Re: [ccp4bb] clashscore question

[Robbie Joosten]

Hi Xiaodi,

Please read the PDB validation report for the individual clashes and see if 
these are symmetry or alternate related. If you have been playing around with 
atomic occupancies, this also affects which atoms are taken into account for 
the clashscore. Also, which hydrogen model did you use? The latter can affect 
the score a bit although I've never seen this much of a difference.

HTH,
Robbie

On 16 Jan 2019 05:22, Xiaodi Yu  wrote:
Hi All:

I have a pdb file and the clashscores reported from both phenix and MolProbity 
were around 5, while the clashscore from the pdb validation server is 17. I 
wonder what may cause the difference? Any suggestion is appreciated.

Thank you.

Xiaodi



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Re: [ccp4bb] clashscore question

[Sharan Karade]

Dear Yu,

I think pdb validation server add hydrogen to the structure and then
calculate the clashscore. The other methods you mentioned calculate
clashscore without adding hydrogen to the structure.

Regards
Sharan


On Tue, Jan 15, 2019, 11:23 PM Xiaodi Yu  Hi All:
>
> I have a pdb file and the clashscores reported from both phenix and
> MolProbity were around 5, while the clashscore from the pdb validation
> server is 17. I wonder what may cause the difference? Any suggestion is
> appreciated.
>
> Thank you.
>
> Xiaodi
>
> --
>
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[ccp4bb] clashscore question

[Xiaodi Yu]

Hi All:

I have a pdb file and the clashscores reported from both phenix and MolProbity 
were around 5, while the clashscore from the pdb validation server is 17. I 
wonder what may cause the difference? Any suggestion is appreciated.

Thank you.

Xiaodi



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Re: [ccp4bb] covalent link to aa

[Bernhard Lechtenberg]

Hi Markus,

Did you load the .cif file into Coot before real space refinement? File -> 
Import CIF dictionary …
When you do that, Coot should be able to refine the link and that might then 
also help for the refinement in Refmac.

Bernhard
Bernhard C. Lechtenberg, PhD
Postdoctoral Associate
Riedl Lab
Cancer Metabolism and Signaling Networks Program
NCI-Designated Cancer Center

[cid:24A04CE0-5418-4257-A8D1-8084CA766BC9@burnham.org]

10901 N. Torrey Pines Road, La Jolla, CA 92037
T  858.646.3100 ext. 4216  E 
blechtenb...@sbpdiscovery.org
Science Benefiting Patients®

On Jan 15, 2019, at 12:49 PM, Markus Heckmann 
mailto:markus.21...@gmail.com>> wrote:

Dear all,
I have a structure where CYS is bound to OCA (octanoic acid). I
started with Jligand and created a CYS-OCA covalent link. It then
output a CIF file (verified looks OK). Add the LINK record to PDB
file:

LINK SG  CYS A 161 C1  OCA A 902CYS-OCA

Place OCA to the model using Coot. When I now use RealSpaceRefinement,
the OCA is placed on top of CYS itself. Coot does not recognise that
OCA-CYS link but why? therefore, I just place OCA at Place it in
*reasonable* position without any overlaps.


All files are located at
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgist.github.com%2Fort163%2Fe6b8411f45e5224f7d46fc36c3324e6f&data=02%7C01%7Cblechtenberg%40SBPDISCOVERY.ORG%7Cddcea39782f54aa79e0008d67b2b4211%7C0b162723004547deb0699f1a7aa955a1%7C0%7C0%7C636831823062844471&sdata=YuhoO%2B6giCrJwZ9R4Njw2UBpkp6c85PZHA%2FSYiBwZnw%3D&reserved=0

Now in REFMAC, input MTZ,PDB and the CIF file (from jligand). After
refinement, I find that the oxygen in the OCA is pointing wrongly. The
thioester bond is also NOT ideal distance (though density is good).

Is there anything wrong with my procedure? *Shouldnt* the refinement
optimise everything in OCA-CYS link?

