from:"Wim Burmeister"

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

2023-12-18 Thread Wim Burmeister

Hello, 
this looks like beta-mercaptoethanol adduct through a S-S bond. 
See 
[ https://pubmed-ncbi-nlm-nih-gov.insb.bib.cnrs.fr/12421561/ | The crystal 
structure of the Epstein-Barr virus protease shows rearrangement of the 
processed C terminus.  ] 
Buisson M, Hernandez JF, Lascoux D, Schoehn G, Forest E, Arlaud G, Seigneurin 
JM, Ruigrok RW, Burmeister WP. J Mol Biol. 2002 Nov 15;324(1):89-103. doi: 
10.1016/s0022-2836(02)01040-9. 

Wim 

De: "Liliana Margent"  
À: "CCP4BB"  
Envoyé: Lundi 18 Décembre 2023 18:03:46 
Objet: [ccp4bb] extra Fo-Fc density in two Cysteines 

Hi there, We’ve been having an issue in trying to clear regions of Fo-Fc 
density from a few cysteines during the refinement process. We were wondering 
if anyone had seen something similar so they could offer some insight on the 
likely chemistry at hand, and a potential refinement solution. Attached are two 
images of the observed extra density at two cysteines, 505 and 518. We have 
modeled acetylated cysteine, s-hydroxycysteine, and s-mercaptocysteine but it 
does not solve the density. The protein in question is a Protein Tyrosine 
Phosphatase known as STEP (PTPN5), with data collected to a resolution of 1.79 
Å. The crystals were grown in bis-tris pH 6.65, 200mM Li2SO4, ~30% PEG3350. Of 
note, prior to data collection the crystal was conserved at room temp for long 
time where it dried, and was subsequently rehydrated with mother liquor. Thank 
you so much. 



To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 

[image/png:Screenshot 2023-12-16 at 3.36.01 PM.png] 

-- 
Wim Burmeister 
Professor 
Institut de Biologie Structurale (IBS) CIBB 
71 avenue des Martyrs / CS 20192 
38044 Grenoble Cedex 9, FRANCE 
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
Mobile: +33 (0) 7 50 49 19 91 
[ 
https://www.ibs.fr/en/research/microbiology-infection-and-immunity/viral-replication-machines-group-m-jamin/team-burmeister/
 | website ] [ 
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
 ] 

[ https://showyourstripes.info/s/europe/france/all | 
https://showyourstripes.info/s/europe/france/all ] 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] 1990s-style stereo viewer

2023-07-24 Thread Wim Burmeister

Hi,
the E PS300 already used LCD-based shutter glasses connected with a wire 
although awfully flickering with a switching frequency in the 8 Hz range!
Wim

- Mail original -
De: "Harry Powell" <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
À: "CCP4BB" 
Envoyé: Lundi 24 Juillet 2023 16:58:26
Objet: [ccp4bb] 1990s-style stereo viewer

Hi folks

I was wondering if anyone has a photo of the old-style head-mounted stereo 
viewers that used to be used to see 3D images from wall-eyed stereo pairs? I 
don’t mean the ones that were used to view the side-by-side stereo images that 
once appeared in printed journals, but the ones that were used for advanced 
computer graphics machines like E PS300.

>From my somewhat dim memory, they had an adjustable mirror on one side so that 
>the two views could be coalesced (with the adjustment knob on the top of the 
>box).

More in hope than expectation…

Harry


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/
-- 
Wim Burmeister 
Professor 
Institut de Biologie Structurale (IBS) CIBB 
71 avenue des Martyrs / CS 20192 
38044 Grenoble Cedex 9, FRANCE 
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
Mobile: +33 (0) 7 50 49 19 91 
[ 
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
 | website ]



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] quantifying electron density

2023-06-29 Thread Wim Burmeister

Hello, 

I think, in principle this is possible if you use about internal controls. I 
used this approach a long time ago : 

Burmeister WP, Guilligay D, Cusack S, Wadell G, Arnberg N. Crystal structure of 
species D adenovirus fiber knobs and their sialic acid binding sites. J Virol. 
2004 Jul;78(14):7727-36. doi: 10.1128/JVI.78.14.7727-7736.2004. PMID: 15220447; 
PMCID: PMC434083. 

Cheers 
Wim 



De: "Hughes, Jonathan"  
À: "CCP4BB"  
Envoyé: Mercredi 28 Juin 2023 18:16:22 
Objet: [ccp4bb] quantifying electron density 

hello everyone, 
is there software that can use an electron density map to quantify the number 
of electrons in a selected volume somewhere in a protein? 
cheers 
jon 

-- 
Professor Jon Hughes, BSc, PhD 
Department of Physics 
Free University of Berlin 
Arnimallee 14 
14195 Berlin 
Germany 
mobile: (+49/0)1757929098 
email: lv...@posteo.de 
homepage: 
http://www.uni-giessen.de/fbz/fb08/Inst/pflphys 
Sent without the use of Apple products 

 

To unsubscribe from the CCP4BB list, click the following link: 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/ 

-- 
Wim Burmeister 
Professor 
Institut de Biologie Structurale (IBS) CIBB 
71 avenue des Martyrs / CS 20192 
38044 Grenoble Cedex 9, FRANCE 
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
Mobile: +33 (0) 7 50 49 19 91 
[ 
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
 | website ] 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] 3d stereo on windows 10/11

2023-02-10 Thread Wim Burmeister

Hello,
you won't find anything better than the old system with the p5000 quadro cards.
Just keep a linux computer running Debian 10 or Ubuntu 20 using the xfce
desktop and hope that the hardware doesn't fail for the next few years.
Best regards
Wim

De: "Krishnan Raman"
À: "CCP4BB"
Envoyé: Vendredi 10 Février 2023 16:34:05
Objet: [ccp4bb] 3d stereo on windows 10/11

What is the best current hardware setup for 3d stereo on windows OS.

Nividia does not support 3d vision anymore.

Iam still hanging onto to the old system with p5000 Quadro cards. Would like to
know what other alternatives are available?

Regards

Krish

CONFIDENTIALITY NOTICE

This email, including any attachments, may contain confidential or legally
privileged information that is intended only for the individual or entity to
whom it is addressed. If you are not the intended recipient, please be advised
that any dissemination, distribution or copying of this email and any
attachment is strictly prohibited. If you have received this email in error,
please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take
corrective measures and then permanently delete this email and any attachment,
including any printed copies. Thank you.

To unsubscribe from the CCP4BB list, click the following link:
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 |
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ]

--
Wim Burmeister
Professor
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs / CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ]
Mobile: +33 (0) 7 50 49 19 91
[
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
| website ]

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Deadline approaching : PhD thesis offer (F/M) "Structure of the vaccinia virus DNA replication machinery..."

2022-09-26 Thread Wim Burmeister

We are looking for a PhD student (f/m) starting on 1 November 2022 or on 1
January 2023 in our team at the Institut de Biologie Structurale ( [
https://www.ibs.fr/ | IBS ] ) in Grenoble, France working on the

Structure of the vaccinia virus DNA replication machinery in complex with DNA
substrates by single-particle cryo-electron microscopy

With the recent spread of monkeypox infections, poxviruses got into the
headlines. Our team works on the elucidation of structure and function of the
poxvirus DNA replication machinery, now mainly by single-particle cryo-electron
microscopy. The DNA replication of vaccinia virus, a safe model system,
involves the DNA polymerase holoenzyme complex E9-A20-D4, furthermore the
hexameric helicase-primase D5. The aim is to determine structures of these
assemblies by cryo-EM with bound DNA substrates, nucleotides, inhibitors and
nucleotide analogues in order to stabilize different functional states for the
understanding of poxvirus DNA replication. The project builds on the team’s
experiences in the structure determination and biophysical characterization of
the partners and their domains, our recent results on the cryo-EM of the
helicase domain of D5 and first results by cryo-EM on the holoenzyme.

The candidate should be computer literate and have some experience in the use
of Linux. Knowledge of relevant software packages used for cryo-EM will be an
asset. Furthermore, a sound background in biochemistry, physics or biophysics
is required as the project comprises multiple methods : protein production in
the baculovirus-insect cell system; protein purification by affinity
chromatography; sample preparation for cryo-EM. structure calculations for
single-particle cryo-EM on a Linux computing cluster; analysis and
visualization of protein structures.

The successful candidate will work in a [
https://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-burmeister/article/burmeister-team
| small team interested in poxvirus DNA
replication ] directed by Prof. Wim Burmeister within the « [
https://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/
| Viral Replication Machines group ] ». Cryo-EM and computing facilities are
available on the research campus, which is shared with international
institutes: the EMBL Grenoble outstation, the ESRF synchrotron and the ILL
research reactor. Working lang u ages of the institu t e are English and
French. Grenoble is a mid-size town with an international atmosphere located in
the middle of the French Alps. The net salary is about 1750 €/month ( ~ 2000 €
gross salary ),

In order to candidate please send a CV, a letter of motivation and a copy of
the Master diploma with marks to [ mailto:wim.burmeis...@ibs.fr |
wim.burmeis...@ibs.fr ] before 30 September, 2022.

Bibliography

Tarbouriech N, Ducournau C, Hutin S, Mas PJ, Man P, Forest E, Hart DJ,
Peyrefitte CN, Burmeister WP & Iseni F. The vaccinia virus DNA polymerase
structure provides insights into the mode of processivity factor binding. Nat
Commun. 2017;8: 1455.* doi:10.1038/s41467-017-01542-z.

Bersch B, Tarbouriech N, Burmeister WP, Iseni F. Solution structure of the
C-terminal domain of A20, the missing brick for the characterization of the
interface between vaccinia virus DNA polymerase and its processivity factor. J
Mol Biol. 2021; 167009.* doi:10.1016/j.jmb.2021.167009.

Hutin, S., Ling, W.L., Tarbouriech, N., Schoehn, G, Grimm, G., Fischer, U. &
Burmeister, W.P. The vaccinia virus DNA helicase structure from combined
single-particle cryo-electron microscopy and AlphaFold2 prediction. Viruses. In
press.
--
Wim Burmeister

Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs / CS 20192
38044 Grenoble Cedex 9 , FRANCE
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ]
Tel: +33 (0) 457 42 87 41 Fax: +33 (0) 476 20 94 00
[
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
| website ] [
https://www.openstreetmap.org/?mlat=45.20762=5.69255#map=17/45.20762/5.69255
| map ]

Changement climatique : «Les autres combats n’ont aucun sens si celui-là est
perdu» ( Aurélien Barrau )

To unsubscribe from the CCP4BB list, click the following link:
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 |
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ]

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] PhD thesis offer (F/M) "Structure of the vaccinia virus DNA replication machinery..."

