased to 3155.393 > *** > * Information from CCP4Interface script > *** > The program run with command: /all/programas/ccp4- > 6.1.2/bin/refmac5 XYZIN > "/data/refmac8-coot-0Wiso.pdb" XYZOUT > "/tmp/lcocri/21_2_pdb_1.tmp" HKLIN > "/data/4_unique1.mtz" HKLOUT "/tmp/lcocri/21_3_mtz_1.tmp" LIBIN > "/data/ligand.cif" LIBOUT "/data/21_lib.cif" > has failed with error message > child killed: SIGABRT > *** > > > #CCP4I TERMINATION STATUS 0 child killed: SIGABRT > #CCP4I TERMINATION TIME 06 sep 2010 15:28:12 > #CCP4I MESSAGE Task failed > Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
Re: [ccp4bb] Refmac bref MIXED failed
Could you please try refmac 5.6. I think we have fixed this problem. It is available from: www.ysbl.york.ac.uk/refmac/latest_refmac.html You need to take experimental version (it is now fairly stable) Regards Garib On 6 Sep 2010, at 15:01, Lionel Costenaro wrote: > Hello, > > When I run Refmac with the mixed iso/anisotripic B-value option (refi bref > MIXED), refmac failed with the error message below. > My pdb comes from previous refmac runs with anisotropic B values for all > atoms (H generated but not written). > I just removed from the pdb the ANISOU lines for all water molecules. > > Refmac with "refi bref ANIS" (all anisotropic B) works fine (normal > termination) with the same input data and pdb - with all ANISOU lines. > CCP4Interface 2.0.5 > Refmac_5.5.0102 > > Any comments, help, fix are welcome. > > Best regards, > Lionel > > ** > CGMAT cycle number = 1 > > . > Trying gamma equal0.00 > Not converging with gamma equal0.00 > Trying gamma equal 5.503E-02 > Not converging with gamma equal 5.503E-02 > Trying gamma equal 0.1155000 > . > Not converging with gamma equal2655.967 > Trying gamma equal2921.619 > Not converging with gamma equal2921.619 > Trying gamma equal3213.836 > Gamma decreased to3155.393 > *** > * Information from CCP4Interface script > *** > The program run with command: /all/programas/ccp4-6.1.2/bin/refmac5 XYZIN > "/data/refmac8-coot-0Wiso.pdb" XYZOUT "/tmp/lcocri/21_2_pdb_1.tmp" HKLIN > "/data/4_unique1.mtz" HKLOUT "/tmp/lcocri/21_3_mtz_1.tmp" LIBIN > "/data/ligand.cif" LIBOUT "/data/21_lib.cif" > has failed with error message > child killed: SIGABRT > *** > > > #CCP4I TERMINATION STATUS 0 child killed: SIGABRT > #CCP4I TERMINATION TIME 06 sep 2010 15:28:12 > #CCP4I MESSAGE Task failed > > > > >
Re: [ccp4bb] fail to install ccp4i task for arp warp
On 31 Aug 2010, at 14:56, Jochen Kuper wrote: > sorry to bother you with this but I just can't figure out what goes wrong ... > > I am running the latest version of snow leopard on a MBP unibody with the > 64bit kernel. > > I have an up to date fink installation for native 64bit. I've seen this too - it seems to be due to problems with 64bit bltwish. There is a workaround here: http://proteincrystallography.org/ccp4bb/message13191.html but that unfortunately requires a 32 bit fink installation of CCP4 alongside the 64bit one. I can confirm that this works and once installed ARP/wARP and 64bit CCP4 work together fine. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
[ccp4bb] Refmac bref MIXED failed
Hello, When I run Refmac with the mixed iso/anisotripic B-value option (refi bref MIXED), refmac failed with the error message below. My pdb comes from previous refmac runs with anisotropic B values for all atoms (H generated but not written). I just removed from the pdb the ANISOU lines for all water molecules. Refmac with "refi bref ANIS" (all anisotropic B) works fine (normal termination) with the same input data and pdb - with all ANISOU lines. CCP4Interface 2.0.5 Refmac_5.5.0102 Any comments, help, fix are welcome. Best regards, Lionel ** CGMAT cycle number = 1 . Trying gamma equal0.00 Not converging with gamma equal0.00 Trying gamma equal 5.503E-02 Not converging with gamma equal 5.503E-02 Trying gamma equal 0.1155000 . Not converging with gamma equal2655.967 Trying gamma equal2921.619 Not converging with gamma equal2921.619 Trying gamma equal3213.836 Gamma decreased to3155.393 *** * Information from CCP4Interface script *** The program run with command: /all/programas/ccp4-6.1.2/bin/refmac5 XYZIN "/data/refmac8-coot-0Wiso.pdb" XYZOUT "/tmp/lcocri/21_2_pdb_1.tmp" HKLIN "/data/4_unique1.mtz" HKLOUT "/tmp/lcocri/21_3_mtz_1.tmp" LIBIN "/data/ligand.cif" LIBOUT "/data/21_lib.cif" has failed with error message child killed: SIGABRT *** #CCP4I TERMINATION STATUS 0 child killed: SIGABRT #CCP4I TERMINATION TIME 06 sep 2010 15:28:12 #CCP4I MESSAGE Task failed
