?
2. Any easier method to generate the "LINK" record between molecules from
different asymmetric units?
Thanks a lot for your help!
Best regards,
Qixu Cai
Email: caiq...@gmail.com
To unsubscribe from the CCP4BB list, c
Yes. I tried to weight those B values by occupancies, but the result is
still not the same as the value reported by refmac5.
Qixu Cai
Email: caiq...@gmail.com
Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
于2023年11月6日周一 14:04写道：
> Are there some atoms with occupanc
I tried both and none of them is the same as reported by refmac5.
Qixu Cai
Email: caiq...@gmail.com
James Holton 于2023年11月6日周一 01:11写道：
> Are you averaging over all ATOM records? Or are you including HETATM as
> well?
>
> On 11/5/2023 5:45 AM, Qixu Cai wrote:
>
> Dear all
Thanks for your reply. Does the refmac5 program weight the mean B value by
the resolution?
Qixu Cai
Email: caiq...@gmail.com
Ian Tickle 于2023年11月5日周日 19:34写道：
> The arithmetic mean B value from the structure as quoted everywhere is
> pretty meaningless anyway and 10 Ang.^2 either
as used in refmac5.
When we prepare the Table 1 of manuscript, which one is correct for the
"average B value"?
Thanks and best regards,
Qixu Cai
Email: caiq...@gmail.com
To unsubscribe from the CCP4BB list, clic
Dear Robbie and Tim，
Thanks a lot for your reply. I just do not understand that if we can change
the R free set during different rounds of refinement, the gap between Rwork
and Rfree would be small, and Rfree would be meaningless, as R-free set is
not "free".
Best regards,
Qixu Cai
E
Dear all,
I'm using the PDB-REDO server to refine my structure. I found that PDB-REDO
said that 5% R-free set is too small and it created a new R-free set.
Is possible for the PDB-REDO server to keep the original R-free set to make
final Rfree value comparable?
Best regards,
Qixu Cai
x27;s the difference between the CCP4
polar angle definition and eulerian angle ZXZ definition?
And what's the definition of polar angle XYK convention in GLRF program?
Thank you very much!
Best wishes,
--
Qixu Cai
Email: caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fuj
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Calculate_average_I/sigma_from_.sca_file
Qixu Cai
Email: caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fujian, China
**from thunderbird**
On 02/13/2014 12:20 AM, Ronald E Stenkamp wrote:
How did people get when using
Dear Tim,
Does the program of O support only the quad-buffered stereo mode, not the
Zalman mode?
Qixu Cai
Email: caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fujian, China
2013/3/1 Tim Gruene
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Jl,
>
Thanks. That's what I need.
Qixu Cai
Email: caiq...@gmail.com
在 2013-2-25，下午9:38，Jon Agirre 写道：
> If you just want to generate symm mates from MTRIX records, you may
> want to give GK's 'xpand' a go:
> http://xray.bmc.uu.se/usf/xpand_man.html
>
> Othe
Dear Harry,
It's a useful function. Could you please added it?
Thanks.
Qixu Cai
Email: caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fujian, China
2013/2/25 Harry Powell
> Hi Richard
>
> I'm afraid it doesn't exist at the moment. It could be added
section and use the matrix in the pdbset.
so I have to convert the matrix from
r11r12r13tx
r21r22r23ty
r31r32r33tz
to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz.
How can I do it?
Thanks.
Qixu Cai
Qixu Cai
Email: caiq...@gmail.com
School of Life Science
; keywords of
the pdbset program?
is it "r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz"?
And how to covert from the "pdb file format" to the "pdbset format"?
What's the matrix format of "apply NCS operators" in phenix GUI?
Thanks a lot!
Qixu Cai
Dear Tim Gruene,
2013/1/24 Tim Gruene
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Rajesh,
>
> first of all, a model is not "true" or "false", it can only be
> "better" or "worse".
>
> The explanation of what you observe depends on what you did:
> - - did you use the identical an
Dear all,
Could you please teach me any method to present the relationship between
resolution and B values of all the x-ray structures in Protein Data Bank.