2022-09-05 Thread Wim Burmeister

We are looking for a PhD
student (f/m) starting on 1 November 2022 or on 1 January 2023
in our team at the Institut de Biologie Structurale (IBS) in Grenoble, France working on the
Structure
of the vaccinia virus DNA replication machinery in complex with
DNA substrates by single-particle cryo-electron microscopy
With
the recent spread of monkeypox infections, poxviruses got into the
headlines. Our team works on the elucidation of structure and
function of the poxvirus DNA replication machinery, now mainly by
single-particle cryo-electron microscopy. The DNA replication of
vaccinia virus, a safe model system, involves the DNA polymerase
holoenzyme complex E9-A20-D4, furthermore the hexameric
helicase-primase D5. The aim is to determine structures of these
assemblies by cryo-EM with bound DNA substrates, nucleotides,
inhibitors and nucleotide analogues in order to stabilize
different functional states for the understanding of poxvirus DNA
replication. The project builds on the team’s experiences in the
structure determination and biophysical characterization of the
partners and their domains, our recent results on the cryo-EM of
the helicase domain of D5 and first results by cryo-EM on the
holoenzyme.
The
candidate should be computer literate and have some experience in
the use of Linux. Knowledge of relevant software packages used for
cryo-EM will be an asset. Furthermore, a sound background in
biochemistry, physics or biophysics is required as the project
comprises multiple methods: protein production in the
baculovirus-insect cell system; protein purification by affinity
chromatography; sample preparation for cryo-EM. structure
calculations for single-particle cryo-EM on a Linux computing
cluster; analysis and visualization of protein structures.
The successful candidate will work in a small team interested in poxvirus DNA
replication directed by Prof. Wim
Burmeister within the « Viral Replication Machines group ». Cryo-EM and computing facilities are available
on the research campus, which is shared with international institutes: the EMBL Grenoble
outstation, the ESRF synchrotron and the ILL research
reactor. Working languages of the
institute are English and French. Grenoble is a mid-size
town with an international atmosphere located in the
middle of the French Alps. The net salary is about 1750 €/month (~2000 € gross salary),
In order to candidate please send a CV, a letter of
motivation and a copy of the Master diploma with marks to wim.burmeis...@ibs.fr
before 30 September, 2022.
Bibliography
Tarbouriech N, Ducournau C,
Hutin S, Mas PJ, Man P, Forest E, Hart DJ, Peyrefitte CN,
Burmeister WP & Iseni F. The vaccinia virus DNA polymerase
structure provides insights into the mode of processivity factor
binding. Nat Commun. 2017;8: 1455.*
doi:10.1038/s41467-017-01542-z.
Bersch B, Tarbouriech N,
Burmeister WP, Iseni F. Solution structure of the C-terminal
domain of A20, the missing brick for the characterization of the
interface between vaccinia virus DNA polymerase and its
processivity factor. J Mol Biol. 2021; 167009.*
doi:10.1016/j.jmb.2021.167009.
Hutin, S., Ling, W.L.,
Tarbouriech, N., Schoehn, G, Grimm, G., Fischer, U. &
Burmeister, W.P. The vaccinia virus DNA helicase structure from
combined single-particle cryo-electron microscopy and AlphaFold2
prediction. Viruses. In press.
--

Wim
Burmeister

Professeur
Institut
de Biologie Structurale (IBS) CIBB
71
avenue des Martyrs / CS 20192

38044 Grenoble Cedex 9,
FRANCE
E-mail: wim.burmeis...@ibs.fr
Tel: +33 (0) 457 42 87 41
Fax: +33 (0) 476 20 94 00
website
map

Changement
climatique : «Les autres comba

Re: [ccp4bb] Unable to reduce the values of R-work and R-free

2022-03-07 Thread Wim Burmeister


  
  
Hello,
the crystal is certainly twinned. Not sure that this explains
  completely the R-factor. Check https://www.ccp4.ac.uk/html/twinning.html.

Check the packing. Maybe you miss a molecule.
Are other spacegroups giving MR solutions ? The assignment of the
  spacegroup may still be wrong. Have a look at the systematic
  absences, whether the information is really sound.
Best wishes
Wim

Le 07/03/2022 à 09:39, Mudassar Ali
  Khan a écrit :


  
  
Dear all,


I am trying to solve an x-ray structure of a protein for
  which the structure is not available. I have performed data
  reduction using XDS followed by Aimless (output file attached
  herewith). Molecular replacement was performed using Phaser MR
  (CCP4i) with modelled structure followed by rigid body and
  restrained refinement. In coot, the electron density is
  fitting well with the structure, however, I am not able to
  reduce the R-work and R-free beyond 0.43 and 0.46
  respectively.


I have also tried the same with Phenix, but the R-work and
  R-free were almost the same as obtained from ccp4i. 

Any suggestion to reduce R-work and R-free will be greatly
  appreciated.


Thanks!


Regards,
Mudassar Ali Khan
Graduate student
KS-101, Varma Lab

Advanced Centre for Treatment Education and Research in
  Cancer (ACTREC)
Navi-Mumbai, India



  
  
  
  To unsubscribe from the CCP4BB list, click the
following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
  

-- 
  
  
  Wim
Burmeister
  

  

  

  

  

  

   Professeur
  Institut
de Biologie Structurale (IBS) CIBB
  71
avenue des Martyrs / CS 20192
  
   38044 Grenoble Cedex 9,
  FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41  
Fax: +33 (0) 476 20 94 00
  website 
                                   
map
  
  
  Changement
climatique : «Les autres combats n’ont
aucun sens si celui-là est perdu» (Aurélien
  Barrau)   
  
  
  

  

  

  

  

  

  

  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

Re: [ccp4bb] Ligand occupancy refinement

2022-03-03 Thread Wim Burmeister

Hello,
at 2.1 A resolution, atomic temperature factors and occupancy are strongly
correlated. So you have to be very careful with the results.
So the best is just to set the inhibitor to the average occupancy and then to
include it into a full positional and B-factor refinement. You can check
whether the result is coherent by comparing the B-factors of the ligand and of
the atoms, which are in contact with it. If this is not the case, you may want
to adjust the occupancy manually. As there are also solvent atoms at the ligand
positions, when it is not bound, there is another source of inaccuracy and
theoretically you would have to model the site with the solvent and an
occupancy 1-q and the ligand with an occupancy q as alternate structures. But
nobody does that and it is not really required.
Best
Wim

De: "Akanksha Tomar"
À: "CCP4BB"
Envoyé: Jeudi 3 Mars 2022 15:15:07
Objet: [ccp4bb] Ligand occupancy refinement

Hi everyone,

I am trying to refine the occupancy of a bound ligand. After fixing the protein
model and water I fitted the ligand into it. Currently, I am using Phenix
Refine with occupancy refinement for individual atoms switched on. After the
refinement, the overall occupancy of the ligand is 0.7 and the RSCC value is
0.86. The resolution of the structure is 2.1 Å.

Now the problem is that the program has assigned different occupancies to
different atoms of the ligand. For some cases, it has assigned 0 occupancies to
atoms for which there is a clear positive peak.

Why it has been done so and is it acceptable?

Any help would be greatly appreciated.

Thank you.

--
Best Regards,
Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India

To unsubscribe from the CCP4BB list, click the following link:
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 |
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ]

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Add hydrogens

2021-09-29 Thread Wim Burmeister

Hello, there is for exemple the "addh" command in chimerax to add hydrogens to 
a structure. Wim 


De: "Mark J. van Raaij"  
À: "CCP4BB"  
Envoyé: Mercredi 29 Septembre 2021 13:11:24 
Objet: Re: [ccp4bb] Add hydrogens 

Dear Sam, 

1CDW is from 1996, when it was not obligatory (or common practice) to upload 
structure factors to the PDB. 
So I think you can't do any refinement, just perhaps some optimisation. 

Mark J van Raaij 
Dpto de Estructura de Macromoleculas, lab 20B 
Centro Nacional de Biotecnologia - CSIC 
calle Darwin 3 
E-28049 Madrid, Spain 
tel. +34 91 585 4616 (internal 432092) 
Section Editor Acta Crystallographica F 
[ https://journals.iucr.org/f/ | https://journals.iucr.org/f/ ] 




On 29 Sep 2021, at 13:03, Sam Tang < [ mailto:samtys0...@gmail.com | 
samtys0...@gmail.com ] > wrote: 

Dear community 

This may appear to be a silly question -- I am trying to add hydrogens to the 
structure in PDB 1CDW. My initial thought is to run a single run of refinement 
with a refinement program. It happens that I cannot locate the map coefficients 
under the entry (am I missing something?) So... is there an easy way to do what 
I want in this case? 

Warm regards 

Sam 




To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 








To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 

-- 
Wim Burmeister 
Professor 
Institut de Biologie Structurale (IBS) CIBB 
71 avenue des Martyrs / CS 20192 
38044 Grenoble Cedex 9, FRANCE 
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
Mobile: +33 (0) 7 50 49 19 91 
[ 
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
 | website ] 

Changement climatique : «Les autres combats n’ont aucun sens si celui-là est 
perdu» ( Aurélien Barrau ) 



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Phosphatase enzymatic assay

2021-09-15 Thread Wim Burmeister

Hello,
try mass spectrometry, either after tryptic digestion into peptides or 
electrospray MS on the entire protein if it is not too big.
Best
Wim

- Mail original -
De: "Andrea Moretti" 
À: "CCP4BB" 
Envoyé: Mercredi 15 Septembre 2021 14:28:45
Objet: [ccp4bb] Phosphatase enzymatic assay

Dear CCP4 community,

sorry for the off topic question but I am struggling with enzymatic 
assays and I would need your help.

I am trying to measure dephosphorylation of a phosphorylated kinase by a 
ser/thr phosphatase. So far I tried to measure it by malachite green 
assay, anti pSer/pThr antibody and PNPase coupled assay but nothing 
really worked for me. NMR is unfortunately not an option since I can't 
make enough of the proteins.

So any hints on phosphatase assays would be helpful.
Thanks!