Best
Markus



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[ccp4bb] covalent link to aa

[Markus Heckmann]

Dear all,
I have a structure where CYS is bound to OCA (octanoic acid). I
started with Jligand and created a CYS-OCA covalent link. It then
output a CIF file (verified looks OK). Add the LINK record to PDB
file:

LINK SG  CYS A 161 C1  OCA A 902CYS-OCA

Place OCA to the model using Coot. When I now use RealSpaceRefinement,
the OCA is placed on top of CYS itself. Coot does not recognise that
OCA-CYS link but why? therefore, I just place OCA at Place it in
*reasonable* position without any overlaps.


All files are located at
https://gist.github.com/ort163/e6b8411f45e5224f7d46fc36c3324e6f

Now in REFMAC, input MTZ,PDB and the CIF file (from jligand). After
refinement, I find that the oxygen in the OCA is pointing wrongly. The
thioester bond is also NOT ideal distance (though density is good).

Is there anything wrong with my procedure? *Shouldnt* the refinement
optimise everything in OCA-CYS link?

Best
Markus



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[ccp4bb] hybrid photon counter in the home lab

[wtempel]

Hi,
I would value your opinions in this equipment-related question.
Allé et al have compared detector types with a molybdemon source for a
small molecule application
. Are there similar
published comparisons for protein crystallography? What benefits can I
expect from replacing a CCD detector with a hybrid photon counter at an
energy of 8 keV and in the absence of the flux that a modern synchrotron
provides?

Thank you in advance.
Wolfram Tempel



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Re: [ccp4bb] translational NCS & twinning

[Donghyuk Shin]

Dear Eleanor,

Many thanks for you comments.

I have run aimless/pointless with those data sets having unit cell (134/67, 
134/67, 183, 90, 90 120) previously integrated with P31 2 1.
Previously, I forced aimless to not determine laue group, to keep the original 
SG, and now I let aimless determine the SG.

Both aimless and pointless re-indexed both data sets to the P63 2 2 for both 
data sets.
Based on the matthews analysis, it seems impossible to put molecule in to small 
cell (67. 67, 183, 90, 90, 120), and truncate analysis for this large cell 
indicates both tNCS and twinning. I am confused..how to interpret my data sets. 
Does it have both tNCS and twinning? 

For curiosity, I have ran the Phaser by turning on/off the tNCS with larger 
cell (134, 134, 180, 90, 90, 120), and only the phaser 'without tNCS' gave me 
the solution, but still it did not give me the 2 molecules/ASU which should be, 
and just 1mol/ASU.
Again for curiosity, I ran Refmac but results were like below.
-> Refmac without twin: 0.51/0.56 (work/free)
-> Refmac with twin: 0.52/0.59

I am also attached the log file of pointless for both cells.

Going back to the previous post, I am very open to accept that my C2 refinement 
is wrong, happy to learn. But, based on L-test, H-test and dropping R-values 
and model with density, I guess this is quite convincing but as you commented 
maybe I am misleading. Please let me know if you have more comments.


Best wishes,
Donghyuk





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#CCP4I VERSION CCP4Interface 7.0.051
#CCP4I SCRIPT LOG pointless
#CCP4I DATE 15 Jan 2019  13:42:04
#CCP4I USER user
#CCP4I PROJECT donghyuk_d011_x024
#CCP4I JOB_ID 135
#CCP4I SCRATCH /tmp/user
#CCP4I HOSTNAME localhost.localdomain
#CCP4I PID 30946

 
 ###
 ###
 ###
 ### CCP4 7.0.051: POINTLESS version 1.11.8 : 19/12/17##
 ###
 User: user  Run date: 15/ 1/2019 Run time: 13:42:04 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

 Input command lines 

XDSIN /home/user/Donghyuk/d011_x024/process_donghyuk/xds_016/XDS_ASCII.HKL
HKLOUT /home/user/Donghyuk/d011_x024/ccp4/XDS_016_pointless.mtz
## This script run with the command   ##
# /home/user/Downloads/destination/ccp4-7.0/bin/pointless


