From: arka chakraborty
Date: 12 December 2011 16:02
--
----------
From: Randy Read
Date: 12 December 2011 16:02
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 run....As 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
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 run....As 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 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 wrote:
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>
> <B><FONT COLOR="#FF0000">
> <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>
> <B><FONT COLOR="#FF0000">
> <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-->
>
>
> <B><FONT COLOR="#FF8800">
> ------------------------------------------
> SYNTAX ERROR: Use SIGFPOS SIGF(+) or SIG+
> ------------------------------------------
> </FONT></B>
>
> --------------------
> EXIT STATUS: FAILURE
> --------------------
>
> CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs)
> Finished: Sat Dec 10 13:45:46 2011
>
> </pre>
> </html>
>
> #CCP4I TERMINATION STATUS 1
> #CCP4I TERMINATION TIME 10 Dec 2011 13:45:46
> #CCP4I MESSAGE Task completed successfully
>
>
>
- --
Dr Tim Gruene
------Randy J. Read
--
ARKA CHAKRABORTY
CAS in Crystallography and Biophysics
University of Madras
Chennai,India
----------
From: Randy Read
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
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