Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
This is very uncommon... Can you look at the final plot of R and Rfree against resolution. Sometimes there is an awful hiccup somewhere - ice rings? high resolution data somewhat fictional - low resolution data saturated and also somewhat fictional .. I also check the completeness which is uin the same loggraph panel. Eleanor On 12/09/2011 08:53 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Petr, there may be a couple of reasons, e.g. - - your data are not really 1.1A, but you simply integrated a lot of noise - - you entered some odd command or another option which allows refmac5 such a deviation - - your model is incomplete - - surely several more. When a well tested program does something unexpected, it is usually the user and not the program which misbehaves... The optimisation of the weighting scheme is based on the geometry of the model and not one the gap between R and Rfree. Cheers, Tim On 12/08/2011 08:43 PM, Petr Leiman wrote: Dear Tim, I agree with you completely. The question then becomes why does the automatic weighting scheme in refmac allow R and R-free to run away from each other by 8% in a 1.1 A resolution structure? Petr On Dec 8, 2011, at 6:50 PM, Tim Gruene wrote: Dear Christopher, if your R/Rfree from Refmac5 really are 10% vs. 18%, you might simply be looking at an electron density map with strong model bias, i.e. the map shows the features of the model and not of the data. Although at 1.1A resolution this seems quite unlikely, but that's what might explain this great gap between R and Rfree. Tim On 12/08/2011 06:36 PM, Christopher Browning wrote: Dear All, Question: Has anybody ever refined the same structure using PHENIX and then tried REFMAC to see what happens? I did and I stumbled on something funny. I'm refining a structure at 1.1A resolution which was solved with Iodine phasing using PHENIX AutoSolve. Got a great map and the structure was built almost completely. I had to build a few residues myself, and using the published sequence, I started filling in the residues, but as I came nearer the N-terminus, it looked like the density did not match residues from the sequence. I kept the residues as in the sequence, but as you can see from the PHENIX refined picture (below is the link) it still looks like the amino acid sequence in the crystal does not match the published protein sequence. Out of interest I refined the same file in REFMAC, and now the electron density is correct, and the sequence of the amino acids in the crystal matches the published sequence (see link for picture below). Not only that. my R/Rfree improved (16.5/19 for PHENIX, 10/18 for REFMAC). I've also refined the occupancies of the iodide, however the the output FO-FC map from PHENIX complains and the REFMAC map is fine. How can this be and what causes this? Link for the pictures: Both maps are at identical Sigma levels in both pictures. PHENIX: http://dl.dropbox.com/u/51868657/PHENIX_refined.png REFMAC: http://dl.dropbox.com/u/51868657/REFMAC_refined.png Cheers, Chris Browning - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO4cyCUxlJ7aRr7hoRAqDTAJkBsSEIp2bH7hZlB23LJadHL2VhVQCg0r38 LGVjgK1z29vPc5V4lUh74vw= =wP9n -END PGP SIGNATURE-
Re: [ccp4bb] Failure in Phaser EP
Dear Arko, Is it possible that your Phaser installation is out of sync with your CCP4 installation? You might like to upgrade both. CCP4 6.2.0 includes Phaser 2.3.0. The Phaser EP module for this release correctly writes 'SIGF(+) =' and 'SIGF(-) =' to the LABIN line. Best regards -- David On 10 December 2011 15:40, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Arko, your input script reads LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) Try and replace SIGF+ with either SIG+ or SIGF(+); same for SIGF-. Tim On 12/10/2011 09:33 AM, arka chakraborty wrote: Hi CCPers! I have a strange problem..I am trying to obtain phases for a dna decamer structure from cobalt SAD data. In the Phaser EP module when I input the mtz generated by Ctruncate and the heavy atom PDB file generated from shlelxC/D and run the program it fails. Below is the log file for one of the runs. Plz help me out! Thanks in advance! ARKO #CCP4I VERSION CCP4Interface 2.0.7 #CCP4I SCRIPT LOG phaser_EP #CCP4I DATE 10 Dec 2011 13:45:46 #CCP4I USER 'UNKNOWN' #CCP4I PROJECT decamer #CCP4I JOB_ID 37 #CCP4I SCRATCH C:/Ccp4Temp #CCP4I HOSTNAME dell-pc #CCP4I PID 3412 pre BFONT COLOR=#FF html!