Can the PDB statistics in RCSB do it?
Thank you very much!
Q. Cai
Dear Andreas Förster,
You can use "ccp4um" (ccp4 update manage) to update CCP4 from command line.
Best wishes,
Q. Cai
Qixu Cai
Email: caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fujian, China
2013/1/14 Andreas Förster
> Dear CCP4 maintainers,
>
> I&#x
/2012 07:32 PM, Paul Emsley wrote:
On 23/11/12 08:54, Qixu Cai wrote:
I have some problems about coot.
1, How to run the "Extensions --> All molecule --> Stepped refine" at
"no-graphic" mode of coot?
(let ((imol (read-pdb "coot-download/3rso.pdb"))
(imo
n these functions?
Thanks for your help.
Best wishes,
Q. Cai
On 11/23/2012 07:32 PM, Paul Emsley wrote:
On 23/11/12 08:54, Qixu Cai wrote:
I have some problems about coot.
1, How to run the "Extensions --> All molecule --> Stepped refine" at
"no-graphic"
Dear all,
I have some problems about coot.
1, How to run the "Extensions --> All molecule --> Stepped refine" at
"no-graphic" mode of coot?
2, Are all of the extensions in coot the scheme/python scripts? If yes,
where the script files store at?
2, And is there any option to prevent coot auto-l
ms that the "SAD data directly" gets a better result for my SAD data.
Best wishes,
Q. Cai
Qixu Cai
Email: caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fujian, China
2012/11/5 Navraj Pannu
>
>
>> I am not sure how you would fare with SAD data directly..
&
Dear all,
What's the difference between "no prior phase information", "phase and
FOM", Hendrickson-Lattman coefficients", and "SAD data directly" in the
refmac5 GUI of CCP4i?
I have a SAD dataset and solve the phase by phenix.autosol. Now I want to
refine the structure by refmac5, which kind of i
C222 means 2 possible space groups C222 and C2221.
P222 means 8 possible space groups.
ps: I don't understand the C2221A and C222A listed by phaser when I chose
the "alternative space groups (listed)" option in C222 space group, because
when I chose "all alternative space group", only C222 and C22
of C2221 is 25% of the P22121. But I cannot index the
data to C2221 space group.
Thanks a lot.
Best wishes,
Qixu Cai
2012/8/1 Eleanor Dodson
> Are your unit cell and SG correct? I think you maybe should reindex to get
> a cell volume 25% of this one, and maybe SG P21
> That patterso
ere any tNCS refinement options in refmac?
Thanks for your help.
Best wishes,
Qixu Cai
2012/7/31 Randy Read
> Hi,
>
> The second Patterson peak is twice the first (considering lattice
> translations, where 1 is equivalent to 0 modulo 1), and then if you triple
> the first vector yo
Dear Lakshmanan Govindasamy,
I cannot find the related information in refmac5 document. Could you
please help me?
Thanks.
Qixu Cai
Email: caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fujian, China
**from thunderbird**
On 08/01/2012 04:43 AM, Lakshmanan Govindasamy wrote
Dear all,
When we are running the rigidbody refinement of refmac5, if we do not
assign the rigidbody group in CCP4i GUI, what's the default rigidbody group
in refmac5?
Is it a rigidbody for each chain?
Thanks a lot.
Thanks a lot for your help.
Best wishes,
Qixu Cai
2012/7/31, Eleanor Dodson :
> More details - what do you mean by pesudo-translational symmetry ?
> Are there two molecules related by a translation vector? or its it
> something more complicated?
> Eleanor
>
> On 31 July 2012 10:47
Dear all,
Can I use the "twin refinement" to refine the pesudo-translational symmetry
dataset?
Thanks a lot for your help.
Best wishes,
Qixu Cai
?
And is that necessary to specify the location of MSE?
Thanks a lot for your help.
Qixu Cai
?
Thanks.
Best wishes,
Qixu Cai
2012/5/30 Laurent Maveyraud
> Hi,
>
> it is therefore likely that your spacegroup is really P321... hopefully,
> your data set is not twinned, did you check that ?
