Hi guys,
Maybe this may address a few of your questions. In 2019 we published a method
to validate structures unbiased from the terms used in refinement and works on
predicted models too.
Pražnikar, J., Tomić, M. & Turk, D. Validation and quality assessment of
macromolecular structures using c
t;>
>>> Possible useful items could be a solvent mask not including that regions,
>>> or a density map
>>>
>>> that includes only features with a certain boundary around that blob.
>>>
>>>
>>>
>>> I pilfered some kludges
regards to all, stay safe
> Celia
>
> --
> Dr Célia Plisson-Chastang, PhD, HDR
> Laboratoire de Biologie Moléculaire Eucaryote - CBI
> UMR CNRS 5099-Université Paul Sabatier Toulouse III
> Bâtiment IBCG, 118 Route de Narbonne
> 31062 Toulouse Cedex, France
> Tel
James,
> On 7 Mar 2020, at 21:01, James Holton wrote:
>
> Yes, that's right. Model B factors are fit to the data. That Boverall gets
> added to all atomic B factors in the model before the structure is written
> out, yes?
Almost true. It depends how the programs are written. In MAIN this is
James,
The case you’ve chosen is not a good illustration of the relationship between
atomic B and resolution. The problem is that during scaling of Fcalc to Fobs
also B-factor difference between the two sets of numbers is minimized. In the
simplest form with two constants Koverall and Bovera
re a mean to support one or more biologically relevant
conclusions.
???
best wishes,
dusan turk
> On 29 Feb 2020, at 01:00, CCP4BB automatic digest system
> wrote:
>
>
> Date:Fri, 28 Feb 2020 16:03:22 +
> From:"Phoebe A. Rice"
> Subject: Re: W
o we have a consensus?
best wishes,
dusan turk
Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://stef.ijs.si/
Head of Centre for Protein and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Scientific Director
http://www.cipk
gt; comment on twinning, but with NCS it would seem that the normal CCP4 way of
>> picking the R-free set is as good as anything else!
>> On Sunday, 26 May 2019, 14:02:50 BST, dusan turk
>> wrote:
>>
>>
>> Dear colleagues,
>>
>>
>>> Do
d Visualization, Protein Crystallography, Methods in
MolecularBiology 1607, Springer protocols).
I hope this helps to clarify a few issues.
dusan turk
> On 25 May 2019, at 01:00, CCP4BB automatic digest system
> wrote:
>
> Date:Fri, 24 May 2019 22:27:28 +
> From:Jonath
Dear Alex,
try MAIN "http://www-bmb.ijs.si/";
it has a two way interface to Ramachandran plot, you can either display
“HIS_RAMA” of individual clicked residues in displayed 3D model and also the
other way around, you can click on residues in Ramachandran plot and center on
the residue in 3D m
wrong and the current coordinates are used directly to get
local "Fc density" by expanding 3D Gaussians without reference to a previously
calculated map from refined phases.
Can anyone clarify exactly what maps are being compared during wwPDB
validation?
Ethan
--
Dr. Dusan Turk
ne. It
>> is in order to avoid the need for that extra time, or for a recourse
>> to various debiasing methods, that the "book-keeping faff" described
>> yesterday has been introduced. Operating without it is perfectly
>> feasible, it is just likely to not be optimally direct.
>&
a
>> lot of reflections, so 5% could be several thousand which would be more
>> than you need to just check Rfree seems OK.
>>
>> Since I really don't know what is the right # reflections to assign to a
>> free set thought I would ask here - what do you think? Essenti
structure of catalytically inactive mutant was published first
and when
- which catalytically inactive enzyme structure in complex with substrate or
part of it as a ligand was published first and when.
help of the community is highly appreciated,
best wishes,
dusan
Dr. Dusan Turk, Prof.
Head of
nly export three decimals, though I'm sure they
> use greater precision under the hood. I'm not opposed to exporting from
> coot or pymol either, I just haven't figured out how to do this yet - what
> would be the simplest way to calculate and export an NCS transformation
&g
not calculate these numbers,
> so they do not seem to be extremely important. If somebody could point me to
> a program which could calculate these number without too much effort, I would
> be happy to do it. Otherwise, I would still be willing to go the extra mile
> if someone could
ed the absence of contacts between layers
> in the crystal. Is it something that has already been observed in other
> crystals?
>
> Best regards,
>
> Fred
> -
> Frédéric Kerff
> Chercheur qualifié F.R.S.-FNRS
> Cristallographie des protéines
> Centre d'Ing
u.se/><http://www.cmps.lu.se <http://www.cmps.lu.se/>>
> Centre for Molecular Protein Science www.maxlab.lu.se/crystal
> <http://www.maxlab.lu.se/crystal>
> Lund University, Box 124, 221 00 Lund, Sweden www.saromics.com
> <http://www.sarom
cta Crys D (2014).
best regards,
dusan
Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://bio.ijs.si/sbl/
Head of Centre for Protein and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Scientific Director
http://www.c
ause there are clash_guard parameter with nonbonded_distance_threshold
> = 0.5 .
>I think I may try to turn of the clash_guard parameter.
>
>
> Best Regards!
> Lu Zuokun
>
>
>
> --
> 卢作焜
> 南开大学新生物站A202
Dr. Dusan Turk, Prof.
Head of Structural Bi
of the 36 characters. Thus
> there was no way to say that alternate conformation A in one residue is or
> is not associated with alternate conformation A in another residue.
>
> Frances
Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://bio.ijs.si/sbl/
l
>
>
> On Wed, Jun 18, 2014 at 9:21 AM, Antony Oliver
> wrote:
>
>> Hi Pavel,
>>
>> Sorry… the current ‘triumvirate’ is, in no particular order:
>>
>> CCP4, Phenix and Buster (Global Phasing).
>>
>> Any suggestions would indeed be u
references) and contact information (E-mail, phone, or Skype) should
be sent by mail or E-mail to
Prof. Dr. Dusan Turk
Jozef Stefan Institute
Dept. of Biochemistry and Molecular and Stuctural Biology
Jozef Stefan Instiutute
Jamova 39
1000 Ljubljana, Slovenia
Dr. Dusan Turk, Prof.
Head of Structural
Dear Guangyu Zhu,
if this is not a hypothetical case you can refine both structures in each
crystal form separately using whatever software and compare them later.
The structure can be refined also in both crystal forms simultaneously using
the multi crystal NCS refinement as implemented in MAIN
tran or C codes with possible suggestion may be
> helpful.
> Thank you.
> TA
>
Dr. Dusan Turk, Prof.
Head of Structural Biology Group
Head of Centre for Protein and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Scientific
nd - input map does not contain a whole ASU.
>
> Thanks!
>
> Niu
>
Dr. Dusan Turk, Prof.
Head of Structural Biology Group
Head of Centre for Protein and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Scientific Director
Pr
ieved this with GRADE.
Do I understand correctly that the CSD license restrain has been removed for
anyone providing such a service or is the use of MOGUL the only way how one can
provide CSDB derived parameters to public?
best wishes,
dusan
Dr. Dusan Turk, Prof.
Head of Structural Biology Gro
ter-deve...@globalphasing.com
>>
>> rather than write to a specific developer.
>>
>>
>>With best wishes,
>>
>>The Global Phasing developers: Gerard Bricogne, Claus Flensburg,
>>Peter Keller, Wlodek Paciorek, Andrew Sharff,
, whereas for a small number of downloads its use is not
restrained.
dusan
Dr. Dusan Turk, Assoc. Prof.
Head of Structural Biology Group
Head of Centre for Protein and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Scientific Director
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