-- CCP4 HTML LOGFILE -- !--SUMMARY_BEGIN-- # # # ### CCP4 PROGRAM SUITE: Phaser 2.2.1 ### # Run time: Sat Dec 10 13:45:46 2011 Version: 2.2.1 Release Date: Tue Aug 24 18:17:37 2010 If you use this software please cite: $TEXT:Reference1: $$ $$ Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni R.J. Read J. Appl. Cryst. (2007). 40, 658-674 $$ !--SUMMARY_END-- !--END--/FONT/B !--SUMMARY_BEGIN-- * *** Phaser Module: PREPROCESSOR 2.2.1 *** * !--SUMMARY_END-- ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT !--SUMMARY_BEGIN-- TITLE phasing_with_phaser_10_12_11 MODE EP_AUTO HKLIN E:/block1plus2_mtzs_10_12_11/ctruncate_BLOCK1PLUS2_INTEGRATION_16_11_11.mtz RESOLUTION 21.659 2.900 HAND BOTH LLGCOMPLETE NCYC 50 LLGCOMPLETE CRYSTAL DECAMER COMPLETE ON LLGCOMPLETE CRYSTAL DECAMER SIGMA 6.0 LLGCOMPLETE CRYSTAL DECAMER CLASH DEFAULT LLGCOMPLETE CRYSTAL DECAMER SCATTERING ELEMENT CO ATOM CRYSTAL DECAMER PDB L:/decamer/scala_NGAT-1-P1X8-pk_1_001_shelx2.pdb CRYSTAL DECAMER DATASET Cobalt LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) CRYSTAL DECAMER DATASET Cobalt SCATTERING WAVELENGTH 1.60428 CRYSTAL DECAMER DATASET Cobalt FIXDP COMPOSITION NUCLEIC MW 9084 NUMBER 1 ROOT L:/manual_model_esrf_NG/ccp4_work/decamer_37 ## This script run with the command ## # phaser !--SUMMARY_END-- EXIT STATUS: SUCCESS CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs) Finished: Sat Dec 10 13:45:46 2011 /pre /html pre BFONT COLOR=#FF html!-- CCP4 HTML LOGFILE -- # # # ### CCP4 PROGRAM SUITE: Phaser 2.2.1 ### # Run time: Sat Dec 10 13:45:46 2011 Version: 2.2.1 Release Date: Tue Aug 24 18:17:37 2010 If you use this software please cite: $TEXT:Reference1: $$ $$ Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni R.J. Read J. Appl. Cryst. (2007). 40, 658-674 $$ !--END--/FONT/B !--SUMMARY_BEGIN-- * *** Phaser Module: READ DATA FROM MTZ FILE 2.2.1 *** * TITLE phasing_with_phaser_10_12_11 HKLIN E:/block1plus2_mtzs_10_12_11/ctruncate_BLOCK1PLUS2_INTEGRATION_16_11_11.mtz RESOLUTION 21.659 2.900 CRYSTAL DECAMER DATASET Cobalt LABIN F+ = F(+) SIGF+ !--SUMMARY_END-- BFONT COLOR=#FF8800 -- SYNTAX ERROR: Use SIGFPOS SIGF(+) or SIG+
Re: [ccp4bb] Failure in Phaser EP
I just realised that my reply on this issue only went to Arko, and not to the BB. I think that the problem was because of an internally out-of-synch CCP4 installation that was made available for Windows for some time. Here's my reply, which makes a similar point to David's. = As Tim says, you can edit the script to make it run. However, I think you've run into the problem that, for a short period of time, incompatible versions of Phaser and the ccp4i GUI were being distributed with the Windows distribution of CCP4-6.1.13. If you install CCP4-6.2, you'll have newer versions of everything and the Phaser GUI will be compatible with the executable. = On 12 Dec 2011, at 12:25, David Waterman wrote: Dear Arko, Is it possible that your Phaser installation is out of sync with your CCP4 installation? You might like to upgrade both. CCP4 6.2.0 includes Phaser 2.3.0. The Phaser EP module for this release correctly writes 'SIGF(+) =' and 'SIGF(-) =' to the LABIN line. Best regards -- David On 10 December 2011 15:40, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Arko, your input script reads LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) Try and replace SIGF+ with either SIG+ or SIGF(+); same for SIGF-. Tim On 12/10/2011 09:33 AM, arka chakraborty wrote: Hi CCPers! I have a strange problem..I am trying to obtain phases for a dna decamer structure from cobalt SAD data. In the Phaser EP module when I input the mtz generated by Ctruncate and the heavy atom PDB file generated from shlelxC/D and run the program it fails. Below is the log file for one of the runs. Plz help me out! Thanks in advance! ARKO #CCP4I VERSION CCP4Interface 2.0.7 #CCP4I SCRIPT LOG phaser_EP #CCP4I DATE 10 Dec 2011 13:45:46 #CCP4I USER 'UNKNOWN' #CCP4I PROJECT decamer #CCP4I JOB_ID 37 #CCP4I SCRATCH C:/Ccp4Temp #CCP4I HOSTNAME dell-pc #CCP4I PID 3412 pre BFONT COLOR=#FF html!