Best wishes,
Andrea


-- 
Andrea Moretti
Structural Plant Biology Laboratory
Department of Botany and Plant Biology
Sciences III
University of Geneva
30 Quai E. Ansermet
1211 Geneva
Switzerland
Email: andrea.more...@unige.ch
Phone: +41 22 379 3029 (office)
web:http://structplantbio.org



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/
-- 
Wim Burmeister 
Professor 
Institut de Biologie Structurale (IBS) CIBB 
71 avenue des Martyrs / CS 20192 
38044 Grenoble Cedex 9, FRANCE 
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
Mobile: +33 (0) 7 50 49 19 91 
[ 
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
 | website ] 

Changement climatique : «Les autres combats n’ont aucun sens si celui-là est 
perdu» ( Aurélien Barrau )



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] chain on 2-fold axis?

2021-09-01 Thread Wim Burmeister

Hello, 
I just would guess that you have twinning and disorder of the 5th subunit 
around the 2-fold axis at the same time. 
The twinning in P3221 with operators HKL and KH-L (involving the full unit cell 
contents) is required to explain the observed twinning fraction whereas only 
the disorder can explain the electron density showing alternate orientations of 
the 5th subunit. 
Greetings 
Wim 





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] malonate and histidine interaction

2021-08-19 Thread Wim Burmeister


  
  
Hello Ana,
it looks very much like a covalent bond with the His. You may get
  some hints from the chemistry of the reaction, which is normally
  catalysed. Are there possible side products involving malonate,
  alternative substrates present in the buffer etc ?
Occupancy refinements of the different atom groups may also yield
  some information.

This looks really interesting
Cheers
Wim

I 

Le 18/08/2021 à 13:13, Ana Ebrecht a
  écrit :


  
  Hello Jon, 
Thanks for the comments. Yes, the His is part of the active
  site, and the distances are very close, like a covalent bond.
  That's why I was wondering if the malonate can be bound to the
  His.


We tried to model the malonate in the different
  conformation, but that didn't work. But I'll check about the
  protease inhibitor. Thanks!


Kind regards
Ana
  
  
  
On Tue, 17 Aug 2021 at 14:48,
  Jon Cooper 
  wrote:

Hello,
  only other thought was that malonate might be binding in two
  conformations, i.e. dual occupancy, and did you use a protease
  inhibitor cocktail, since the constituents can react? The
  density looks a bit like citrate, but too close to the His. I
  couldn't read the distances to the His in your figure. Is it
  part of the active site and if so can you say what the enzyme
  is? Anomalous difference maps are popular here, too. Is the
  surrounding structure totally OK because odd features in the
  difference map can indicate problems nearby e.g. I did see a
  leucine which looked slightly strained on the left, but maybe
  I am wrong. Good luck. Cheers, Jon.C.
  
  
  Sent from ProtonMail mobile
  
  
  
   Original Message 
  On 17 Aug 2021, 12:11, Ana Ebrecht < anaebre...@gmail.com> wrote:
  
Hi Jon,
  Thanks for the reply. I don't think this is
acetylation, because I only see this density in the
crystals that grew with malonate. In other conditions
doesn't show anything like that. So I thought it'd be
the malonate. But I'll check on that. 
  Thanks for the suggestion.
  
  
  Kind regards
  Ana



  On Mon, 16 Aug 2021 at
16:56, Jon Cooper 
wrote:
  
  Hello, could the His
be partially acetylated? 

Best wishes Jon.C.


Sent from ProtonMail mobile



 Original Message 
On 16 Aug 2021, 14:52, Ana Ebrecht < anaebre...@gmail.com>
wrote:

  
Dear all, 

  
I am building
the structure of a protein that was
crystallized in 0.2 M sodium malonate pH 5.0,
20% w/v polyethylene glycol 3,350.
During
the refinement, we found what we think is a
malonate molecule in the active site, but it
seems like is bound
somehow to the histidine (this His is the
catalytic residue of the enzyme), almost like a
covalent interaction. Under other
  conditions of crystallization, the protein bound a
  sulfate and an acetate in the site but did not
  show this type of interaction with the histidine. 

  
We
couldn't find anything that explains a reaction
between the malonate and the histidine.

Does anyone have
experience with this reaction or have seen
something similar before? 


Thanks 
Kind regards
Ana











  
  
  
  To unsubscribe from the CCP4BB list,

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

2020-12-03 Thread Wim Burmeister

Hello, 
we had a 124 aa target in Casp14, without any detectable homology to a known 
structure. Within the experimental errors, the AlphaFold2 model is identical to 
the NMR model we got. That was very convincing. 
Best wishes 
Wim 


De: "Jon Cooper" <488a26d62010-dmarc-requ...@jiscmail.ac.uk> 
À: "CCP4BB"  
Envoyé: Jeudi 3 Décembre 2020 21:55:38 
Objet: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?) 

Hello. A quick look suggests that a lot of the test structures were solved by 
phaser or molrep, suggesting it is a very welcome improvement on homology 
modelling. It would be interesting to know how it performs with structures of 
new or uncertain fold, if there are any left these days. Without resorting to 
jokes about artificial intelligence, I couldn't make that out from the CASP14 
website or the many excellent articles that have appeared. Best wishes, Jon 
Cooper. 


Sent from ProtonMail mobile 



 Original Message  
On 3 Dec 2020, 11:17, Isabel Garcia-Saez < isabel.gar...@ibs.fr> wrote: 





Dear all, 

Just commenting that after the stunning performance of AlphaFold that uses AI 
from Google maybe some of us we could dedicate ourselves to the noble art of 
gardening, baking, doing Chinese Calligraphy, enjoying the clouds pass or 
everything together (just in case I have already prepared my subscription to 
Netflix). 

[ https://www.nature.com/articles/d41586-020-03348-4 | 
https://www.nature.com/articles/d41586-020-03348-4 ] 

Well, I suppose that we still have the structures of complexes (at the moment). 
I am wondering how the labs will have access to this technology in the future 
(would it be for free coming from the company DeepMind - Google?). It seems 
that they have already published some code. Well, exciting times. 

Cheers, 

Isabel 


Isabel Garcia-Saez PhD 
Institut de Biologie Structurale 
Viral Infection and Cancer Group (VIC)-Cell Division Team 
71, Avenue des Martyrs 
CS 10090 
38044 Grenoble Cedex 9 
France 
Tel.: 00 33 (0) 457 42 86 15 
[ mailto:isabel.gar...@ibs.fr | e-mail: isabel.gar...@ibs.fr ] 
FAX: 00 33 (0) 476 50 18 90 
http://www.ibs.fr/ 





To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 



To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] R free rising

2020-11-02 Thread Wim Burmeister

...or your dataset may have a much lower resolution than the one your initial 
model was based upon. The discrepancy between Rfree and Rwork seem to indicate 
this. 
Best 
Wim 

De: "Eleanor Dodson" <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> 
À: "CCP4BB"  
Envoyé: Lundi 2 Novembre 2020 12:08:17 
Objet: Re: [ccp4bb] R free rising 

Yes, as Dale says when the FreeR goes up after minor rebuilding you have 
usually somehow picked up a different FreeR set.. 
This is almost certainly what causes this to happen - you say 

This results in R free slightly lower than R work. 

Small changes in a well refined structure dont change r factors very much! 
Eleanor 

On Mon, 2 Nov 2020 at 10:57, Dale Tronrud < [ mailto:de...@daletronrud.com | 
de...@daletronrud.com ] > wrote: 

On 11/2/2020 2:26 AM, Nika Žibrat wrote: 
> 
> Hello, 
> 
> 
> 
> I am trying to solve an X-ray structure of a protein of which the 
> structure is already known. My aim is to only seek for ligands (soaking) 
> and interpret any conformational changes. Since I am using a model with 
> 100% sequence identity from PDB I am not doing Autobuild after Molecular 
> phasing and continue directly with phenix.refine according to 
> reccomendations (10 rounds). In accordance with X-triage I am also using 
> NCS default settings in the refinement. 
> 
> 
> 
> This refinement produces solid R free and R work values around 0.29 and 
> 0.22. The problem becomes when I want to manually edit the structure, 
> correct the loops which are changed upon binding of the ligand, and 
> correct any outliers. This results in R free slightly lower than R work. 
> Upon refining, R work drops normally while R free rises significantly 
> (for 0.2 -0.3). I have been trying to crack this for a few days with no 
> success. 
> 
> 
> 
> I read that slightly lower R free can be normal in such cases but 
> nevertheless both R values should drop, and haven’t found anything about 
> the big rise of this value after refinement. It feels like I am missing 
> something, since this is my first time solving a structure. Any advice? 

This is not normal behavior at all. Rwrk and Rfree will be roughly 
equal only before you perform any refinement. The R's you report before 
your model building sound quite reasonable. When you manually change 
the model you will likely cause both to increase, but you would have to 
perform massive changes to get them to equalize at some larger value. 

The only thing I can think of that would cause this is for your 
second refinement to be working with a newly created test set. It is 
possible that somehow you have reset your R free flags? In an MTZ the 
full data set is divided into twenty subsets -- one is the test set 
while the other nineteen are the working set. When you ran Refmac the 
second time could you have told it to use a different segment as the 
test set? 

Dale Tronrud 

> 
> 
> 
> Thank you, 
> 
> Nika 
> 
> 
> 
> 
>  
> 
> To unsubscribe from the CCP4BB list, click the following link: 
> [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 
> 

To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 

This message was issued to members of [ http://www.jiscmail.ac.uk/CCP4BB | 
www.jiscmail.ac.uk/CCP4BB ] , a mailing list hosted by [ 
http://www.jiscmail.ac.uk/ | www.jiscmail.ac.uk ] , terms & conditions are 
available at [ https://www.jiscmail.ac.uk/policyandsecurity/ | 
https://www.jiscmail.ac.uk/policyandsecurity/ ] 

To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] font issues in imosflm under xubuntu 18

2020-09-29 Thread Wim Burmeister

Thank you very much, this solved the problem !
I am actually working on a portable xubuntu 18 linux USB key with
  a part of the SBgrid distribution for teaching purposes.
Best 

Wim

Le 29/09/2020 à 18:16, David Waterman a
  écrit :

  Dear Wim,

Are you using imosflm distributed by CCP4, the LMB build,
  or something else?

I don't see the same problem with the version in the
  current CCP4 on standard Ubuntu 18.04.5 (not xubuntu). I do
  remember seeing similar issues in the past though. It used to
  be the case that having the package gsfonts-x11 installed made
  an absolute mess of things, so if you do have that please try
  removing it.

