er TLS
>>>>> group selections and see if these give nicer results. Things
>>>>> to try: TLSMD, including or excluding ligands and
>>>>> carbohydrates, other common-sense or gut-feeling structure
>>>>> partitionings. If you have a lot of differ
other common-sense or gut-feeling structure
>>>> partitionings. If you have a lot of different groupings to
>>>> test, you can reset the B-factor and do pure TLS refinement
>>>> (i.e. 0 cycles of restrained refinement) for all of them. You
>>>> c
all TLS groups selections.
>>>
>>> Cheers,
>>> Robbie
>>>
>>> Sent from my Windows Phone
>>>
>>> Van: Omid Haji-Ghassemi
>>> Verzonden: 8-8-2013 21:55
>>> Aan: CCP4BB@JISCMAIL.AC.UK
hen trying your final
> > refinement with all TLS groups selections.
> >
> > Cheers,
> > Robbie
> >
> > Sent from my Windows Phone
> >
> > Van: Omid Haji-Ghassemi
> > Verzonden: 8-8-2013 21:55
> > Aan: CCP4
assemi
> Verzonden: 8-8-2013 21:55
> Aan: CCP4BB@JISCMAIL.AC.UK
> Onderwerp: Re: [ccp4bb] TLS refinement and ANISOU records
>
> Dear Ethan,
>
> Thank you for your reply.
>
> I will try to review my refinement protocol once more; however, I am still
> perplexed at what
inal refinement with all TLS groups selections.
Cheers,
Robbie
Sent from my Windows Phone
Van: Omid Haji-Ghassemi
Verzonden: 8-8-2013 21:55
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: Re: [ccp4bb] TLS refinement and ANISOU records
Dear Ethan,
Thank you for your reply.
Dear Ethan,
Thank you for your reply.
I will try to review my refinement protocol once more; however, I am still
perplexed at what lies at the heart of the problem.
Overestimation of average B-factor using TLS is perfectly sound, but I am
not sure why all my structures the average increases trem
On Thursday, August 08, 2013 11:39:22 am Omid Haji-Ghassemi wrote:
> Dear all,
>
> I was about to deposit a few structures to the pdb when I noticed the mean
> B-factors were larger than one might expect.
>
> All the structures were refined using TLS refinement.
>
> During refinement in Refmac t
Dear all,
I was about to deposit a few structures to the pdb when I noticed the mean
B-factors were larger than one might expect.
All the structures were refined using TLS refinement.
During refinement in Refmac the average temperature factors for each
structure is reasonable. For example, a str
---
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor
> Dodson [eleanor.dod...@york.ac.uk]
> *Sent:* Wednesday, July 17, 2013 6:05 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] TLS refinement refmac
>
>Oh dear - you should always s
anor Dodson
[eleanor.dod...@york.ac.uk]
Sent: Wednesday, July 17, 2013 6:05 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] TLS refinement refmac
Oh dear - you should always start refinement against the original processed
data - but others have told you that already..
The TLS files will n
Stefan
>>>
>>>
>>> -Ursprüngliche Nachricht-
>>> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
>>> Guenter Fritz
>>> Gesendet: Mittwoch, 17. Juli 2013 10:39
>>> An: CCP4BB@JISCMAIL.AC.UK
>>> Betreff:
richt-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
von Guenter Fritz
Gesendet: Mittwoch, 17. Juli 2013 10:39
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] TLS refinement refmac
Dear all,
one gets different R values, if you re-read in the mtz written out by
refmac afte
Dear all,
one gets different R values, if you re-read in the mtz written out by
refmac after TLS refinement. I think this issue had been a while ago in
ccp4bb, but I can't find the right track.
Here are the details.
1st run:
If we do TLS + restr. refinement in refmac
we get:
InitialFina
On Wednesday 30 June 2010 11:57:45 am Pavel Afonine wrote:
> Hi Ethan,
>
> On 6/30/10 11:43 AM, Ethan Merritt wrote:
> > On Wednesday 30 June 2010 11:15:51 am Pavel Afonine wrote:
> >
> >> Just a remark/precaution: if you remove ANISOU records then you will
> >> basically invalidate the refine
Hi Ethan,
On 6/30/10 11:43 AM, Ethan Merritt wrote:
On Wednesday 30 June 2010 11:15:51 am Pavel Afonine wrote:
Just a remark/precaution: if you remove ANISOU records then you will
basically invalidate the refinement results (the refined model).
If that is true then I would say there i
On Wednesday 30 June 2010 11:15:51 am Pavel Afonine wrote:
> Just a remark/precaution: if you remove ANISOU records then you will
> basically invalidate the refinement results (the refined model).
If that is true then I would say there is a deeper problem.
The description of the TLS groups in th
Just a remark/precaution: if you remove ANISOU records then you will
basically invalidate the refinement results (the refined model). Make
sure you recompute the R-factors after removing ANISOU and be prepared
to see (much) higher values.
Pavel.
On 6/30/10 11:09 AM, Nat Echols wrote:
On Wed,
On Wed, Jun 30, 2010 at 10:59 AM, Pavel Afonine wrote:
> I am refining a structure at 2.25 A using Phenix.refine. I am using TLS
> parameters for refinement but as i use TLS, phenix does individual
> anisotropic refinemnt also.
>
> No, it doesn't: it does not do "individual anisotropic refinement
Hi Mirage,
I am refining a structure at 2.25 A using Phenix.refine. I am using
TLS parameters for refinement but as i use TLS, phenix does individual
anisotropic refinemnt also.
No, it doesn't: it does not do "individual anisotropic refinement"
unless you specifically asked for this.