-- CCP4 HTML LOGFILE -- !--SUMMARY_BEGIN-- # # # ### CCP4 PROGRAM SUITE: Phaser 2.2.1 ### # Run time: Sat Dec 10 13:45:46 2011 Version: 2.2.1 Release Date: Tue Aug 24 18:17:37 2010 If you use this software please cite: $TEXT:Reference1: $$ $$ Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni R.J. Read J. Appl. Cryst. (2007). 40, 658-674 $$ !--SUMMARY_END-- !--END--/FONT/B !--SUMMARY_BEGIN-- * *** Phaser Module: PREPROCESSOR 2.2.1 *** * !--SUMMARY_END-- ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT !--SUMMARY_BEGIN-- TITLE phasing_with_phaser_10_12_11 MODE EP_AUTO HKLIN E:/block1plus2_mtzs_10_12_11/ctruncate_BLOCK1PLUS2_INTEGRATION_16_11_11.mtz RESOLUTION 21.659 2.900 HAND BOTH LLGCOMPLETE NCYC 50 LLGCOMPLETE CRYSTAL DECAMER COMPLETE ON LLGCOMPLETE CRYSTAL DECAMER SIGMA 6.0 LLGCOMPLETE CRYSTAL DECAMER CLASH DEFAULT LLGCOMPLETE CRYSTAL DECAMER SCATTERING ELEMENT CO ATOM CRYSTAL DECAMER PDB L:/decamer/scala_NGAT-1-P1X8-pk_1_001_shelx2.pdb CRYSTAL DECAMER DATASET Cobalt LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) CRYSTAL DECAMER DATASET Cobalt SCATTERING WAVELENGTH 1.60428 CRYSTAL DECAMER DATASET Cobalt FIXDP COMPOSITION NUCLEIC MW 9084 NUMBER 1 ROOT L:/manual_model_esrf_NG/ccp4_work/decamer_37 ## This script run with the command ## # phaser !--SUMMARY_END-- EXIT STATUS: SUCCESS CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs) Finished: Sat Dec 10 13:45:46 2011 /pre /html pre BFONT COLOR=#FF html!-- CCP4 HTML LOGFILE -- # # # ### CCP4 PROGRAM SUITE: Phaser 2.2.1 ### # Run time: Sat Dec 10 13:45:46 2011 Version: 2.2.1 Release Date: Tue Aug 24 18:17:37 2010 If you use this software please cite: $TEXT:Reference1: $$ $$ Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams,
Re: [ccp4bb] Failure in Phaser EP
Hi all! Thanks a lot to Randy and Tim and David and to all who found it worthy giving a thought! As Randy said it was due to an internally out of sink CCP4 installation. The CCP4 6.1.2 is working fine However I would like to bring into discussion another problem...While trying to generate heavy atom positions by ShelX C, D, E from the same DNA cobalt SAD data the output PDB is showing the atoms as sulfur inspite of specifying cobalt in the runAs the data was highly twinned(non-merohedral!) the images with no twinning(and offcourse corresponding to one of the two lattices) were used which obviously reduced the completeness. I am using a Linux-redhat5 specific version of CCP4..also the heavy atom sites do not match with a previously PDB generated using the entire data The reason for redoing it was that the previous map had a lot of noise even after density modification and was generated using shelxE which I felt might have made it worse because it is a DNA data and the density modification regime of ShelxE involves C alpha tracing which is protein specific. Also using the ShelX D generated PDB and mtz generated from the untwinned dataset in Phaser EP produced a totally uninterpretable map while the previous trial was atleast interpretable.So the questions are: What might be the reason behind ShelXD marking the atoms as sulfur and not cobalt? Is my assumption about the effect of ShelX E right? What might be the cause behind Phaser failing even with untwinned data while the twinned data gave an interpretable map?- is it completeness? Is using the ShelXD subtructure PDB in phaser EP a good idea? What can be done to get a better interpretable map? Thanks in advance! ARKO On Mon, Dec 12, 2011 at 8:40 PM, Randy Read rj...