Cheers

-- David

On Tue, 29 Sep 2020 at 15:39,
  Kay Diederichs <kay.diederi...@uni-konstanz.de>
  wrote:

hmm,
  should have looked more carefully! Now I see the letters that
  should be greek (e.g. phi) and look like a strike-through
  epsilon.

  Maybe somebody else has xubuntu 18 without this problem?
  Do you use non-standard repositories?

  Kay

  On Tue, 29 Sep 2020 14:34:07 +0100, Kay Diederichs <kay.diederi...@uni-konstanz.de>
  wrote:
  ...
  >However, the screenshot looks as expected (i.e. good) to
  me; no tiny fonts. Not sure what I overlook.
  >

  To unsubscribe from the CCP4BB list, click the following link:
  https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

  This message was issued to members of www.jiscmail.ac.uk/CCP4BB,
  a mailing list hosted by www.jiscmail.ac.uk,
  terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/

  To unsubscribe from the CCP4BB list, click the
following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

-- 

  Wim
Burmeister

 Professeur
Institut
  de Biologie Structurale (IBS) CIBB
71
  avenue des Martyrs / CS 20192

 38044
Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
  Tel:    +33 (0) 457 42 87 41  
  Fax: +33 (0) 476 20 94 00
website 

   map

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

[ccp4bb] Font issues in imosflm under xubuntu 18

2020-09-29 Thread Wim Burmeister


  
  
Hello,
Running imosflm under xubuntu 18 linux get a lot of small font
  problems in the graphical user interface involving greek and
  special characters which are incorrectly translated.
I suppose its a problem of a missing font or incorrect font
  substitution at the Tcl/Tk level. 

Does anybody have any idea how to solve the problem ?
On request I can send the screenshot showing the font problems
  but it seemed that as attachment it blocked the distribution on
  the mailing list.

Best wishes
Wim


-- 
  
  
  Wim
Burmeister
  

  

  

  

  

  

  
 Professeur
Institut
  de Biologie Structurale (IBS) CIBB
71
  avenue des Martyrs / CS 20192

 38044
Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
  Tel:    +33 (0) 457 42 87 41  
  Fax: +33 (0) 476 20 94 00
website 
                              
   map


   



  

  

  

  

  

  

  

  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

[ccp4bb] font issues in imosflm under xubuntu 18

2020-09-29 Thread Wim Burmeister


  
  
Hello,
Running imosflm under xUbuntu 18 linux get a lot of small font
  problems in the graphical user interface involving greek and
  special characters.
I suppose its a problem of a missing font or incorrect font
  substitution at the Tcl/Tk level. I join a screenshot of the
  interface.

Does anybody have any idea how to solve the problem ?

Best wishes
Wim


-- 
  
  
  Wim
Burmeister
  

  

  

  

  

  

  
 Professeur
Institut
  de Biologie Structurale (IBS) CIBB
71
  avenue des Martyrs / CS 20192

 38044
Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
  Tel:    +33 (0) 457 42 87 41  
  Fax: +33 (0) 476 20 94 00
website 
                              
   map


   



  

  

  

  

  

  

  

  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

Re: [ccp4bb] Lattice-translocation defect (LTD)

2020-02-11 Thread Wim Burmeister


  
  
Hello,
do you have some details about the space group ? Did the
  integration not miss any sports ? I would rather think of an ncs
  close to crystallographic symmetry, or maybe some twinning
  problem. 

I guess these are Pilatus data, can you combine the frames into 1
  degree oscillations and try Mosflm processing to see how the
  patterns integrate ?
Greetings
Wim

Le 11/02/2020 à 22:31, Daniele de
  Sanctis a écrit :


  
  
Hi all,


I'm currently dealing with what I think it is a case of LTD
  (off-origin Patterson peak, with vector along w of ~ 7A and
  electron density map showing a "ghost" map shifted by 7 A). I
  saw there are quite a few cases reported in literature  (for
  example Hare et al, 2006), but what I could not find is how I
  can demodulate the data. Is there any software that can be
  used for this?


Thank you


Daniele


-- 
ἀρετή
  ---
  Daniele de Sanctis, PhD
  
  Structural Biology Group
  ESRF, Grenoble, France
  Tel 33 (0)4 76 88 2869
  
  
  
  To unsubscribe from the CCP4BB list, click the
following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  

-- 
  
      
  Wim
    Burmeister
  

  

  

  

  

  

   Professeur
  Institut
de Biologie Structurale (IBS) CIBB
  71
avenue des Martyrs / CS 20192
  
   38044 Grenoble Cedex 9,
  FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41  
Fax: +33 (0) 476 20 94 00
  website 
                                   
map
  
  
  Changement
climatique : «Les autres combats n’ont
aucun sens si celui-là est perdu» (Aurélien
  Barrau)   
  
  
  

  

  

  

  

  

  

  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

2019-12-16 Thread Wim Burmeister

Hello, 
I would guess that the badly fitting molecule may be upside down (related my an 
2-fold axis). 
I would use the first, partially refined structure for another round of 
molecular replacement in P212121 with molrep, using the model as well as a 
partial solution as as asearch model. 
The translational self peak in the native Patterson may be misleading. I came 
recently across a similar problem. 
Regards 
Wim 


De: "Jessica Besaw"  
À: "CCP4BB"  
Envoyé: Lundi 16 Décembre 2019 20:29:38 
Objet: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric 
unit does not fit density 

There have been two potential space groups: 
P212121 - Rfree = 36% 
P21212 - Rfree = 45% 

Xtriage reports that twinning is unlikely. 

Cheers! 

Jessica 





On Mon, 16 Dec 2019 at 13:56, Jürgen Bosch < [ mailto:jxb...@case.edu | 
jxb...@case.edu ] > wrote: 



What’s your spacegroup ? RWork / RFree? 
Twinning by any chance? 

Jürgen 

__ 
Jürgen Bosch, Ph.D. 
Division of Pediatric Pulmonology and Allergy/Immunology 
Case Western Reserve University 
2109 Adelbert Rd, BRB 835 
Cleveland, OH 44106 
Phone: 216.368.7565 
Fax: 216.368.4223 
[ https://www.linkedin.com/in/jubosch/ | https://www.linkedin.com/in/jubosch/ ] 

CEO & Co-Founder at InterRayBio, LLC 

Johns Hopkins University 
Bloomberg School of Public Health 
Department of Biochemistry & Molecular Biology 


BQ_BEGIN

On Dec 16, 2019, at 1:50 PM, Jessica Besaw < [ mailto:jbesaw1...@gmail.com | 
jbesaw1...@gmail.com ] > wrote: 

I am crystallizing this membrane protein in a medium (bicelles) that forms 
lamella like sheets that stack on top of each other. 
The layer packing is shown below. Is this structure unreasonable? 

 

On Mon, 16 Dec 2019 at 13:38, Reza Khayat < [ mailto:rkha...@ccny.cuny.edu | 
rkha...@ccny.cuny.edu ] > wrote: 

BQ_BEGIN



Hi Jessica, 





The gap between the two proteins is a bit troubling. Perhaps it's the image, 
but why would a crystal form if there is no crystal contact between the two 
proteins? 





Reza 



Reza Khayat, PhD 
Assistant Professor 
City College of New York 
Department of Chemistry 
New York, NY 10031 

From: CCP4 bulletin board < [ mailto:CCP4BB@JISCMAIL.AC.UK | 
CCP4BB@JISCMAIL.AC.UK ] > on behalf of Ashish Kumar < [ 
mailto:mail2ashish...@gmail.com | mail2ashish...@gmail.com ] > 
Sent: Monday, December 16, 2019 1:24 PM 
To: [ mailto:CCP4BB@JISCMAIL.AC.UK | CCP4BB@JISCMAIL.AC.UK ] 
Subject: [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does 
not fit density 
Hi Jessica, 

It may be possible because of wrong MR solution as well. How were your stats 
after MR. 
Also it is correct that it could be possible because of wrong space group. 
Try changing the Space group and repeat MR. 

Best Regards 
Ashish 

On 16 Dec 2019 22:56, "Jessica Besaw" < [ mailto:jbesaw1...@gmail.com | 
jbesaw1...@gmail.com ] > wrote: 

BQ_BEGIN

Dear community, 

I am having a lot of trouble solving a protein structure. I think my problem 
may caused by incorrectly placed proteins in molecular replacement. I have two 
proteins in my asymmetric unit. It appears that one protein fits perfectly, and 
the other one has many errors. (See snapshots below). I have tried deleting the 
parts of the protein (and even the whole protein) to try and rebuild it in 
COOT, but it was a bit too difficult for me to solve. 

I would appreciate any and all suggestions for potential strategies moving 
forward. 

Other information: 
(1) 2.4 Angstrom 
(2) 99% complete 
(3) "Translational NCS may be present at a level that may complicate 
refinement" 

Cheers! 

Jessica 

 
 










To unsubscribe from the CCP4BB list, click the following link: 
[ 
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI=
 | https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 ] 







To unsubscribe from the CCP4BB list, click the following link: 
[ 
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI=
 | https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 ] 




To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 ] 
BQ_END





To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 ] 

BQ_END



BQ_END





To unsubscribe from the CCP4BB list,

Re: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04

2019-11-08 Thread Wim Burmeister

Hello,
The desktop changed in the passage from Ubuntu16 to Ubuntu18.
I think Nvidia stereo now works only with a xfce desktop.
The passage from debian 8 to debian 9 was not a problem as long as xfce is kept.
Best regards
Wim 

- Mail original -
De: "Chris Richardson" 
À: "CCP4BB" 
Envoyé: Vendredi 8 Novembre 2019 13:18:44
Objet: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04

Apologies for the only slightly relevant question.

Does anyone know the correct incantations to get nVidia 3D Vision glasses and 
emitter working with Ubuntu 18.04?

None of the tricks that work with 16.04 are helping with the new release.  In 
particular, disabling composite in the extensions makes the display blank while 
X11 restarts itself every few seconds.

Thanks in advance,

Chris
-- 
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
 
 
 


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Calculating RMSD of a loop

2019-09-17 Thread Wim Burmeister


  
  
Hello,
I admit that I only found the solution to import the pdb's after
alignment of the body of the protein into a spreadsheet (LibreOffice
Calc) and then to calculate the rms of the atoms of the loop (or of
the CA atoms of the loop).
Best wishes
Wim

On 17/09/2019 15:31, Kyle Gregory
  wrote:


  
  
   Hi all, 

What is the best/easiest way to calculate RMSD of a loop for 2
c-alpha aligned structures?
Thought I could do this in Coot but I only see this if I align
the specific loops, which I don't want to do. 

