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 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:
>> -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
>> >
>> >
>> >
>> >
>> >
>> >
>> > #
>> > #
>> > #
>> > ### CCP4 PROGRAM SUITE: Phaser
>> > 2.2.1 ###
>> > ##
