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
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>
>> > <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
>> 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/
>>
>> iD8DBQFO431lUxlJ7aRr7hoRAgHbAJ469ptgbbHe28e68X6qQ5hOuznexQCcDHuR
>> vyl455GlQ+1gFLffPpxXxm4=
>> =q4ro
>> -----END PGP SIGNATURE-----
>>
>
>
> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: + 44 1223 336500
> Wellcome Trust/MRC Building Fax: + 44 1223 336827
> Hills Road E-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
>
>
--
*ARKA CHAKRABORTY*
*CAS in Crystallography and Biophysics*
*University of Madras*
*Chennai,India*
--
*ARKA CHAKRABORTY*
*CAS in Crystallography and Biophysics*
*University of Madras*
*Chennai,India*