@cam.ac.uk wrote: I just realised that my reply on this issue only went to Arko, and not to the BB. I think that the problem was because of an internally out-of-synch CCP4 installation that was made available for Windows for some time. Here's my reply, which makes a similar point to David's. = As Tim says, you can edit the script to make it run. However, I think you've run into the problem that, for a short period of time, incompatible versions of Phaser and the ccp4i GUI were being distributed with the Windows distribution of CCP4-6.1.13. If you install CCP4-6.2, you'll have newer versions of everything and the Phaser GUI will be compatible with the executable. = On 12 Dec 2011, at 12:25, David Waterman wrote: Dear Arko, Is it possible that your Phaser installation is out of sync with your CCP4 installation? You might like to upgrade both. CCP4 6.2.0 includes Phaser 2.3.0. The Phaser EP module for this release correctly writes 'SIGF(+) =' and 'SIGF(-) =' to the LABIN line. Best regards -- David On 10 December 2011 15:40, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Arko, your input script reads LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) Try and replace SIGF+ with either SIG+ or SIGF(+); same for SIGF-. Tim On 12/10/2011 09:33 AM, arka chakraborty wrote: Hi CCPers! I have a strange problem..I am trying to obtain phases for a dna decamer structure from cobalt SAD data. In the Phaser EP module when I input the mtz generated by Ctruncate and the heavy atom PDB file generated from shlelxC/D and run the program it fails. Below is the log file for one of the runs. Plz help me out! Thanks in advance! ARKO #CCP4I VERSION CCP4Interface 2.0.7 #CCP4I SCRIPT LOG phaser_EP #CCP4I DATE 10 Dec 2011 13:45:46 #CCP4I USER 'UNKNOWN' #CCP4I PROJECT decamer #CCP4I JOB_ID 37 #CCP4I SCRATCH C:/Ccp4Temp #CCP4I HOSTNAME dell-pc #CCP4I PID 3412 pre BFONT COLOR=#FF html!-- CCP4 HTML LOGFILE -- !--SUMMARY_BEGIN-- # # # ### CCP4 PROGRAM SUITE: Phaser 2.2.1 ### # Run time: Sat Dec 10 13:45:46 2011 Version: 2.2.1 Release Date: Tue Aug 24 18:17:37 2010 If you use this software please cite: $TEXT:Reference1: $$ $$ Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni R.J. Read J. Appl. Cryst. (2007). 40, 658-674 $$ !--SUMMARY_END-- !--END--/FONT/B !--SUMMARY_BEGIN-- * *** Phaser Module: PREPROCESSOR 2.2.1 *** * !--SUMMARY_END-- ENTER KEYWORD INPUT FROM FILE OR FROM
[ccp4bb] Failure in Phaser EP-and a new problem!
Hi all! Thanks a lot to Randy and Tim and David and to all who found it worthy giving a thought! As Randy said it was due to an internally out of sink CCP4 installation. The CCP4 6.1.2 is working fine However I would like to bring into discussion another problem...While trying to generate heavy atom positions by ShelX C, D, E from the same DNA cobalt SAD data the output PDB is showing the atoms as sulfur inspite of specifying cobalt in the runAs the data was highly twinned(non-merohedral!) the images with no twinning(and offcourse corresponding to one of the two lattices) were used which obviously reduced the completeness. I am using a Linux-redhat5 specific version of CCP4..also the heavy atom sites do not match with a previously PDB generated using the entire data The reason for redoing it was that the previous map had a lot of noise even after density modification and was generated using shelxE which I felt might have made it worse because it is a DNA data and the density modification regime of ShelxE involves C alpha tracing which is protein specific. Also using the ShelX D generated PDB and mtz generated from the untwinned dataset in Phaser EP produced a totally uninterpretable map while the previous trial was atleast interpretable.So the questions are: What might be the reason behind ShelXD marking the atoms as sulfur and not cobalt? Is my assumption about the effect of ShelX E right? What might be the cause behind Phaser failing even with untwinned data while the twinned data gave an interpretable map?