Let m
Dear all,
I am refining a structure at 2.25 A using Phenix.refine. I am using TLS
parameters for refinement but as i use TLS, phenix does individual anisotropic
refinemnt also. Is there some setting by which i can close anisotropic
refinment?
Looking forward for your answers.
Regards
Mirage sin
Dear Martin,
this should be fixed in the latest refmac version
http://www.ysbl.york.ac.uk/~garib/refmac/latest_refmac.html
Please let us know if it is not!
Pavol.
--
Sent from: Leiden ZH Netherlands.
On Tuesday 03 March 2009, Nalam, Madhavi wrote:
> Hello:
> I am trying to refine a structure at 3 A resolution using TLS refinement.
> After 8-10 cycles of TLS refinement, R-free and R-factor converges. But
> R-free starts going up again from the first round of restrained refinement.
> My questi
Hello:
I am trying to refine a structure at 3 A resolution using TLS refinement. After
8-10 cycles of TLS refinement, R-free and R-factor converges. But R-free starts
going up again from the first round of restrained refinement. My question now
is can I stop just after TLS refinement without doi
Hi Folks,
If anyone wants to do this on an Intel mac you will need a fortran
compiler, which is not installed by XCode. There is a compatible
gfortran here:
http://r.research.att.com/tools/
which in my experience works fine, though is completely incapable of
producing static binaries.
There are
Child killing and/or wrong bus seems to be related with static
compilation on Mac intel OS 10.5. Existence of this bug is the reason
why the version with bug fixes was not announced.
If you build from source code then this bug can be overcomed
Download source files and copy them to ccp4 source
Yes - I found that irritating bug; it is a disaster for less experienced
users..
It doesnt seem to happen with the linux installation..
Eleanor
Anita Lewit-Bentley wrote:
Hi Ian,
A bug was reported with that version of Refmac, though I've no idea
if that would cause your problem: you shou
Hi Ian,
A bug was reported with that version of Refmac, though I've no idea
if that would cause your problem: you should upgrade to the latest
version from the York website.
Done - and here is what happens:
1) the latest CCP4 package (6.1.1) runs the same version of Refmac
(5.5.0066) and
Hi Anita
A bug was reported with that version of Refmac, though I've no idea if that
would cause your problem: you should upgrade to the latest version from the
York website.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On
Dear ccp4 folks,
I am refining a structure in several crystal forms, with several
molecules in the asymmetric unit. The structure is rather flexible, so
I am using TLS refinement, having first submitted the coordinates to
the TLSMD server (http://skuld.bmsc.washington.edu/~tlsmd/).
The TL
The residual B factors are only one contribution to the mean square
displacements, so don't read too much into the numbers. In particular,
there is an ambiguity between the trace of T and the mean residual B
factor - you can take a chunk out of Tr(T) and give it to all the atoms
in the TLS group. T
Hello everyone,
I have two structures of a protein bound to two different small molecules I
am trying to refine with REFMAC5 from CCP4 v6.0.0. One has a resolution of
3.2 and the other has a resolution of 2.9. If I use TLS refinement
parameters on these structures I can get the Rwork/Rfree down
> Chaudhry, Charu (NIH/NICHD) [F]
> Sent: Monday, August 25, 2008 10:29 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] TLS refinement
>
> Hello,
>
> I have a question about comparing anisotropic displacement parameters for a
> series of 6 mutant and a wt structure with
Hello,
I have a question about comparing anisotropic displacement parameters for a
series of 6 mutant and a wt structure with diffraction from 1.2-1.5 Å. The
space group and unit cell for the series is the same, and most xtals were
obtained by seeding from a hit for one mutant. There are two
Hi Alexei,
at this resolution you most likely need to refine isotropic group B (one
B per residue or so) or/and do TLS refinement (on top of it).
Cheers,
Pavel.
---
Pavel V. Afonine, Ph.D.
Lawrence Berkeley National Lab, Berkeley CA, USA (http://www.lbl.gov/)
CCI: Computational Crystallograph
Hi,
I have a question with B-factor and TLS refinement. My protein diffracts
only to modest/low resolutions (3.4 A). I've been refining isotropic
B-factors for main chain and side chain (not individual atoms) because I'm
worried at this resolution I don't have enough observations to justify
indiv
Dear Yogesh
Could you please try the version from York
www.ysbl.york.ac.uk/refmac/latest_refmac.html
You need to take appropriate refmac 5.4 (it is current stable
version) and dictionary. I remember that in older version there was a
problem in one of RNA bases and it has now
been corrected
Dear CCP4 users,
I refined my final model (protein-RNA complex) using TLS refinement in
Refmac but when i am validating the coordinates I am having an issue
with Bond Distances and Bond Angles of some of the bases of RNA, these
values for some of the bases are higher ( >6 times) then the standard
This parameter is MAXTLSGRP in $CCP4/src/refmac5_/tls.fh
You can increase it here BUT you have to then re-compile Refmac.
It doesn't have phenix.refine's dynamic allocation ;-(
Note that it is already increased to 200 in Refmac 5.3 available from
York or from http://www.ccp4.ac.uk/prerelease/
H
Hi,
phenix.refine allows unlimited number of TLS groups of any size.
More :
general info: http://www.phenix-online.org/
refinement info: http://www.phenix-online.org/download/cci_apps/ (click
"Documentation" or "QuickFacts" right next to phenix.refine link).
or write me back with your questi
hello-
i am refining a structure with six copies of a complex (one dimer and
one monomer) in the asu. the output of the TLSMD server suggests to
me that i should use six TLS groups for each protomer in the dimer
and four TLS groups for the monomer. when i ran REFMAC, however, i
an encoun
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