Thanks,

Kyle 
  
  
  
  To unsubscribe from the CCP4BB list, click the
following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  


-- 
  
  
  




  Changement climatique : «Les autres
combats n’ont aucun sens si celui-là est perdu» (Aurélien
  Barrau)
  

  

  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

2019-08-20 Thread Wim Burmeister


  
  

  Hello,
  I transmit this initiative for those who feel that there is
  also life outside reciprocal space and and not only scientist
  in specialist disciplines have a responsibility in real space.
  
  The graphs in the paper mentioned below are sufficiently
  explicit to understand that there is a big problem.
  Best wishes
  Wim
   
  Dear Colleague,
We are inviting you and all scientists to sign our new in-press
BioScience  paper "World Scientists' Warning of a
  Climate Emergency" which we want to present to world
leaders.

The article is short and can be read in fewer than eight
minutes. Just go to  http://scientistswarning.forestry.oregonstate.edu/
to read and sign the paper (you can also read a condensed
version of the article below).

Please forward this email to other scientists within your
network or use social media as suggested below. 
    
Thanks, Bill  
  
  
William J. Ripple, Distinguished Professor of Ecology, Oregon
State University

To promote the initiative on social media (Facebook and
  Twitter), please consider using the following text:

The #ScientistsWarningToHumanity is
speaking out about the climate emergency. If you are a scientist
you can support this new initiative by sharing this and adding
your signature here: http://scientistswarning.forestry.oregonstate.edu/


Or

Scientists can support the #ScientistsWarningToHumanity
climate emergency initiative by sharing this and adding your
signature here:  http://scientistswarning.forestry.oregonstate.edu/

Or

I just signed the #ScientistsWarningToHumanity climate emergency initiative. If you are
a scientist you can support this new initiative by sharing this
and adding your signature here: http://scientistswarning.forestry.oregonstate.edu/
   
   World

Scientists’ Warning of a Climate Emergency (Condensed

  Version) 
   William J. Ripple, Christopher
  Wolf, Thomas M. Newsome,  scientist signatories from xxx
  countries 
  We

  scientists have a moral obligation to clearly warn humanity of
  any great existential threat. In this paper, we present a
  suite of graphical vital signs of climate change over the last
  40 years. Results show greenhouse gas emissions are still
  rising, with increasingly damaging effects. With few
  exceptions, we are largely failing to address this
  predicament. The climate crisis has arrived and is
  accelerating faster than many scientists expected. It is more
  severe than anticipated, threatening natural ecosystems and
  the fate of humanity. We suggest six critical and interrelated
  steps that governments and the rest of humanity can take to
  lessen the worst effects of climate change, covering 1)
  Energy, 2) Short-lived pollutants, 3) Nature, 4) Food, 5)
  Economy, and 6) Population. Mitigating and adapting to climate
  change entails transformations in the ways we govern, manage,
  feed, and fulfill material and energy requirements. We are
  encouraged by a recent global surge of concern. Governmental
  bodies are making climate emergency declarations. The Pope
  issued an encyclical on climate change. Schoolchildren are
  striking. Ecocide lawsuits are proceeding in the courts.
  Grassroots citizen movements are demanding change. As
  scientists, we urge widespread use of our vital signs and
  anticipate that graphical indicators will better allow
  policymakers and the public to understand the magnitude of
  this crisis, track progress, and realign priorities to
  alleviate climate change. The good news is that such
  transformative change, with social and ecological justice,
  promises greater human wellbeing in the long-run than business
  as usual. We believe that prospects will be greatest if policy
  makers and the rest of humanity promptly respond to our
  warning and declaration of a climate emergency, and act to
  sustain life on planet Earth, our only home.
   
  William J. Ripple email:
  scientistswarn...@oregonstate.edu
   
   
   
   

  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Better Beamline suggestion!

2019-08-20 Thread Wim Burmeister


  
  
Hello,
the problem can rather be due to mechanical deformations of the
crystal upon mounting and freezing (bent needle, for example). If
the crystals are needle shaped, aligning the long axis with the
spindle axis and using a beamline with a very small beamsize
"microfocus" and a helical scan in order to expose a sufficient
volume will help.
Best
Wim

On 19/08/2019 17:08, Chandramohan
  Kattamuri wrote:


  
  
  
  Dear All
  

  




We recently collected a data set at
  APS, Chicago with unit
  cell dimensions of 68.4; 68.4 and 991.6 A. Our diffraction
  data extends to 3A
  with the APS set up, however, the long axis has been
  problematic, resulting in
  streaking of the diffraction data and requires a very
  specific orientation of
  the crystal for usable diffraction. Can anyone recommend
  beamlines that can
  give us higher resolution, or a source with a better
  goniometer allowing for
  more angle manipulation after looping?
Thank a lot
Chandra K


  

  
  
  
  
  To unsubscribe from the CCP4BB list, click the
following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  


-- 
  
      
  Wim
    Burmeister
  

  

  

  

  

  

   Professeur
  Institut


de Biologie Structurale (IBS) CIBB
  71
avenue des Martyrs / CS 20192
  
   38044 Grenoble Cedex 9,
  FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41  
Fax: +33 (0) 476 20 94 00
  website 
                                   
map
  
  
  Changement
climatique : «Les autres combats n’ont
aucun sens si celui-là est perdu» (Aurélien
  Barrau)   
  
  
  

  

  

  

  

  

  

  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] ORCID

2019-08-19 Thread Wim Burmeister

Hello, 
like a lot of items in the pdb entry, the entry is not mandatory. But using the 
ORCID is a good idea in order to be able to claim easily your work if you have 
a very common name and it may be difficult to find your authorship 
unambigously. 
Best 
Wim 


De: "Jie Liu"  
À: "CCP4BB"  
Envoyé: Lundi 19 Août 2019 21:54:52 
Objet: [ccp4bb] ORCID 

Dear all, 

It's been a while since last time I deposited structures to PDB. Do I really 
need an ORCID (Open Researcher and Contributor IDentifier) now to submit files? 
Is it mandatory? 

Thank you! 
Jie 




To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 ] 

-- 
Changement climatique : «Les autres combats n’ont aucun sens si celui-là est 
perdu» ( Aurélien Barrau ) 



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

2019-03-25 Thread Wim Burmeister

?SUBED1=CCP4BB=1

  

  
  
  
  To unsubscribe from the CCP4BB list,
click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  

  
  
  
  To unsubscribe from the CCP4BB list,
click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  

  

  
  
  
  To unsubscribe from the CCP4BB list, click the
following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  


-- 
  
  
  Wim
    Burmeister
  

  

  

  

  

   Professeur
  Institut
de Biologie Structurale (IBS) CIBB
  71
avenue des Martyrs / CS 20192
  
   38044 Grenoble Cedex 9,
  FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41   Fax:
+33 (0) 476 20 94 00
  website 
                                    map
  
  
  Changement climatique :
«Les autres combats n’ont aucun sens si
celui-là est perdu» (Aurélien Barrau)   






  
  
  

  

  

  

  

  

  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Partially occupied C-terminus

2019-01-17 Thread Wim Burmeister


  
  
Hello,
can you do some ES-mass spectrometry on your sample ?
There may be a truncated form in the sample and in this case the
occupancy refined C-terminus would be a good solution.
Otherwise I would invent an alternative conformation with 30 %
occupancy and assign very high B-factors so that it won't show up.
Best
Wim

On 17/01/2019 16:40, Andreas Heine
  wrote:

Dear CCP4-BB,
  
  
  after refining a fairly high resolution aldose reductase structure
  (0.96 A) we observed negative Fo-Fc density (-3.0 sigma) for the
  three C-terminal residues (314-316). However, the 2Fo-Fc density
  clearly showed the position of these residues without indication
  of a second conformation for these residues. Therefore, we decided
  to refine the occupancy for the entire 3 residues, which refined
  to 70%. After occupancy refinement the negative density
  disappeared. We are now courious if it is acceptable to deposit
  the structure with 3 residues only partially occupied without
  indication of a second conformation or how to proceed otherwise?
  
  
  Thanks for any advice,
  
  
  Lea and Andreas
  
  

  
  
  To unsubscribe from the CCP4BB list, click the following link:
  
  https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  


-- 
  
  
  Wim
Burmeister
  

  

  

   Professeur
  Institut de Biologie
Structurale (IBS) CIBB
  71 avenue des Martyrs
/ CS 20192
  
   38044 Grenoble Cedex 9, FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41   Fax: +33 (0)
476 20 94 00
  website 
                                    map
  
  
  Changement climatique : «Les
autres combats n’ont aucun sens si celui-là est
perdu» (Aurélien Barrau)   


  
  
  

  

  

  

  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation - Fwd: 3D graphics under linux for coot, pymol and chimera

2018-12-20 Thread Wim Burmeister


  
  
Hello,
I re-post my contribution from 17 may 2017.
Software versions and hardware may be obsolete, but some of the
information may still help.
Best
Wim

  
   Forwarded Message 
  

  
Subject:

3D graphics under linux for coot, pymol and chimera
  
  
Date: 
Wed, 17 May 2017 12:27:21 +0200
  
  
From: 
Wim Burmeister 
  
  
To: 
CCP4 Bulletin Board 
  

  
  
  
  
  
  Hello,
   
  we just wanted to share our experience in
finding a configuration which allows to use 3D graphics
under linux using Nvidia GeForce 3D glasses.
   
  We had quite a hard time to find a
configurations which works correctly.
   
  We finally used Debian linux with a xfce
desktop. Other recent desktops use a tiling which is not
compatible with 3D graphics.
   
  The hardware consists of
  
  
a DELL Precision T5810 
desktop computer with an Nvidia Quadro M4000 (8 Gbyte
memory, 4 DP) graphics card
Nvidia
GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT)
active stereo glasses
a stereo
connector PNY Quadro 4000 3D for the synchronization of
graphics card and glasses
an ASUS
24" LED 3D - VG248QE display
a
DisplayPort-DisplayPort cable
  
  
  The Nvidia linux drivers from version 367.57
can handle the current version of the Nvidia glasses.
   
  For an obscure reason a direct DP-DP connection
between graphics card and display is absolutely required in
order to obtain fully working stereo. If a DP-DVI dual link
adapter is used, the stereo does not work on the top and the
bottom part of the screen. This is true for a native DELL
active adaptor or generic models. The exact reason remains
unresolved, but the solution is to use a direct DP-DP
connection. This limits the available choice of displays
which require 120 Hz for 1080*1980 screen resolution and a
DP input. We have been choosing a “Nvidia 3D ready” model.
   