 End of input

Release Date: 19th December 2017


**
**
* POINTLESS  *
*   1.11.8   *
**
*   Determine Laue group from unmerged intensities   *
* Phil Evans MRC LMB, Cambridge  *
* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
**
**


Reading XDS ascii file from file /home/user/Donghyuk/d011_x024/process_donghyuk/xds_016/XDS_ASCII.HKL

Header lines:

!FORMAT=XDS_ASCIIMERGE=FALSEFRIEDEL'S_LAW=FALSE
!OUTPUT_FILE=XDS_ASCII.HKLDATE=11-Jan-2019
!Generated by CORRECT   (VERSION Jan 26, 2018  BUILT=20180808)
!PROFILE_FITTING= TRUE 
!NAME_TEMPLATE_OF_DATA_FRAMES=/home/user/Donghyuk/d011_x024/x024_C11_1_??.h5 GENERIC
!DATA_RANGE=   1 900
!ROTATION_AXIS=  0.99  0.001086 -0.000195
!OSCILLATION_RANGE=  0.15
!STARTING_ANGLE= 0.000
!STARTING_FRAME=   1
!INCLUDE_RESOLUTION_RANGE=50.000 1.582
!SPACE_GROUP_NUMBER=  152
!UNIT_CELL_CONSTANTS=   134.222   134.222   182.665  90.000  90.000 120.000
!UNIT_CELL_A-AXIS=-9.656   -13.195   133.223
!UNIT_CELL_B-AXIS=36.958   117.512   -53.297
!UNIT_CELL_C-AXIS=  -175.05651.620-7.575
!REFLECTING_RANGE_E.S.D.= 0.163
!BEAM_DIVERGENCE_E.S.D.= 0.029
!X-RAY_WAVELENGTH=  0.87
!INCIDENT_BEAM_DIRECTION= -0.002009 -0.001292  1.10
!FRACTION_OF_POLARIZATION=   0.990
!POLARIZATION_PLANE_NORMAL=  0.00  1.00  0.00
!AIR=  0.000339
!SILICON=  3.942720
!SENSOR_THICKNESS=  0.45
!DETECTOR=EIGER 
!OVERLOAD=   300
!NX=  4150  NY=  4371QX=  0.075000  QY=  0.075000
!ORGX=   2066.92  ORGY=   2186.64
!DETECTOR_DISTANCE=   260.894
!DIRECTION_OF_DETECTOR_X-AXIS=   1.0   0.0   0.0
!DIRECTION_OF_DETECTOR_Y-AXIS= 

[ccp4bb] MRC-IMPaCT PhD -LISCB Leicester & MPL Diamond

[Peter Moody]

*Deadline Sunday 20 January 2019*.

The theme for the MRC IMPaCT programme is complex disease.  This project
studies membrane protein complexes relevant to fibrosis, and funding is for
3.5 years. It will be based within LISCB (Leicester Institute for
Structural & Chemical Biology), and is a partnership with NIHR Leicester
BRC-Respiratory, and the Membrane Protein Lab at Diamond/Harwell.
Prospective applicants are encouraged contact *Bibek Gooptu*

/Andrew Quigley to discuss and can access the application form via this
link (one among various listed projects):

https://more.bham.ac.uk/mrc-impact/phd-opportunities/
Converting insult into injury: Cellular and structural biology studies of a
macromolecular complex that links inflammation with scarring in fibrotic
disease

Supervisors: Bibek Gooptu (UoL) and and Andrew Quigley (Diamond)

45% of deaths in the developed world arise as a result of fibrosis –
replacement of normal tissue with scar. Fibrosis is a basic response to
severe or sustained insult. If confined, fibrosis can limit further tissue
damage, but when widespread it leads to organ failure, cancer risk, and
death. We study how different insults cause fibrosis, focusing on lung and
liver disease. We have recently identified a molecular complex that
represents a junction between acute inflammation and chronic scarring
pathways, and may be an important target for future drug therapies. This
project will use state-of-the-art cellular and structural biology
approaches to understand the molecular details of how the complex
assembles, works, and may be targeted by drugs. It will be studied in the
context of intracellular (glycoprotein misfolding) and extracellular
(bacterial molecule) insults. The work is excitingly cross-disciplinary
(membrane protein crystallography, cryo-EM, cell biology, and integration
within clinical/translational studies). It is also cross-institutional
(Leicester Institute of Structural and Chemical Biology, NIHR Leicester
BRC, Research Complex at Harwell, Diamond Light Source). The supervisors
span these institutions and areas of expertise, from clinical to atomic
resolution studies, and can offer outstanding training and support.