- is it completeness? Is using the ShelXD subtructure PDB in phaser EP a good idea? What can be done to get a better interpretable map? Thanks in advance! ARKO On Mon, Dec 12, 2011 at 8:40 PM, Randy Read rj...@cam.ac.uk wrote: I just realised that my reply on this issue only went to Arko, and not to the BB. I think that the problem was because of an internally out-of-synch CCP4 installation that was made available for Windows for some time. Here's my reply, which makes a similar point to David's. = As Tim says, you can edit the script to make it run. However, I think you've run into the problem that, for a short period of time, incompatible versions of Phaser and the ccp4i GUI were being distributed with the Windows distribution of CCP4-6.1.13. If you install CCP4-6.2, you'll have newer versions of everything and the Phaser GUI will be compatible with the executable. = On 12 Dec 2011, at 12:25, David Waterman wrote: Dear Arko, Is it possible that your Phaser installation is out of sync with your CCP4 installation? You might like to upgrade both. CCP4 6.2.0 includes Phaser 2.3.0. The Phaser EP module for this release correctly writes 'SIGF(+) =' and 'SIGF(-) =' to the LABIN line. Best regards -- David On 10 December 2011 15:40, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Arko, your input script reads LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) Try and replace SIGF+ with either SIG+ or SIGF(+); same for SIGF-. Tim On 12/10/2011 09:33 AM, arka chakraborty wrote: Hi CCPers! I have a strange problem..I am trying to obtain phases for a dna decamer structure from cobalt SAD data. In the Phaser EP module when I input the mtz generated by Ctruncate and the heavy atom PDB file generated from shlelxC/D and run the program it fails. Below is the log file for one of the runs. Plz help me out! Thanks in advance! ARKO #CCP4I VERSION CCP4Interface 2.0.7 #CCP4I SCRIPT LOG phaser_EP #CCP4I DATE 10 Dec 2011 13:45:46 #CCP4I USER 'UNKNOWN' #CCP4I PROJECT decamer #CCP4I JOB_ID 37 #CCP4I SCRATCH C:/Ccp4Temp #CCP4I HOSTNAME dell-pc #CCP4I PID 3412 pre BFONT COLOR=#FF html!-- CCP4 HTML LOGFILE -- !--SUMMARY_BEGIN-- # # # ### CCP4 PROGRAM SUITE: Phaser 2.2.1 ### # Run time: Sat Dec 10 13:45:46 2011 Version: 2.2.1 Release Date: Tue Aug 24 18:17:37 2010 If you use this software please cite: $TEXT:Reference1: $$ $$ Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni R.J. Read J. Appl. Cryst. (2007). 40, 658-674 $$ !--SUMMARY_END-- !--END--/FONT/B !--SUMMARY_BEGIN-- * *** Phaser Module: PREPROCESSOR 2.2.1 *** * !--SUMMARY_END-- ENTER KEYWORD INPUT FROM FILE OR FROM
Re: [ccp4bb] Failure in Phaser EP-and a new problem!
Hi, For reasons best known to George, SHELXD calls everything a sulphur. For some phasing programs (no doubt including SHELXE) that doesn't matter, but it does for Phaser. For this reason, the Phaser GUI allows you to substitute the SHELXD atom with your own atom type. If you prefer scripts, you can put in the command that the GUI would generate, e.g. if you were looking for Se when you ran SHELXD, this is an example of the command: ATOM CRYSTAL SeMet PDB shelxd.pdb SCATTERING Se Regards, Randy On 12 Dec 2011, at 16:02, arka chakraborty wrote: Hi all! Thanks a lot to Randy and Tim and David and to all who found it worthy giving a thought! As Randy said it was due to an internally out of sink CCP4 installation. The CCP4 6.1.2 is working fine However I would like to bring into discussion another problem...While trying to generate heavy atom positions by ShelX C, D, E from the same DNA cobalt SAD data the output PDB is showing the atoms as sulfur inspite of specifying cobalt in the runAs the data was highly twinned(non-merohedral!) the images with no twinning(and offcourse corresponding to one of the two lattices) were used which obviously reduced the completeness. I am using a Linux-redhat5 specific version of