  There has been a considerate about of exchange
about this problem on
   
  https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/
   
  The setup comes with a price tag of about 1600
€ free of taxes.
   
  coot, pymol and chimera work straight without
problems in hardware stereo mode. The experience is
absolutely great.
   
  Best
   
  Wim 
  
  
  
  
  
  
  
  
  
  -- 


      Wim Burmeister
Professeur
  Institut de Biologie Structurale (IBS) CIBB
  71 avenue des Martyrs
  CS
  20192
  38044 Grenoble Cedex 9, FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20
94 00
  website
  
  
  

  
  


  



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] OFF TOPIC

2018-11-13 Thread Wim Burmeister

Hello,
you probably purified a contaminant. Do a blot with an anti-biotin
antibody or get electro-spray mass spectrometry done in order to
confirm the identity of your protein.
Wim

On 13/11/2018 11:13, Anamika Singh
wrote:

Hi All,

I am purifying the biotinylated protein (cloned into the pET28a vector) using Avidin beads. Since I need the protein for SPR but when I used the purified protein to interact with Streptavidin coated onto the SPR chip. There was no signal. Can anybody tell me why is it so or how can I make sure that the purified protein is biotinylated enough to interact and give the signal? Because when I ran the SDS-PAGE there was a band of purified protein.

I have used the elution buffer (20mM Tris, 5mM Mgcl2, 500mM Nacl, and 2mM Biotin).
PS: I have included the biotin during overexpression of the protein also.
Please suggest.
Thanks
--

Anamika
Post-Doctoral Fellow
Silberman Institute of Life Sciences
Hebrew University of Jerusalem, Israel

To unsubscribe from the CCP4BB list, click the
following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Wim Burmeister
Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs
CS
20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Tel: +33 (0) 457 42 87 41 Fax: +33 (0) 476 20
94 00
website
map

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

2018-11-04 Thread Wim Burmeister

Hello, 
it looks if the density is located around a 2-fold axis. 
It cannot be the superposition of a bis-tris methane molecule bound 
asymmetrically and its symmetry mate ? 
Best 
Wim 


De: "Deborah Harrus"  
À: "CCP4BB"  
Envoyé: Vendredi 2 Novembre 2018 22:14:32 
Objet: [ccp4bb] help needed with a rabbit-head-shaped blob 




Dear all, 

I came across an unidentified rabbit-head-shaped blob and would need help for 
its identification. There are 2 molecules of protein per asymmetric unit but 
there are some differences between the two chains. The blob is located in 
between the two chains, and is surrounded by residues Asp, Pro, and Val. 

The protein, a glycosyltransferase, was expressed in E. coli BL21(DE3) and 
purified on Ni-NTA followed by gel filtration. The purification buffer included 
Sodium phosphate and NaCl. The crystallization condition had Bis-Tris, ammonium 
acetate and PEG 2, and glycerol was used as cryoprotectant. From the size, 
bis-tris was the most probable, but I have tried to fit it and it is not 
convincing. 

The structure is 1.6 angstrom resolution and this is the only thing left to be 
done, it's driving me crazy! 

Pictures attached show the face, bottom and top of the head. 2Fo-Fc is at 1.1 
sigma, Fo-Fc at 3 sigmas. 

Many thanks in advance for your suggestions! 

Regards, 
Deborah. 






= 
Deborah Harrus, PhD. 

University of Oulu / Faculty of Biochemistry and Molecular Medicine 
Aapistie 7 A, 90220 Oulu 
Finland 

office: F123B 
email: deborah.har...@oulu.fi 
phone: +358 50 3502387 / +358 44 2386351 
http://www.oulu.fi/fbmm/node/20603 
= 




To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 ] 



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

2018-10-09 Thread Wim Burmeister

Hello, 
at that resolution, the refinement of anisotropic atomic B-factors is 
absolutely required, as is the modelisation of alternate conformations for 
surface residues. Optimize also the weight of different restraints (for exemple 
on B-factors) in order to get the lowest Rfree. 
Best 
Wim 


De: "Robbie Joosten"  
À: CCP4BB@JISCMAIL.AC.UK 
Envoyé: Mardi 9 Octobre 2018 20:02:17 
Objet: Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset 
(1.05 Ang) 

Hi Hugo, 

Perhaps you should play with your refinement strategy. Use a decent number of 
cycles and a sensible restraint weight (something that gives you rmsZ < 1.0 and 
good R-factors). Anisotropic B-factors are probably needed and make your model 
as complete as your maps allow. 

You could try pdb-redo to see if this can help you on your way. 

Cheers, 
Robbie 

On 9 Oct 2018 19:12, Guto Rhys  wrote: 




Hi all, 

I have a 1.05 Angstrom dataset that I was able to phase but the refined model 
only has an Rfree of approximately 0.25. The dataset includes 1800 images and, 
as the crystal did not suffer significantly from radiation damage, comprises 
all 360 deg. Auto-processing pipelines at diamond light source all suggest 
I222. I have also indexed the data in iMOSFLM, which has the highest-symmetry 
Laue group that is least penalised of I422. Subsequent scaling and merging in 
AIMLESS strongly indicates that I222 is the likely space group (see below). I 
have ran the refined model through ZANUDA, which has similar R values to lower 
symmetry space groups (see below). The output from Phenix Xtriage does not find 
any specific crystal pathologies and if twinning is present it is very low (2 
to 4%, see below). The difference map suggests that the model accounts for 
nearly all the density. Any ideas or direction would be greatly appreciated. 

Best, 
Guto 


AIMLESS Summary 
Overall InnerShell OuterShell 
Low resolution limit 27.75 27.75 1.07 
High resolution limit 1.05 5.75 1.05 

Rmerge (within I+/I-) 0.050 0.078 0.466 
Rmerge (all I+ and I-) 0.051 0.080 0.536 
Rmeas (within I+/I-) 0.055 0.086 0.591 
Rmeas (all I+ & I-) 0.054 0.085 0.613 
Rpim (within I+/I-) 0.023 0.034 0.359 
Rpim (all I+ & I-) 0.017 0.028 0.288 
Rmerge in top intensity bin 0.049 - - 
Total number of observations 107950 779 1972 
Total number unique 11315 88 486 
Mean((I)/sd(I)) 19.7 46.2 1.8 
Mn(I) half-set correlation CC(1/2) 0.998 0.994 0.796 
Completeness 99.1 99.2 90.4 
Multiplicity 9.5 8.9 4.1 

Anomalous completeness 98.1 100.0 79.1 
Anomalous multiplicity 5.0 6.4 2.2 
DelAnom correlation between half-sets -0.067 0.286 0.097 
Mid-Slope of Anom Normal Probability 0.789 - - 

Estimate of maximum resolution for significant anomalous signal = 1.14A, from 
CCanom > 0.15 

Estimates of resolution limits: overall 
from half-dataset correlation CC(1/2) > 0.30: limit = 1.05A == maximum 
resolution 
from Mn(I/sd) > 1.50: limit = 1.05A == maximum resolution 
from Mn(I/sd) > 2.00: limit = 1.07A 

Estimates of resolution limits in reciprocal lattice directions: 
Along h axis 
from half-dataset correlation CC(1/2) > 0.30: limit = 1.06A 
from Mn(I/sd) > 1.50: limit = 1.09A 
Along k axis 
from half-dataset correlation CC(1/2) > 0.30: limit = 1.11A 
from Mn(I/sd) > 1.50: limit = 1.13A 
Along l axis 
from half-dataset correlation CC(1/2) > 0.30: limit = 1.05A == maximum 
resolution 
from Mn(I/sd) > 1.50: limit = 1.05A 

Anisotropic deltaB (i.e. range of principal components), A^2: 6.40 

Average unit cell: 29.12 29.26 55.50 90.00 90.00 90.00 
Space group: I 2 2 2 
Average mosaicity: 0.36 

AIMLESS Laue Group prediction 

Laue Group Lklhd NetZc Zc+ Zc- CC CC- Rmeas R- Delta ReindexOperator 

= 1 I m m m *** 0.987 6.25 9.19 2.94 0.92 0.29 0.07 0.49 0.0 [h,k,l] 
2 I 1 2/m 1 0.004 4.36 9.32 4.96 0.93 0.50 0.07 0.30 0.0 [-h,-k,l] 
3 I 1 2/m 1 0.004 4.14 9.24 5.10 0.92 0.51 0.07 0.30 0.0 [k,-h,l] 
4 I 1 2/m 1 0.004 4.05 9.23 5.18 0.92 0.52 0.06 0.31 0.0 [h,-l,k] 
5 I 4/m m m 0.000 6.35 6.35 0.00 0.64 0.00 0.22 0.00 0.3 [h,k,l] 
6 I 4/m 0.000 0.90 6.83 5.93 0.68 0.59 0.17 0.26 0.3 [h,k,l] 
7 P -1 0.000 3.69 9.36 5.67 0.94 0.57 0.06 0.26 0.0 [-h,k,1/2h-1/2k-1/2l] 
8 I 1 2/m 1 0.000 0.08 6.40 6.33 0.64 0.63 0.23 0.22 0.3 
[-1/2h+1/2k-1/2l,-h-k,-1/2h+1/2k+1/2l] 
9 F m m m 0.000 -0.43 6.17 6.60 0.62 0.66 0.24 0.20 0.3 [h+k,-h+k,l] 
10 I 1 2/m 1 0.000 0.75 6.89 6.14 0.69 0.61 0.22 0.22 0.3 
[-1/2h-1/2k-1/2l,h-k,-1/2h-1/2k+1/2l] 


Xtriage Summary 

Twinning and intensity statistics summary (acentric data): 

Statistics independent of twin laws 
/^2 : 2.126 (untwinned: 2.0, perfect twin: 1.5) 
^2/ : 0.774 (untwinned: 0.785, perfect twin: 0.885) 
<|E^2-1|> : 0.761 (untwinned: 0.736, perfect twin: 0.541) 
<|L|>, : 0.490, 0.323 
Multivariate Z score L-test: 1.303 

The multivariate Z score is a quality measure of the given 
spread in intensities. Good to reasonable data are expected 
to have a Z score lower than 3.5. 
Large values can indicate twinning, but small values do not 
necessarily

Re: [ccp4bb] Unidentified electron density blob

2018-07-06 Thread Wim Burmeister

Hello,
a really molecule should show up also in the 2Fo-Fc type map. This
appears not to be the case.
So indeed it is likely that your density corresponds to some
alternate conformation of the surrounding residues present with low
occupancy. The glutamic acid sidechain could be modelled, but I have
some doubts about the rest.
If the refinement is almost finished, it could simply be noise.
Best
Wim

On 03/07/2018 04:23, Uma Gabale wrote:

Dear all,

We came across a blob of
unidentified electron density in a shallow cavity
of a bacterial protein
structure (pictures attached). It is surrounded by residues Asp, Arg, Gln, His, Glu, Thr, and Trp.