Posted on behalf of *Bibek Gooptu **Professor of Respiratory Biology, LISCB
and NIHR BRC-Respiratory, University of Leicester*

* Consultant in Respiratory Medicine, Glenfield Hospital*

*Please do not reply to me, I'm not very good at looking after this account
-Peter*



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[ccp4bb] Group Leader position in CryoEM at eBIC - Diamond closing date this wednesday 16th January!

[martin.wa...@diamond.ac.uk]

Dear all

For all the cryoEM people who clearly avidly follow ccp4 this is a reminder of 
an exciting opportunity to join eBIC at Diamond as a group leader in CryoEM

Full details here:
https://vacancies.diamond.ac.uk/vacancy/principal-electron-microscopy-scientist-ebic-368475.html

Informal inquires please direct to Peijun Zhang 
peijun.zh...@diamond.ac.uk

Thanks!
Martin







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[ccp4bb] Postdoc position in Structural Biology at the Francis Crick Institute

[Katrin Rittinger]

Dear Colleagues,



We are looking for a highly motivated structural biologist to join the group of 
Katrin Rittinger at the Francis Crick Institute as a postdoctoral fellow. Work 
in the group is focused on defining the regulatory mechanisms that underlie 
protein ubiquitination.
The successful applicant will use a wide range of approaches including 
structural biology techniques (X-ray crystallography and cryoEM), biochemistry, 
structural mass spectrometry (XL-MS, HDX and native MS) and cell biology to 
study the structure and function of TRIM family E3 ubiquitin ligases.



Further information about the position can be found at 
https://www.crick.ac.uk/research/labs/katrin-rittinger/vacancies

Informal inquiries are welcome 
(katrin.rittin...@crick.ac.uk)



Best wishes,



Katrin

-
Katrin Rittinger PhD
The Francis Crick Institute
Molecular Structure of Cell Signalling Laboratory
1 Midland Road
London NW1 1AT
Tel: ++44 (0)20 37962274
katrin.rittin...@crick.ac.uk
https://www.crick.ac.uk/research/labs/katrin-rittinger

The Francis Crick Institute Limited is a registered charity in England and 
Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
with its registered office at 1 Midland Road London NW1 1AT



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Re: [ccp4bb] translational NCS & twinning

[Eleanor Dodson]

Donghyuk - testing your "twinning" in a lower symmetry space group can be
misleading.
Many checks look to see if twin related reflections are similar.
But the twin laws are often the same as the symmetry operators, so if you
have ignored the true symmetry, you will wrongly assume you have twinning.

In this case I would do the following.
Look at the small trigonal cell in pointless/aimless etc.  (134.223/2
134.223/2 182.666, 90, 90, 120)
(You can just input the data integrated in C2 I think and pointless will
check alternate cells.
Your C2  data with these cell dimensions can be reindexed into a trigonal
cell
67.2  67.2 182.9  90.0  90.0 120.0 )

Then pointless will check the likely pointgroup symmetrys -  P3 ?  P3/mmm
?  P6?  etc and give you a score for each symmetry operator.

And since you now have no non-cryst translation you can believe the twin
tests much more.