CCP4..also the heavy atom sites do not match with a previously PDB generated using the entire data The reason for redoing it was that the previous map had a lot of noise even after density modification and was generated using shelxE which I felt might have made it worse because it is a DNA data and the density modification regime of ShelxE involves C alpha tracing which is protein specific. Also using the ShelX D generated PDB and mtz generated from the untwinned dataset in Phaser EP produced a totally uninterpretable map while the previous trial was atleast interpretable.So the questions are: What might be the reason behind ShelXD marking the atoms as sulfur and not cobalt? Is my assumption about the effect of ShelX E right? What might be the cause behind Phaser failing even with untwinned data while the twinned data gave an interpretable map?- is it completeness? Is using the ShelXD subtructure PDB in phaser EP a good idea? What can be done to get a better interpretable map? Thanks in advance! ARKO On Mon, Dec 12, 2011 at 8:40 PM, Randy Read rj...@cam.ac.uk wrote: I just realised that my reply on this issue only went to Arko, and not to the BB. I think that the problem was because of an internally out-of-synch CCP4 installation that was made available for Windows for some time. Here's my reply, which makes a similar point to David's. = As Tim says, you can edit the script to make it run. However, I think you've run into the problem that, for a short period of time, incompatible versions of Phaser and the ccp4i GUI were being distributed with the Windows distribution of CCP4-6.1.13. If you install CCP4-6.2, you'll have newer versions of everything and the Phaser GUI will be compatible with the executable. = On 12 Dec 2011, at 12:25, David Waterman wrote: Dear Arko, Is it possible that your Phaser installation is out of sync with your CCP4 installation? You might like to upgrade both. CCP4 6.2.0 includes Phaser 2.3.0. The Phaser EP module for this release correctly writes 'SIGF(+) =' and 'SIGF(-) =' to the LABIN line. Best regards -- David On 10 December 2011 15:40, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Arko, your input script reads LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) Try and replace SIGF+ with either SIG+ or SIGF(+); same for SIGF-. Tim On 12/10/2011 09:33 AM, arka chakraborty wrote: Hi CCPers! I have a strange problem..I am trying to obtain phases for a dna decamer structure from cobalt SAD data. In the Phaser EP module when I input the mtz generated by Ctruncate and the heavy atom PDB file generated from shlelxC/D and run the program it fails. Below is the log file for one of the runs. Plz help me out! Thanks in advance! ARKO #CCP4I VERSION CCP4Interface 2.0.7 #CCP4I SCRIPT LOG phaser_EP #CCP4I DATE 10 Dec 2011 13:45:46 #CCP4I USER 'UNKNOWN' #CCP4I PROJECT decamer #CCP4I JOB_ID 37 #CCP4I SCRATCH C:/Ccp4Temp #CCP4I HOSTNAME dell-pc #CCP4I PID 3412 pre BFONT COLOR=#FF html!-- CCP4 HTML LOGFILE -- !--SUMMARY_BEGIN-- # # # ### CCP4 PROGRAM SUITE: Phaser 2.2.1 ### # Run time: Sat Dec 10 13:45:46 2011
Re: [ccp4bb] Efficient way of showing residue conservation
I input the alignment in ESPript. Add the template PDB file and it makes a Bcol.pdb file where temperature factors are replaced my sequence similarity. I open this file in Pymol in Surface and color B-Factors as rainbow. Ivan On 12/7/11, Yuri Pompeu yuri.pom...@ufl.edu wrote: I once saw a figure showing the protein as surface, but instead of having it coloured by atom type or potential, it was shown by percent conservation in the family. Something like red highly conserved, all the way to white, not conserved at all... Now, I assume the figure was done by uploading aligned sequnces of several members of a family, and the colouring the generated surface accordingly. Does anyone know a way to do this more elegantly than what I tried doing? ps. I quit colouring them manually after I remebered my protein was 407 aa long...
