u have a solution which refines (Free
> >> Rfactor drops below say 40% in P1) you can try to figure out what the
> >> true, higher symmetry space group may be. Your true space group may even
> >> be P1, with pseudo P21 symmetry!
> >>
> >> Good lu
AC.UK Subject: Re: [ccp4bb] Help! weird thing
Dear all, Thank you very much for all the great suggestions on my case.
Yes, I run the latest version of Phaser in Phenix. The analysis showed
that there is one non-origin distinct peak more than 15 angstroms from
the origin. 44.1% origin: FRAC 0.000
or drops
>> below say 40% in P1) you can try to figure out what the true, higher
>> symmetry space group may be. Your true space group may even be P1, with
>> pseudo P21 symmetry!
>>
>> Good luck!
>> Herman
>>
>> From: CCP4 bulletin board [mail
space group may
> be. Your true space group may even be P1, with pseudo P21 symmetry!
>
> Good luck!
> Herman
>
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> xiaoyazi2008
> Sent: Thursday, March 15, 2012 6:12 AM
> To: CCP4BB@JISCMAIL.AC.UK
&
Subject: Re: [ccp4bb] Help! weird thing
Dear all,
Thank you very much for all the great suggestions on my case.
Yes, I run the latest version of Phaser in Phenix. The analysis
showed that there is one non-origin distinct peak more than 15 angstroms
Dear all,
Thank you very much for all the great suggestions on my case.
Yes, I run the latest version of Phaser in Phenix. The analysis showed that
there is one non-origin distinct peak more than 15 angstroms from the origin.
44.1% origin:FRAC 0.000 0.042 0.500 (ORTH -15.72.8 103.5)
That difference density looks too good to be true..
There is obviously a very strong non-crystallographic translation.
Is the spacegroup and/or cell correct?
Eleanor
On Mar 11 2012, xiaoyazi2008 wrote:
Hi All,
I have an interesting thing to share. 2.3A dataset with good quality, P21
Par
Airlie points out that what I said about the ccp4i interface wasn't correct!
In order to keep the ccp4i interface in synch with the version of Phaser, we've
started distributing the ccp4i files with the source code. The ones on our
website are for an older version of Phaser, but the latest one
Yes, the current version of Phaser will do the same test that xtriage carries
out, and if it finds a sufficiently high non-origin Patterson peak, it will
automatically characterise the translational NCS and use this for molecular
replacement. This is working pretty well in our tests.
In the ne
Hi -
I agree with Garib that its likely a pseudo-translation issue.
I also agree with that the advice he gives is correct, but ...
... since I am evidently less smart to follow all these steps,
I like to use phenix.xtriage that will tell me if there is pseudo-
translation or not,
and will give
Hi
Could you please check:
1) If there is psedotranslation. It could be done by using sfcheck, molrep,
ctruncate or calculating patterson map and displaying using coot at 8-10 sigma
level (it is my favourite method for analysis of pseudo translations), whole
unit cell ( a bit bigger than whole
It could be that your partial model has a loop, not present
in the true solution, that is causing a clash. You could run
Phaser again with the anti-bumping restraint weakened or disabled,
or more carefully edit your partial model.
Dale Tronrud
On 3/10/2012 11:33 PM, xiaoyazi2008 wrote:
Hi A
12 matches
Mail list logo