OK?
Eleanor









On Tue, 15 Jan 2019 at 10:57, Donghyuk Shin  wrote:

> Dear all,
>
> Thank you very much for all of your constructive comments.
> Based on all of your comments, I have done several treatment on my data
> sets, and here are some questions related with both your comments and my
> results.
>
> First of all, I would like to make a short note summarizing all of your
> comments for the people who will have similar problem.
>
> 1) Twinning and tNCS has opposite effects to each other, and one should
> carefully analyze the data if one of them present.
> 2) Simple tNCS can be automatically analyzed and corrected during Phaser,
> but if it does not work, you may try to lower symmetry, decrease the size
> of the Uni cell, or turning off the tNCS option during phaser.
> 3) If one think there is twinning in the crystal, to make sure whether
> your data is twinned, it is better to take a look twinning test than seeing
> the R-values from refinement with twin operators. Applying twin operators
> always give you better R- values.
>
> Then, here are some questions related to my current analysis.
> Q1. As many of you concerned and I also had speculation on my C2 cell
> refinement with twin operators, I tried to analyze twinning of my datasets.
> (ATTACHED)
> As you can see the log file from truncate, I guess my crystal is twinned.
> In addition to this, I also followed the discussion between Randy and Lan.
> I wanted to make sure whether my refinement with twin operators is correct
> or not.  As Randy recommend and based on the paper from Garib N. Murshudov (
> http://www.ysbl.york.ac.uk/refmac/papers/Rfactor.pdf), I could see the
> drop of R-values with twin operators is always possible, however, in this
> paper, I could see the gap between refinements w/ or w/o twin operators is
> quite smaller than my case. (0.49-> 0.41 or 0.58 -> 0.52 vs my case 0.39 ->
> 0.23). Together, based on both twinning-test and good R-values, I now
> believe C2 refinement with twin operators are true. What do you think?
>
> Q2-1. Because some of you asked me about the original spots and
> re-indexing the data sets with high symmetry SG,  I went back to mosflm,
> and here are some images from my analysis. As you can clearly see there are
> strong/weak spots in the frames, and if you increase the threshold you can
> pick the strong spots (ATTACHED). Based on this, initially, I assumed that
> my crystal has tNCS, because I thought this strong - weak pattern is caused
> by tNCS. or Am I wrong?
>
> Q2-2. During new indexing, I choose two unit cells (large and small) and
> integrated them into 2 SG (P31 1 2 or P31 2 1) as Lijun commented. (four
> data sets)
> All of these data sets indicated twinning, while smaller one showed higher
> twinning fractions. Then, I ran phaser, and found that phaser only found
> the solution from P31 2 1SG from both large and small cells. However, I
> could see crash of molecules from large cell, and I decided to stick with
> small cell again. Then, during refinement with twin operators the R-values
> drops from (0.46/0.49) to (0.37/0.42), even the map looks already good. I
> assume that applying high symmetry SG is not possible for this case, and
> again C2 refinement might be correct.
>
> Q2-3. Related to Q1 and 2-1, Now, I think C2 (small cell) refinement with
> twin operator is right solution. Then, here I have another question.
> Based on the observations from frames, I guessed my crystal has tNCS, and
> I only followed strong spots. (Maybe I am wrong ?)
> Then, data sets with only strong spots suggests my crystal is twinned.
> Together, I am thinking my crystal has both tNCS and twinning, and I could
> solve the structure by following strong spots with twin operators.
>
> Again, I would like to express my special thanks to you all for giving me
> valuable comments.
> I hope this post will also useful for others in the future.
>
> Donghyuk
>
>
> 
>
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[ccp4bb] PostDoc AD

[Isabelle BILLAS MASSOBRIO]

Hello
Please find enclosed an ad for a postdoc position in our laboratory.
Many thanks in advance.
Best regards,

Dr. Isabelle M.L. BILLAS, Ph.D.
Institute of Genetics and of Molecular and Cellular Biology (IGBMC)
Department of Integrated Structural Biology
Team 'Large complexes involved in gene expression'
UMR7104 CNRS-UDS, INSERM U1258
1, rue Laurent Fries, BP 10142
F-67404 ILLKIRCH CEDEX

[http://archive.igbmc.fr/annuaire/images/tel_icon.gif]+33 3 69 48 52 71 
(Office: E-2014)
Email : bil...@igbmc.fr




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2019_Postdoc Ad Chan-Kastner.pdf
Description: 2019_Postdoc Ad Chan-Kastner.pdf