[ccp4bb] artificial tetramer
Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred
Re: [ccp4bb] Efficient way of showing residue conservation
Hi Yuri, I once saw a figure showing the protein as surface, but instead of having it coloured by atom type or potential, it was shown by percent conservation in the family. Something like red highly conserved, all the way to white, not conserved at all... Now, I assume the figure was done by uploading aligned sequnces of several members of a family, and the colouring the generated surface accordingly. Does anyone know a way to do this more elegantly than what I tried doing? ps. I quit colouring them manually after I remebered my protein was 407 aa long... PyMOL can do this pretty easily now. First you need to calculate an alignment, then you need to do the coloring. The alignment step is done like this: align protA, protB, object=aln I then wrote a script to automate the coloring of residues by conservation in the sequence alignment. You can find the script on the PyMOLWiki, here http://pymolwiki.org/index.php/Color_by_conservation. The script does a couple other useful things like showing the conservation not only by color but by cartoon putty radius, and expanding the alpha-carbon conservation to surface colors. You can find an example to copy/paste into PyMOL on that page. Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] artificial tetramer
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
at few Angstrons of the protein. Em 12-12-2011 19:01, Jacob Keller escreveu: How do you know where to put the axis? JPK On Mon, Dec 12, 2011 at 2:34 PM, Fredccp4bb.l...@gmail.com wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
[ccp4bb] Calibration question
All- We are reevaluating the frequency of our pipette calibrations and were tasked with determining the norm. How often do you calibrate your pipettes? Do you have different schedules for different purposes (i.e. crystallization pipettes get calibrated every 18 months, while purification pipettes are calibrated every 2 years)? Who do you use for the calubration? Thanks, everyone! Jackie
Re: [ccp4bb] artificial tetramer
Hi James, In my first post arbitrary orientation into the cell only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
Can you clarify your reason for doing this? JPK On Mon, Dec 12, 2011 at 3:36 PM, Fred ccp4bb.l...@gmail.com wrote: Hi James, In my first post arbitrary orientation into the cell only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE- -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] artificial tetramer
I only want to produce an artificial tetramer. Em 12-12-2011 19:41, Jacob Keller escreveu: Can you clarify your reason for doing this? JPK On Mon, Dec 12, 2011 at 3:36 PM, Fredccp4bb.l...@gmail.com wrote: Hi James, In my first post arbitrary orientation into the cell only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
[ccp4bb] Expression of a Selenomethionine Variant in E. coli
Hi List, I want to preprare sel-met labeling protein. Could someone can tell me if it is necessary to add DTT or BME to medium, which contains sel-met, when growing cells? Thanks in advance, Yibin Lin
Re: [ccp4bb] Expression of a Selenomethionine Variant in E. coli
Generally no, only in the subsequent protein purification steps. Tony. Sent from my iPhone On 12 Dec 2011, at 21:57, Yibin Lin yyb...@gmail.com wrote: Hi List, I want to preprare sel-met labeling protein. Could someone can tell me if it is necessary to add DTT or BME to medium, which contains sel-met, when growing cells? Thanks in advance, Yibin Lin
Re: [ccp4bb] artificial tetramer
Coot can do this using the Rubik's Cube principle: transform to some state where the operation can be performed, perform the operation, then transform back. So, in coot, I would (1) rotate the molecule to the appropriate orientation (2) move to the appropriate place in the unit cell (3) change the symmetry to P4 (3) apply P4 symmetry (4) change the symmetry back to whatever (5) move the tetramer back to the appropriate place in the unit cell (6) rotate the molecule back Then, your original molecule will be in the original place surrounded by it's symmetry mates. James On Dec 12, 2011, at 2:36 PM, Fred wrote: Hi James, In my first post arbitrary orientation into the cell only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] Calibration question
I suppose you mean the pipetman and similar, and having it calibrated by a professional rather than pipetting into a weighing boat to see if it is OK- Unless i'm missing something, there is very little that can be done in the way of calibration- the diameter of the stainless steel shaft and the pitch of the screw can't be changed (and won't get out of calibration anyway). This leaves only the zero point to adjust, and that is unlikely to get off either, except by a clumsy attempt to calibrate it. What does need attention is the seal, which can get worn and allow air to leak. This is noticed (in very bad cases) when you fill the pipet, hold it up, and solution slowly drips out; or if you are pipetting a viscous solution and the solution stops flowing in long before the indicated volume has been taken up. The seals are available from the manufacturer (Rainin) and can be changed rather easily by yourself. As for testing when the seal needs changing, the drip test mentioned above works for large volume pipets, for P2 or p10 you might need to wick the water out of the tip with a kimwipe- if the seal is good a little will flow and then stop, if the entire volume flows out into the kimwipe the seal needs replacing. To check the zero point, turn the counter toward zero checking the play (to first position) as you approach. The play should go to zero as the counter does. More practically, pipet a volume into a weighing boat tared on the analytic balance, and see if the correct volume was delivered. If either of these tests fails, it's time to have the pipet calibrated. If there is a bent shaft or cracked plastic, then it needs repair. Just my opinion, Ed Jacqueline Day wrote: All- We are reevaluating the frequency of our pipette calibrations and were tasked with determining the norm. How often do you calibrate your pipettes? Do you have different schedules for different purposes (i.e. crystallization pipettes get calibrated every 18 months, while purification pipettes are calibrated every 2 years)? Who do you use for the calubration? Thanks, everyone! Jackie