Re: [ccp4bb] Fd-3m with pdbset
> > There seem to be a few CCP4 Fortran files that have character spgnam*10 > > from the good old days ... > > What good old days were those? The Cryst1-format for PDB-files in the ccp4 > documentation says > 56-66Space group symbol, left justified (not used) > which is eleven characters. Were there days when this was different? > > Tim I remember when we didn't bother with spacegroup on the CRYST1 line at all, let alone formatting it correctly. And what about 'P 42/n n m :2' which is more than 11 characters? I realise my answer doesn't help with Coot problems, but I will clean up CCP4 Fortran programs at least. m -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] Fd-3m with pdbset
On Mon, Sep 06, 2010 at 02:45:49PM +0100, Martyn Winn wrote: > > Yes, I can reproduce this, and I think I have found the bug. > It is simply that PDBSET dimensions the spacegroup name to 10 > characters. Increasing that to 20 allows you to use either > > spac 'F d -3 m :1' > or > spac 227 > > However, it still won't recognise 'F d -3 m' because this is not in the > syminfo file (at least, not in a field that is read). > > There seem to be a few CCP4 Fortran files that have character spgnam*10 > from the good old days ... What good old days were those? The Cryst1-format for PDB-files in the ccp4 documentation says 56-66Space group symbol, left justified (not used) which is eleven characters. Were there days when this was different? Tim > > Cheers > Martyn > > On Mon, 2010-09-06 at 13:38 +0200, Tim Gruene wrote: > > Hello, > > I tried to assign a cell with space group F d -3 m to a PDB file using > > pdbset. > > Since it did not recognize the string 'F d -3 m' (nor 'F d -3 m :1') , I > > used > > the space group number 227. This resulted in the space group string 'F d -3 > > m :' > > in the PDB-file instead of 'F d -3 m :1' as it is listed in syminfo.lib, and > > hence coot refused to display the symmetry mates for the molecule. > > > > When I add the missing '1' in the resulting PDB-file, coot does display the > > cell, but when I ask to display the symmetry mates, coot chokes and > > consumed all > > my cpu power (for 8 molecules present in the unit cell...) until I killed > > it. > > > > I was wondering if this is a known bug in syminfo.lib (and/or the dependent > > programs) and if there is a way around it (without using > > phenix.get_me_out_of_here, I could of course use xp instead of coot for > > such a > > small molecule). > > > > Kind regards, Tim > > > > P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3 > > > > -- > *** > * * > * Dr. Martyn Winn * > * * > * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * > * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* > * Fax: +44 1925 603634Skype name: martyn.winn * > * URL: http://www.ccp4.ac.uk/martyn/ * > *** -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Fd-3m with pdbset