The protein was expressed in E. coli BL21(DE3)
and purified on Ni-NTA followed by gel filtration.
The purification buffers included Tris,
crystallization condition had HEPES and PEG3350;
perfluoropolyether was used as a cryoprotectant.
We would appreciate any help in identifying it.

Thanks and regards,

Uma.

--
Uma
Gabale, PhD
Research
Associate
Molecular
and Cellular Biochemistry
Indiana
University Bloomington

To unsubscribe from the CCP4BB list, click the
following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

2018-05-18 Thread Wim Burmeister


  
  
Hello,
thank you very much for the different answers.

In order to close the discussion, the solution is to expand first
the I213 asymmetric unit to a full I213 unit
cell contents (24 asu, 12 from the rotational symmetry and 12 from
the body-centering) using pdbset.

Then the coordinates have to be rotated using again pdbset and the
matrix :



   

  -0,577335655
  0,5773878412
  0,5773878412


  0,4083025328
  -0,4082287321
  0,816531265


  0,7071581216
  0,7071581216
  0

  




This matrix combines the passage from the cubic to the primitive
triclinic P1 (or actually rhombohedral R3) unit cell (a=b=c,
alpha=beta=gamma=109.47°) and the re-orthogonalization of the
structure in the triclinic unit cell.

Finally, the symmetry information in the pdb header has to be
changed from I213 to P1 and the 12 excess molecules
(asu's) have to be removed manually to stay with 12 molecules
(asu's) filling the primitive triclinic unit cell ( or 4 ones
filling the rhombohedral R3 asymmetric unit.

Greetings
Wim

Re: [ccp4bb] 3D stereo and pymol

2018-05-18 Thread Wim Burmeister

Dear Christine,
here you can find my xorg.conf file.
https://app.box.com/v/xorg-conf
I gave some replies below.
Sorry for the late answer, I do not read the ccp4bb every day.
Best
Wim

On 16/05/2018 19:56, Christine Gee
wrote:

Hi Wim

Would you mind letting me know which stereo option you
selected in your xorg.conf file,

Option "Stereo" "10"

and if you needed the option composite disable?

Yes

It would be very helpful. We are just setting up a new
system.

Regards

Christine

On Wed, Jan 3, 2018 at 1:42 AM, Wim
Burmeister <wim.burmeis...@ibs.fr>
wrote:

I answer a bit late,
but I repost a message on 3D graphics from Mai 2017 :

Hello,

we just
wanted to share our experience in finding a
configuration which allows to use 3D graphics under
linux using Nvidia GeForce 3D glasses.

We had quite
a hard time to find a configurations which works
correctly.

We finally
used Debian linux with a xfce desktop. Other recent
desktops use a tiling which is not compatible with
3D graphics.

The hardware
consists of

a DELL Precision
T5810 desktop computer with an Nvidia Quadro M4000
(8 Gbyte memory, 4 DP) graphics card
Nvidia GeForce 3D Vision 2
(NVIDIA GEF 3D VISION 2 GLASSES KIT) active stereo
glasses
a stereo connector PNY Quadro
4000 3D for the synchronization of graphics card and
glasses
an ASUS 24" LED 3D - VG248QE
display
a DisplayPort-DisplayPort cable

The Nvidia
linux drivers from version 367.57 can handle the
current version of the Nvidia glasses.

For an
obscure reason a direct DP-DP connection between
graphics card and display is absolutely required in
order to obtain fully working stereo. If a DP-DVI
dual link adapter is used, the stereo does not work
on the top and the bottom part of the screen. This
is true for a native DELL active adaptor or generic
models. The exact reason remains unresolved, but the
solution is to use a direct DP-DP connection. This
limits the available choice of displays which
require 120 Hz for 1080*1980 screen resolution and a
DP input. We have been choosing a “Nvidia 3D ready”
model.

There has
been a considerate about of exchange about this
problem on

https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/

The setup
comes with a price tag of about 1600 € free of
taxes.

coot, pymol
and chimera work straight without problems in
hardware stereo mode. The experience is absolutely
great.

Best

Wim
--
Wim Burmeister
Professeur
Institut de Biologie
Structurale (IBS) CIBB
71
avenue des Martyrs
CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Tel: +33 (0) 457 42 87 41 Fax: +33 (0)
476 20 94 00
website

Wim Burmeister
Profe

[ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

2018-05-15 Thread Wim Burmeister


  
  
Hello,
does anybody have a script which transforms the pdb file of a
structure in I-centred I213 into a pdb file based on the
corresponding primitive P1 unit cell ? A rotation matrix would also
do  which uses the matrix of the transformation from one coordinate
system to the other combined with the orthogonalisation convention
for the P1 cell.
Best
Wim
-- 
Wim Burmeister
  Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs
CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
  Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
website
map

Re: [ccp4bb] 3D stereo and pymol

2018-01-03 Thread Wim Burmeister

I answer a bit late, but I repost a message on 3D graphics from Mai
2017 :

Hello,

we just wanted to share our experience in finding
a configuration which allows to use 3D graphics under linux
using Nvidia GeForce 3D glasses.

We had quite a hard time to find a configurations
which works correctly.

We finally used Debian linux with a xfce desktop.
Other recent desktops use a tiling which is not compatible
with 3D graphics.

The hardware consists of

a DELL Precision T5810
desktop computer with an Nvidia Quadro M4000 (8 Gbyte memory,
4 DP) graphics card
Nvidia
GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT)
active stereo glasses
a stereo
connector PNY Quadro 4000 3D for the synchronization of
graphics card and glasses
an ASUS 24"
LED 3D - VG248QE display
a
DisplayPort-DisplayPort cable

The Nvidia linux drivers from version 367.57 can
handle the current version of the Nvidia glasses.

For an obscure reason a direct DP-DP connection
between graphics card and display is absolutely required in
order to obtain fully working stereo. If a DP-DVI dual link
adapter is used, the stereo does not work on the top and the
bottom part of the screen. This is true for a native DELL
active adaptor or generic models. The exact reason remains
unresolved, but the solution is to use a direct DP-DP
connection. This limits the available choice of displays which
require 120 Hz for 1080*1980 screen resolution and a DP input.
We have been choosing a “Nvidia 3D ready” model.

There has been a considerate about of exchange
about this problem on

https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/

The setup comes with a price tag of about 1600 €
free of taxes.

coot, pymol and chimera work straight without
problems in hardware stereo mode. The experience is absolutely
great.

Best

Wim
--
Wim Burmeister
Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs
CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Tel: +33 (0) 457 42 87 41 Fax: +33 (0) 476 20 94 00
website

Re: [ccp4bb] ITC data clarification.

2017-12-08 Thread Wim Burmeister


Hello,
only a test of the biological function of mutants will tell whether  
your interface is an artefact or not.
It is very well possible that an alanine mutations increases binding;  
you have to inspect the interface carefully whether there were for  
example buried hydrogen donors or flexible residues in the WT  
interface which made the interaction less than optimal.

Regards
Wim

Dharma  a écrit :


Hello CCP4 users,
Based on the crystal structure of a two molecule protein complex, I  
have mutated (alanine substitutions) one of the putative binding  
interface. The mutant binds with much higher affinity than the wild  
type.
However, the signature plot of ITC data reveals a decrease in the  
enthalpy but increase on the entropy (deltaS). Thus overall increase  
in deltaG.

I want to know if it’s relevant biological interface or a crystal artifact.
Suggestions please.

Thanks
Regards
Dharma
Sent from my iPhone

Re: [ccp4bb] 3D graphics under linux for coot, pymol and chimera

2017-05-22 Thread Wim Burmeister


  
  
Dear Ray,
below the contents of the file.
Best
Wim

ps. There are actually still some lines for the monitor we used
previously (Benq) in the file. This model does not work correctly
for stereo as it does not have a DP input.

# nvidia-settings: X configuration file generated by nvidia-settings
# nvidia-settings:  version 375.39 
(buildmeister@swio-display-x86-rhel47-09)  Tue Jan 31 20:46:35 PST
2017

# nvidia-xconfig: X configuration file generated by nvidia-xconfig
# nvidia-xconfig:  version 340.46  (buildd@brahms)  Tue Oct  7
08:00:32 UTC 2014

Section "ServerLayout"
    Identifier "Layout0"
    Screen  0  "Screen0" 0 0
    InputDevice    "Keyboard0" "CoreKeyboard"
    InputDevice    "Mouse0" "CorePointer"
    Option "Xinerama" "0"
EndSection

Section "Files"
EndSection

Section "InputDevice"

    # generated from default
    Identifier "Mouse0"
    Driver "mouse"
    Option "Protocol" "auto"
    Option "Device" "/dev/psaux"
    Option "Emulate3Buttons" "no"
    Option "ZAxisMapping" "4 5"
EndSection

Section "InputDevice"

    # generated from default
    Identifier "Keyboard0"
    Driver "kbd"
EndSection

Section "Monitor"
    Identifier "Monitor0"
    VendorName "Unknown"
    ModelName  "BenQ XL2411Z"
    HorizSync   30.0 - 160.0
    VertRefresh 56.0 - 144.0
    Option "DPMS"
EndSection

Section "Device"
    Identifier "Device0"
    Driver "nvidia"
    VendorName "NVIDIA Corporation"
    BoardName  "Quadro M4000"
EndSection

Section "Screen"

# Removed Option "metamodes" "1920x1080_120 +0+0"
    Identifier "Screen0"
    Device "Device0"
    Monitor    "Monitor0"
    DefaultDepth    24
    Option "AllowGLXWithComposite" "True"
    Option "Stereo" "10"
    Option         "nvidiaXineramaInfoOrder" "DFP-6"
    Option "metamodes" "1920x1080_100 +0+0"
    Option "SLI" "Off"
    Option "MultiGPU" "Off"
    Option "BaseMosaic" "off"
    SubSection "Display"
    Depth   24
    EndSubSection
EndSection

Section "Extensions"
    Option "Composite" "Disable"
EndSection


-- 
  
  
Wim Burmeister
  Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs
CS
20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
  Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94
  00
website

[ccp4bb] 3D graphics under linux for coot, pymol and chimera

2017-05-17 Thread Wim Burmeister

Hello,

we just wanted to share our experience in finding
a configuration which allows to use 3D graphics under linux
using Nvidia GeForce 3D glasses.