>
> You are left with 2 possible indexing schemes, as already mentionn
90 90
120Rfactor to native: 29%
The Rfactor at low resolution is larger than in high resolution.
Could you please to help me figure out where the heavy atoms had been
soaked into the crystal?
Thank you very much.
Best wishe,
Qixu Cai
2012/5/30 Laurent Maveyraud
>
SIR to get some information
about the phase.
so I think for peak dataset, anomalous processing is necessary, and for
edge and remote dataset, anomalous processing is not necessary.
Is my understanding correct?
Thank you very much for your help.
Best wish,
Qixu Cai
2012/5/29 Tim Gruene
&
At first, I processed the data at P3 space group. But after phenix.xtriage
analysis, the Xtriage told me the space group must be P321, so I used P321
to process my data, and got an acceptable Rmerge.
Qixu Cai
2012/5/29 Phil Evans
> How do you know the point group is 321? What does Pointl
space group?
2, I have carryed out some suggestion of yours, such as use pointless （use
native data as reference for derivant2 reindex）, or reindex the derivant2
dataset by （k, h, -l）, and I always got the high R factor 59% between derivant2
and native.
Any suggestion?
thanks a lot!
Qixu Cai
;> invert the hand; this will depend on the reciprocal space asymmetric
> >> unit chosen by the processing program. One could imagine a situation
> >> where the a.u. chosen by one processing program was on a different
> >> hand from the a.u. required by another
t; hand from the a.u. required by another. In such a situation you would
> > have no choice but to invert the hand of the indices, though I suspect
> > you would be better off doing it with CAD which will do it reliably,
> > rather than reindex which may not (judging by the comments
would
> have no choice but to invert the hand of the indices, though I suspect
> you would be better off doing it with CAD which will do it reliably,
> rather than reindex which may not (judging by the comments in the
> reindex code!). Whether such a situation ever occurs in practice, I
-data when we want to use MAD method?
Thank you very much!
Best wishes,
Qixu Cai
o the native dataset,
if I chose "Automatically check and enforce consistent indexing between
different files",
the index would be changed back to the original index. Why?
Thank you very much for your attention.
Best wishes,
Qixu Cai
gt; we're measuring.
>
> this fits, don't you see?
>
> Cheers,
> Tim
>
> On 04/24/12 05:21, Qixu Cai wrote:
> > Dear Johan,
> >
> > "the standard deviation is defined as the square root of the
> > variance." while "The standard deviat
e.
http://mathworld.wolfram.com/StandardDeviation.html
The standard deviation has the same unit as the values you're measuring, which
makes its interpretation a tad easier.
// Best wishes; Johan
On 23 Apr 2012, at 18:13, Qixu Cai wrote:
Dear Ed,
Why the variance is the square of standard deviati
Dear Ed,
Why the variance is the square of standard deviation?
thank you very much!
在 2012年4月23日，20:53，Ed Pozharski 写道：
> On Sun, 2012-04-22 at 12:47 +0530, Arka Chakraborty wrote:
>> baverage program in ccp4 gave average bfactor of 25.0 for the residue
>> but coot is showing 150!
>
> Varia
Dear all,
I have solved a 3.5ang structure with R/Rfree = 0.23/0.32 (refmac5.6 result).
But when I used sfcheck to validate the coordinates and structure factors, I
got a high R factor > 0.38 !
Could anybody tell me the reason? Is that possible to deposit the coordinate to
PDB?
Thank you ver
Dear all,
Recently, I refine two low resolution structures in refmac 5.5. Their
resolutions are 3A and 3.5A respectively.
For 3A structure, after MR by phaser and rigidbody refinement&restraint
refinement by refmac5.5, I got R factor 25% and R free 35%. And then
each time, after my model build
te the carboxy terminus
File "/usr/lib64/python2.7/site-packages/pymol/selecting.py", line
162, in pop
if _self._raising(r,_self): raise pymol.CmdException
CmdException:
---
Can anybody t
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