Dear Herman, thanks for the tip. Unfortunately it does not help with my version of coot (linux, 0.6.1). Coot eats up all my memory (8GB RAM + 4GB swap) until it is being terminated by the OS. Which version of coot are you using? Could you send me your PDB-file that works for you, please (you could even send it plain text to the bb to avoid an attachment...) ? The same happens when I read in an .ins-file which does not contain the space group name or symbol, but provides the symmetry operators themselves. Cheers, Tim P.S.: I'll skip sending a copy to the coot-list since Paul is also reading this one, I am sure. On Mon, Sep 06, 2010 at 02:43:34PM +0200, herman.schreu...@sanofi-aventis.com wrote: > Hi Tim, > > The string 'Fd-3m:1' is recognized by pdbset, but still produces 'F d -3 > m :'. I did a test with a single small ligand with coot and if you > delete the ':' from the CRYST1 card to make 'F d -3 m' coot happily > accepts it and seems to produce the correct symmetry mates. I hope that > this way you are able to display your molecule. I agree that there must > be a bug somewhere. > > Best, > Herman > > -Original Message- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > Tim Gruene > Sent: Monday, September 06, 2010 1:38 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Fd-3m with pdbset > > Hello, > I tried to assign a cell with space group F d -3 m to a PDB file using > pdbset. > Since it did not recognize the string 'F d -3 m' (nor 'F d -3 m :1') , I > used the space group number 227. This resulted in the space group string > 'F d -3 m :' > in the PDB-file instead of 'F d -3 m :1' as it is listed in syminfo.lib, > and hence coot refused to display the symmetry mates for the molecule. > > When I add the missing '1' in the resulting PDB-file, coot does display > the cell, but when I ask to display the symmetry mates, coot chokes and > consumed all my cpu power (for 8 molecules present in the unit cell...) > until I killed it. > > I was wondering if this is a known bug in syminfo.lib (and/or the > dependent > programs) and if there is a way around it (without using > phenix.get_me_out_of_here, I could of course use xp instead of coot for > such a small molecule). > > Kind regards, Tim > > P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3 > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Fd-3m with pdbset
Yes, I can reproduce this, and I think I have found the bug. It is simply that PDBSET dimensions the spacegroup name to 10 characters. Increasing that to 20 allows you to use either spac 'F d -3 m :1' or spac 227 However, it still won't recognise 'F d -3 m' because this is not in the syminfo file (at least, not in a field that is read). There seem to be a few CCP4 Fortran files that have character spgnam*10 from the good old days ... Cheers Martyn On Mon, 2010-09-06 at 13:38 +0200, Tim Gruene wrote: > Hello, > I tried to assign a cell with space group F d -3 m to a PDB file using pdbset. > Since it did not recognize the string 'F d -3 m' (nor 'F d -3 m :1') , I used > the space group number 227. This resulted in the space group string 'F d -3 m > :' > in the PDB-file instead of 'F d -3 m :1' as it is listed in syminfo.lib, and > hence coot refused to display the symmetry mates for the molecule. > > When I add the missing '1' in the resulting PDB-file, coot does display the > cell, but when I ask to display the symmetry mates, coot chokes and consumed > all > my cpu power (for 8 molecules present in the unit cell...) until I killed it. > > I was wondering if this is a known bug in syminfo.lib (and/or the dependent > programs) and if there is a way around it (without using > phenix.get_me_out_of_here, I could of course use xp instead of coot for such a > small molecule). > > Kind regards, Tim > > P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3 > -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
[ccp4bb] Post-doc vacancy in the Integral Membrane Protein group, SGC, Oxford
Dear All, The Integral Membrane Protein group at the SGC in Oxford is looking for a post-doctoral research scientist with experience in purification and crystallisation of membrane proteins. In the past year we have developed a pipeline for the production of human membrane proteins in the baculovirus/insect cell expression system. We are now optimizing purification and crystallisation protocols for a series of well-expressed and purified membrane proteins in a broad spectrum of families, including GPCRs, channels, solute carriers, ABC transporters and enzymes. We are looking for an enthusiastic and highly motivated scientist to join our team of 12 membrane protein scientists to help with this work. For further information on this post, please follow this link http://www.sgc.ox.ac.uk/jobs/H910012/H910012.html. For informal enquiries please contact Dr Liz Carpenter, the Principal Investigator for the IMP group: liz.carpen...@sgc.ox.ac.uk. Liz