[ccp4bb] Phenix version 1.7.3 released
The Phenix developers are pleased to announce that version 1.7.3 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: - New GUIs: MR-Rosetta - viewer for diffraction images (also available as phenix.image_viewer) - editable heavy-atom sites in HySS and AutoSol General: - New commands: phenix.ncs_average, phenix.model_vs_sequence, phenix.image_viewer, phenix.find_alt_orig_sym_mate, phaser.MRage - support for CNS v1.3 reflection files Refinement: === - Reduced memory requirement for map related calculations - Improved handling of parameter files in the GUI - RNA geometry target now includes pucker base type-specific Chi 1 parameters - TLS group definitions from PDB file header will be automatically used if no groups are provided by the user - Bug fix in clashscore calculation for large structures with duplicate chain IDs plus SEGIDs - Torsion NCS restraints uses SEGIDs if present in input PDB file Molecular Replacement: == - phaser (version 2.4): - support for pseudo-translational non-crystallographic symmetry (tNCS) in molecular replacement - detects presence of tNCS from inspection of native Patterson - characterizes tNCS parameters (translation, small rotational difference between copies) - accounts for effect of tNCS in molecular replacement calculations - note: support currently limited to one tNCS operator relating two molecules (or sets of molecules) - FAST search method turned on by default, replacing FULL search method - MR possible with a model containing a single atom - B-factor refinement turned on by default in molecular replacement - Bug fix for occasional and irreproducible segmentation faults for 32 bit binary running on 64 bit Linux - Packing function accepts cases where an ensemble with internal point group symmetry is on a special position, and pdb file output deletes atoms overlapped due to the symmetry of special position - phaser.MRage (version 0.1.0) - automated MR: - New command-line switches for common actions, e.g. setting the verbosity, getting PHIL parameters, etc - Define component by sequence, but calculate molecular weight from available models if sequence is omitted - Calculate number of copies to find from Matthews coefficient - Ability to perform homology search (currently only BLAST is supported, either local installation or NCBI service) - alignments automatically generated for template if target sequence is known - various options for queueing systems, e.g. qslot - option to automatically write out solutions - fully parallel space group exploration - phenix.find_alt_orig_sym_mate (new command): - For different molecular replacement solutions from the same dataset, finds the copy of moving_pdb closest to reference_pdb with respect to all symmetry operations and alternative origin shifts permitted by the spacegroup in moving_pdb Experimental Phasing and Model Building: - AutoSol: - Fixed problems with clean_up=True deleting overall_best.pdb - Allow data file names of any length - Use NCS in scoring by default if ncs copies 2 - Correct anisotropy and sharpen by default - AutoBuild: - Automatic anisotropy correction and sharpening for all maps - phenix.multi_crystal_average: - Automatic anisotropy correction and sharpening - Automatic filling of reflections to highest resolution of any dataset - Masking heavy-atom sites from averaging - Inputs grouped by crystal Miscellaneous: == - phenix.ready_set/phenix.reduce: - Improved handling of alternate conformations - phenix.cif_as_mtz - Support for files containing multiple datasets - Extraction of Hendrickson-Lattman coefficients and anomalous arrays - New map_to_asu and remove_systematic_absences options - phenix.maps: - Added atom selection parameter for simple omit maps (omit.selection) - phenix.ligand_identification: - Implemented methods to generate custom ligand library based on parent protein's SCOP or CATH terms, Pfam accession numbers, GO accession numbers, or InterPro ID - Improved ligand geometry after real-space refinement For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010).
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
Hi Ed, I just had a chance of looking at your comment more closely. You are right it only uses PHIC if in refmacs set up you choose to refine with prior phase information -AFAIU. So what exactly is the info contained in the output refmacX.mtz besides map coefficients for COOT? If it is not just the raw xray data Fo, is it Fc only, or Fc that are filled in for missing Fo? I guess I am not really sure. I was under the impression that model´s PHIC would cause the problems, if they were present. Best,
[ccp4bb] strange MR problem
Hi All I have a 3.0A dataset of a protein-protein complex. I used one of the protein structure solved previously as a template and used phaser in CCP4 as well as in phenix. I used the sca file in phenix which gave a solution with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the converted .mtz file which gave 6 molecules in ASU but with a different packing. In both the cases map fits well in the model and there is some extra density that may correspond to second protein partner of the complex molecule. when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes. what kind of approach should i take so as to resolve this ambiguity. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