We had quite a hard time to find a configurations
which works correctly.

We finally used Debian linux with a xfce desktop.
Other recent desktops use a tiling which is not compatible
with 3D graphics.

The hardware consists of

a DELL Precision T5810
desktop computer with an Nvidia Quadro M4000 (8 Gbyte memory,
4 DP) graphics card
Nvidia
GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT)
active stereo glasses
a stereo
connector PNY Quadro 4000 3D for the synchronization of
graphics card and glasses
an ASUS 24"
LED 3D - VG248QE display
a
DisplayPort-DisplayPort cable

The Nvidia linux drivers from version 367.57 can
handle the current version of the Nvidia glasses.

For an obscure reason a direct DP-DP connection
between graphics card and display is absolutely required in
order to obtain fully working stereo. If a DP-DVI dual link
adapter is used, the stereo does not work on the top and the
bottom part of the screen. This is true for a native DELL
active adaptor or generic models. The exact reason remains
unresolved, but the solution is to use a direct DP-DP
connection. This limits the available choice of displays which
require 120 Hz for 1080*1980 screen resolution and a DP input.
We have been choosing a “Nvidia 3D ready” model.

There has been a considerate about of exchange
about this problem on

https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/

The setup comes with a price tag of about 1600 €
free of taxes.

coot, pymol and chimera work straight without
problems in hardware stereo mode. The experience is absolutely
great.

Best

Wim

Re: [ccp4bb] Temperature factor discrepancy

2008-12-03 Thread Wim Burmeister





I should have given the precision that the problem remains unaffected
by a change of the resolution range (even if I use for example only 4.5
to 3 A resolution).
I am not using TLS and the data are quite isotropic. Rcryst values are
as expected for such a structure.
Anopther 3.5 A dataset does not show the problem (right column).

  

  
  Wilson plot B-factor [2]
  
  
  66
  
  
  43
  


  
  Refinement
  
  
  
  
  
  
  


  
  Rcryst
  
  
  0.186 (0.259)
  
  
  0.190 (0.239)
  


  
  Rfree
  
  
  0.268 (0.408)
  
  
  0.256 (0.278)
  


  
  Rms deviations
from ideal bondlengths ()
  
  
  0.020
  
  
  0.018
  


  
  Rms deviations
from ideal bond angles ()
  
  
  2.0
  
  
  1.9
  


  
  Average B-factor [2]
  
  
  39
  
  
  46
  

  

Values for
the highest resolution bin are given in brackets.


Cheers

Wim

Wim Burmeister a crit:
Dear all,
  
  
I have a 3 A structure refined with REFMAC which gives consistently
average atomic B-factors of 40 A2, whereas the B factor from a Wilson
plot is about 60 A2. Is there any explanation for such a discrepancy?
  
There are no obvious problems:
  
No twinning, spacegroup P21 with two molecules in the asu, no proper
ncs symmetry. No pathologic Wilson plot, complete and redundant dataset
(although collected on several crystals with serious problems due to
radiation damage).
  
Interestingly, the Wilson plot of the Fcalc values is about 60 A2 as
for Fobs in the output dataset.
  
  
Yours
  
  
Wim
  
  



-- 
***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
E-mail: [EMAIL PROTECTED]
Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
http://www.uvhci.fr
***

[ccp4bb] Temperature factor discrepancy

2008-12-02 Thread Wim Burmeister


Dear all,

I have a 3 A structure refined with REFMAC which gives consistently 
average atomic B-factors of 40 A2, whereas the B factor from a Wilson 
plot is about 60 A2. Is there any explanation for such a discrepancy?

There are no obvious problems:
No twinning, spacegroup P21 with two molecules in the asu, no proper ncs 
symmetry. No pathologic Wilson plot, complete and redundant dataset 
(although collected on several crystals with serious problems due to 
radiation damage).
Interestingly, the Wilson plot of the Fcalc values is about 60 A2 as for 
Fobs in the output dataset.


Yours

Wim

--
***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
E-mail: [EMAIL PROTECTED]
Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
http://www.uvhci.fr
***

Re: [ccp4bb] Lower completeness, decent R factors, but low B factor...

2008-08-20 Thread Wim Burmeister


James Pauff a écrit :

Hello all,

I have a refined structure at 2.6 angstroms that at about 73% completeness at 
this resolution.  The I/sigma is about 2.0 at 2.6 angstroms, and the omit 
density for my ligands is great contoured at 3.0sigma.  My Rcryst is 19 or so 
and the Rfree is 24.5 or so.

HOWEVER, my mean B value is 13.9, whereas my other 2 structures (at 2.2 and 2.3 
angstroms, same protein, 95% completeness) have mean B values of 22+.  Any 
suggestions as to what is going on here?  I'm having trouble explaining this.

Thank you,
Jim


  



  

Dear Jim,

probably you did not collect your data to the highest possible 
resolution. Did you use an inhouse source? You would expect that a 
crystal with an average temperature factor of 14 A2 would diffract to 
1.6 A on a synchrotron source.


Regards

Wim

--
***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
E-mail: [EMAIL PROTECTED]
Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
http://www.uvhci.fr
***

Re: [ccp4bb] refmac, twin - really low Rfactors

2008-08-14 Thread Wim Burmeister


Jan Abendroth a écrit :

Hi all,
kind of a weird problem - the R-factors of a refinement using the new 
twin refinement in refmac are low, almost suspiciously low:
A good 1.9AA data set, space group H3/R3, many statistics starting 
with truncate's cumulative intensity distribution clearly suggest 
twinning. The structure (SSGCID target) was solved by MR, very rigid 
beta-helix (see 3bxy, very cool fold!), maps nice. I use refmac 
5.5.0046 for refinement, with and without the new TWIN flag.


Here my concerns:
Despite 0.3/0.7 twin domains as suggested by various programs and 
refined by refmac, the difference of between the Rs of the twinned 
refinement and the non-twinned refinement are constantly rather 
little: 0.143/0.174 for the twinned case, 0.218/0.275 for the 
non-twinned case. This seems rather low to me for a quite high twin 
fraction. Plus the R-factors for the twinned case are really low for a 
1.9AA structure. As expected, the maps from the twin treatment are a 
bit nicer that  for the non-twinned treatment.
Any reasons for concerns or just a very rigid structure that refines 
really well or refmac handling twinning really nicely?


Thanks for any input
Jan

--
Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island WA, USA
work: JAbendroth_at_decode.is
home: Jan.Abendroth_at_gmail.com



Dear Jan,

The result looks reasonable to me.
Twinning has two effects:
The effective ration of observations/variables decreases with increasing 
twinning fraction.

The datasets become better as there are less weak and strong reflections.
This leads to a better fit so that your results do not surprise me.

Yours

Wim Burmeister


--
***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
E-mail: [EMAIL PROTECTED]
Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
http://www.uvhci.fr
***

Re: [ccp4bb] self-rotation interpretation, 5 minutes

2007-08-20 Thread Wim Burmeister


Yanming Zhang a écrit :

Hi,

Would some experts help me to interpretate the attached self rotation 
function ps graph? The cell: 84.847 84.847 172.485 P4 indexing. In 
perticular, I was puzzled by:


1,Does the peak (90 45 180) a crystallographic 2-fold or 
non-crystallographic 2-fold?
2,Why there is no crystallographic peak on the section kappa=90? 
Giving P4 space group, there should be some high crystallographic 
4-fold peaks appear on the section.


It probably takes you only 5 minutes. Your help is greatly appreciated.

Yanming

Deqr Yanming
The north pole of the diagramm corresponds to the direction of the z 
axis. There is well a crystallographic 4-fold (and automatically 2- 
fold) peak in this direction. Then there are non-crystallographic 2-fold 
axes in the x,y plane, spaced by 45 degrees, as all the peaks appear to 
have the same height.




Greetings

Wim Burmeister

--
***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
E-mail: [EMAIL PROTECTED]
Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro
***

Re: [ccp4bb] packing

2007-06-29 Thread Wim Burmeister


Tassos Papageorgiou wrote:

Dear all,

I am looking for examples of different packing arrangements in crystals of the
same protein with similar unit cell parameters and space group (eg the protein
adopts different packing although the crystals remain the same both in unit
cell dimensions and space group). Can this happen, for example, during flash
cooling?

Thank you in advance

Tassos Papageorgiou



--
A.C.(Tassos) Papageorgiou, PhD  phone: +358 2 333 8012 (office)
Senior Scientist, Group leader  fax:   +358 2 333 8000
Turku Centre for Biotechnology  E-mail: [EMAIL PROTECTED]
BioCity, Turku  URL: http://www.btk.utu.fi/~apapageo
FIN-20521, Finland



  

Dear Tassos,

I would guess that you rather have a problem of different choices of 
origins between your datasets which can happen for a number of 
spacegroups. This can make that the packing appears different on the 
first glimpse, but you should be able to translate one arrangement on 
top of another.


Yours

 Wim

--
***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
E-mail: [EMAIL PROTECTED]
Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro
***

Re: [ccp4bb] His-His H-bond

2007-05-23 Thread Wim Burmeister


david lawson (JIC) wrote:

Dear All,

We have solved a structure that has an intersubunit His-His H-bond
(ND1---NE2). The protein most likely undergoes conformational changes
that involve the making and breaking of H-bonds at this interface. In
all the protein structures I have previously studied I don't recall ever
seeing such a bond - His-His ring stacking yes, but never H-bonding. I
was wondering if anyone else had seen this type of interaction and
whether it had any functional significance. The crystals were grown at
pH 5.6. 


Many thanks

Dave Lawson

---

Dr. David M. Lawson
Biological Chemistry Dept.,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: [EMAIL PROTECTED]
Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm 
 




  

Dear David,

why not, as long as the histidine residues are not fully protonated, and 
at pH 5.6 this is still possible, the nitrogen atoms act as hydrogen 
bond donors or acceptors. Look for example in pdb 1FL1 KSHV protease, 
where there is a catalytic triad Ser114-His46-His134.


Yours

Wim Burmeister

--
***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
E-mail: [EMAIL PROTECTED]
Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro
***

45 matches

Mail list logo