Thank you for the tips Brent.
I will try what you suggest. There are actually multiple lattices. And I
actually only processed the dominant one in XDS.
On May 8, 2014 2:26 PM, "Segelke, Brent W." wrote:
> Completeness looks pretty good and you have a good enough resolution
> that you should be
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Refinement of a model with only 50% completeness is problematic, but
you have four copies of a molecule (in P1) so your molecular
replacement is only looking for 24 parameters. You should be able to
get a solution with 50% completeness.
Dale Tron
Hi Brent,
I forgot to mention the resolution and other statistics. Here they are (XDS
-unmerged data P2 below). Overall completeness is 93.4(85.2)% for 2.2A.
I do have some anisotropy in the b-direction. I have tried running phaser
with data scaled by the UCLA anisotropy server and obtained the sa
Hi Jacob. I am worried that I would dramatically suffer in data
completeness. I am not sure how reliable the data is when you are have 50%
completeness. These crystals are also pretty much impossible to reproduce
at the moment.
On Thu, May 8, 2014 at 1:30 PM, Keller, Jacob wrote:
> Since your s
Hi Randy,
Again, sorry about the mis-quote. From a quick look I thought the NCS
2-fold was parallel or close enough. I didn't know that 10 degrees would
change the patterson that much. I have tried refinement with both sets of
data and get the same results. I will investigate the space group
assig
Sorry Dale. I left that out. I thought that it was almost parallel or very
close. I guess that is not enough. This is after all an exact science. My
fault.
On Thu, May 8, 2014 at 10:54 AM, Dale Tronrud wrote:
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>
>
> By the way... I did not say
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Co-Organizers
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The b and c cell constants look remarkably similar
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read
Sent: Thursday, May 08, 2014 3:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] stalled refinement after MR solution
Hi Yarr
Hi Yarrow,
If Dale said that, he probably wasn’t saying what he meant clearly enough! The
NCS 2-fold axis has to be parallel to the crystallographic 2-fold (screw) axis
to generate tNCS. In your case, the NCS is a 2-fold approximately parallel to
the y-axis, but it’s nearly 9 degrees away fro
Dear Colleagues,
Please pardon the shotgun distribution of this query. It may only
directly concern a few beam-line scientists and software developers,
but comments from all interested parties are welcome.
Many people have happily used the IUCr imgCIF dictionary definitions
in data collecti
Hi Tim,
That's a good question. The negative density vanished and the model
itself has not changed much. I still plan to set up
soaking/cocrystallization experiments with the metal ion. I am hoping
this will increase occupancy. That is the only solution that comes to
mind.
Regards,
Chris
On 5/8/
Hi Chris,
this certainly improved your model with respect to the data including
all their errors. How do you know this did not make your model worse
with respect to chemistry, respectively to what is inside your crystal?
Best,
Tim
On 05/08/2014 07:26 PM, Chris Fage wrote:
> Hi Everyone,
>
> Tha
That is probably the culprit. The two unit cell dimensions are...
dataset #1: 68.8295 75.9597 83.3998 65.4000 88.8500 64.9000
dataset #2: 68.3005 75.7100 83.1299 65.3601 88.8900 65.2600
I can't believe I didn't look at that. I know better. Thanks for all of
your quick response
Hi Everyone,
Thank you for the advice, especially Pavel's. My issue has been
resolved. I lowered the occupancy and B-factors of the metal ions in
the .pdb and ran phenix.refine for 10 cycles. This removed most of the
negative Fo-Fc density. Anisotropic refinement of the metal ion
B-factors was als
Hello CCP4 community,
I am stumped and would love some help. I have a molecular replacement
solution that has Rfree stuck around 40% while Rwork is aorund 30%. The
model is actually the same enzyme with a similar inhibitor bound. Relevant
information is below.
-Yarrow
I have solved a structure i
How close are the cell constants?
On May 8, 2014, at 12:17 PM, Katherine Sippel
wrote:
> I forgot to mention the space group is P1. Sorry about that.
>
> Thanks,
> Katherine
>
>
> On Thu, May 8, 2014 at 12:02 PM, Katherine Sippel
> wrote:
> Hi all,
>
> I have two nice, but a hair under-co
I forgot to mention the space group is P1. Sorry about that.
Thanks,
Katherine
On Thu, May 8, 2014 at 12:02 PM, Katherine Sippel <
katherine.sip...@gmail.com> wrote:
> Hi all,
>
> I have two nice, but a hair under-complete data sets that I am trying to
> merge together. If I run aimless on them
Hi all,
I have two nice, but a hair under-complete data sets that I am trying to
merge together. If I run aimless on them separately everything looks
beautiful. When I merge them together the CC1/2 is still good but all the
various and sundry Rs sky rocket. When I go to the log file and look at th
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On Thu, 8 May 2014 16:56:01 +0200, Christophe Wirth
wrote:
>Dear all,
>
>To add another bit to the discussion, I would say that an increase of Rmerge
>and Rmeas is just expected in such a case, isn't it?
>
>According to your tables, in P1, the multiplicity is about 4. In P2, it's
>about 7. In
Dear all,
To add another bit to the discussion, I would say that an increase of Rmerge
and Rmeas is just expected in such a case, isn't it?
According to your tables, in P1, the multiplicity is about 4. In P2, it's about
7. In P3, it's 10. And in P6, it's approaching 20. I would say that this le
Hi,
please post the pointless table "Analysing rotational symmetry in lattice
group P 6/m m m". This gives a quite clear information about the
presence/absence of rotational symmetry axes.
Look at at the following example
Analysing rotational symmetry in lattice group P 6/m m m
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Dear Rain,
Maybe a little late, but here are some more comments:
1) What is the deal? For me, one can only know the space group after the
structure has been solved. I have seen quite few cases (e.g. twinning,
non-crystallographic symmetry etc.) that all programs (XDS, pointless) and
statistics
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Maria,
>From my experience with co-crystallization experiments, if crystals appear
>immediately
after setting up the
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