Behalf Of Kay
Diederichs
Sent: Thursday, March 21, 2013 10:02 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution limit of index in XDS
On Thu, 21 Mar 2013 08:28:27 +, herman.schreu...@sanofi.com wrote:
>Dear Tim,
>
>It could be that COLSPOT does not rely on experimen
N_RANGE .
best,
Kay
>
>Best regards,
>Herman
>
>
>
>-Original Message-
>From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de]
>Sent: Wednesday, March 20, 2013 11:17 PM
>To: Schreuder, Herman R&D/DE
>Cc: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] Resolution limit o
o:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim
>Gruene
>Sent: Tuesday, March 19, 2013 11:06 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] Resolution limit of index in XDS
>
>-BEGIN PGP SIGNED MESSAGE-
>Hash: SHA1
>
>Dear Niu,
>
>indexing relies on strong reflect
March 20, 2013 11:17 PM
To: Schreuder, Herman R&D/DE
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution limit of index in XDS
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Dear Herman,
the short answer might be that at the stage of COLSPOT the term 'resolution'
has a limi
solution cutoff for COLSPOT as
> well.
>
> Best, Herman
>
>
> -Original Message- From: CCP4 bulletin board
> [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent:
> Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject:
> Re: [ccp4bb] Reso
, March 19, 2013 11:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution limit of index in XDS
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Dear Niu,
indexing relies on strong reflections only, that is (in very brieft) why
INCLUDE_RESOLUTION_RANGE indeed does not affect the relections
Hello,
The way I do it is by manually editing the SPOT.XDS file (generated by
the COLSPOT step). Spots are arranged by order of decreasing intensity
in that file. So if you do down the file, select an appropriate
intensity cutoff and then remove all spots below that value, it will
have the ef
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Dear Niu,
indexing relies on strong reflections only, that is (in very brieft)
why INCLUDE_RESOLUTION_RANGE indeed does not affect the relections
collected in COLSPOT which in turn are used by IDXREF. You can work
around this, however, by making use o
Dear All,
Is there any command can set the resolution limit for index step in XDS? I
only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to be a
definition of resolution range after index step
as it says:
INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by
DEFPIX,INTEGRATE,CORRECT
Than
Hi Narayan,
there's nothing wrong with using data with I/sigmaI 2.5, Rsym 224.3 % for
multiplicity 7.8 and completeness 98.2 %.
However, when you discarded frames you might have made the data worse - one
should only reject data if they deviate systematically (e.g. from radiation
damage). Weak
I was [too] obliquely alluding to this thread...
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27056.html
JPK
On Wed, Jul 18, 2012 at 12:32 PM, Edwin Pozharski wrote:
> http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html
>
>
>
> > Rsym...what's that?
> >
> > JPK
> >
> > On Wed, Jul 18
http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html
>
Rsym...what's that?
>
> JPK
>
> On Wed,
Jul 18, 2012 at 9:12 AM, Edwin Pozharski
>
wrote:
>
>> As has been
shown recently (and discussed on this board), Rsym is not
>>
the
>> best measure of data quality (if any measure at all):
>>
>>
ht
Rsym...what's that?
JPK
On Wed, Jul 18, 2012 at 9:12 AM, Edwin Pozharski wrote:
> As has been shown recently (and discussed on this board), Rsym is not the
> best measure of data quality (if any measure at all):
>
> http://www.sciencemag.org/content/336/6084/1030.abstract
>
>
>
> > narayan viswa
As has been shown recently (and discussed on this board), Rsym is not the
best measure of data quality (if any measure at all):
http://www.sciencemag.org/content/336/6084/1030.abstract
> narayan viswam wrote:
>> Hello CCP4ers,
>>
In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI
narayan viswam wrote:
Hello CCP4ers,
In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & Rsym
224.3 %
for multiplicity 7.8 and completeness 98.2 %. I solved the structure by MAD &
refined it
to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not twinned.
The
Hi Narayan
My only comment would be that P622 is a fairly uncommon space group
(currently 43 PDB entries excl homologs), but obviously that doesn't
mean it's wrong - just worth double-checking! Just out of interest
what's the CC(1/2) statistic for your highest shell?
Personally I specify more bi
Hello CCP4ers,
In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & Rsym
224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the
structure by MAD & refined it to Rfree 27.3 %. Ths crystal belongs to P622
space group and it is not twinned. The water content is 68%. I low
Hi Jon
On 30 Oct 2010, at 00:46, Tom Huxford wrote:
Hi all,
I'm working with good quality relatively complete x-ray diffraction
data collected to a resolution limit 2.6 Å from a crystal of a protein
with a small molecule ligand bound. I ran MR from 10-4 Å and then did
maximum likelihood rigid
I guess you are using as input mtz the output mtz from the previous cycle?
This will be limited to the requested previous resolution..
it is good practice to always use as input the full data - eg
mystuff-scala.mtz output from the scala/ctruncate step..
If the input file has the full resolutio
On Fri, Oct 29, 2010 at 5:46 PM, Tom Huxford wrote:
> I'm working with good quality relatively complete x-ray diffraction data
> collected to a resolution limit 2.6 Å from a crystal of a protein with a
> small molecule ligand bound. I ran MR from 10-4 Å and then did maximum
> likelihood rigid bod
Hi all,
I'm working with good quality relatively complete x-ray diffraction
data collected to a resolution limit 2.6 Å from a crystal of a protein
with a small molecule ligand bound. I ran MR from 10-4 Å and then did
maximum likelihood rigid body refinement in Refmac5 against data from
50-3.
Hi All,
I read some literature for phasing by molecular replacement performed with
reflections upto 3.5 Angstroms. Can anybody tell me why? I would prefer
deleting low resolutions so as to reduce contribution from the solvent that
might affect RF search and obtaining a solution. Your responses to
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