Re: [ccp4bb] Problem with NCS detection in Parrot
Florian Schmitzberger wrote: Dear All, I am encountering a problem when using Parrot (for combined density modification and non crystallographic symmetry (NCS) averaging) in ccp4 6.1.13, run via ccp4i. Parrot does not detect the (2-fold) NCS present among my heavy atom substructure with 20 seleniums (the pdb was output by Phaser-EP, single chain ID, and is read by Parrot from what I can tell). I have tried a to split the NCS related heavy atoms into separate chains, but Parrot does still not appear to detect any NCS (error message: WARNING: No NCS found from heavy atoms). Can I try it? The Professs program seems to detect the NCS readily. Unfortunately, I don't think it is possible to input externally determined NCS operators into Parrot. Yup, you can, but you have to 'run and edit com file'. ncs-operator alpha,beta,gamma,x,y,z,x,y,z First set of x,y,z are the centre of mass of the source molecule, second are the target molecule. This info is provided by recent versions of professs. -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm
Re: [ccp4bb] Fd-3m with pdbset
Hi Tim, The string 'Fd-3m:1' is recognized by pdbset, but still produces 'F d -3 m :'. I did a test with a single small ligand with coot and if you delete the ':' from the CRYST1 card to make 'F d -3 m' coot happily accepts it and seems to produce the correct symmetry mates. I hope that this way you are able to display your molecule. I agree that there must be a bug somewhere. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene Sent: Monday, September 06, 2010 1:38 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fd-3m with pdbset Hello, I tried to assign a cell with space group F d -3 m to a PDB file using pdbset. Since it did not recognize the string 'F d -3 m' (nor 'F d -3 m :1') , I used the space group number 227. This resulted in the space group string 'F d -3 m :' in the PDB-file instead of 'F d -3 m :1' as it is listed in syminfo.lib, and hence coot refused to display the symmetry mates for the molecule. When I add the missing '1' in the resulting PDB-file, coot does display the cell, but when I ask to display the symmetry mates, coot chokes and consumed all my cpu power (for 8 molecules present in the unit cell...) until I killed it. I was wondering if this is a known bug in syminfo.lib (and/or the dependent programs) and if there is a way around it (without using phenix.get_me_out_of_here, I could of course use xp instead of coot for such a small molecule). Kind regards, Tim P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] Fd-3m with pdbset
Hello, I tried to assign a cell with space group F d -3 m to a PDB file using pdbset. Since it did not recognize the string 'F d -3 m' (nor 'F d -3 m :1') , I used the space group number 227. This resulted in the space group string 'F d -3 m :' in the PDB-file instead of 'F d -3 m :1' as it is listed in syminfo.lib, and hence coot refused to display the symmetry mates for the molecule. When I add the missing '1' in the resulting PDB-file, coot does display the cell, but when I ask to display the symmetry mates, coot chokes and consumed all my cpu power (for 8 molecules present in the unit cell...) until I killed it. I was wondering if this is a known bug in syminfo.lib (and/or the dependent programs) and if there is a way around it (without using phenix.get_me_out_of_here, I could of course use xp instead of coot for such a small molecule). Kind regards, Tim P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
