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

from the CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] [image/png:Screenshot 2023-12-16 at 3.36.01 PM.png] -- Wim Burmeister Professor Institut de Biologi

Re: [ccp4bb] 1990s-style stereo viewer

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 Cede

Re: [ccp4bb] quantifying electron density

p;A=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 d

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

d 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&A=1 | https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1

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

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..

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

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

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

://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Wim Burmei

Re: [ccp4bb] Ligand occupancy refinement

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&A=1 | https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] -- Wim Burmeister Pro

Re: [ccp4bb] Add hydrogens

e CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] -- Wim Burmeister Professor Institut de Biologie Structurale (IBS) CIBB 71 avenue des Martyrs / CS 20192 38044 Grenobl

Re: [ccp4bb] Phosphatase enzymatic assay

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

[ccp4bb] chain on 2-fold axis?

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 ca

Re: [ccp4bb] malonate and histidine interaction

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 ? Occup

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

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

Re: [ccp4bb] R free rising

...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 12:08:1

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

mp; 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&A=1 --

[ccp4bb] Font issues in imosflm under xubuntu 18

-- Wim Burmeister

[ccp4bb] font issues in imosflm under xubuntu 18

screenshot of the interface. Does anybody have any idea how to solve the problem ? Best wishes Wim -- Wim Burmeister

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

BED1=CCP4BB&A=1 -- Wim Burmeister

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

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 tra

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

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: V

Re: [ccp4bb] Calculating RMSD of a loop

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

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

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 belo

Re: [ccp4bb] Better Beamline suggestion!

uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Wim

Re: [ccp4bb] ORCID

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" Envo

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

scmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Wim Burmeister

Re: [ccp4bb] Partially occupied C-terminus

B&A=1 -- Wim Burmeister Professeur Institut de Biologie Structurale (IBS) CIBB 71 avenue de

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

: 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

Re: [ccp4bb] OFF TOPIC

&A=1 -- Wim Burmeister Professeur Institut de Biologie Structurale (IBS) CIBB 71 avenue des Martyrs CS 20192 38044 Grenoble Cedex 9, FR

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

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 wit

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

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 D

Re: [ccp4bb] Unidentified electron density blob

: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Wim Burmeister Professeur Institut de Biologie Structurale (IBS) CIBB 71 avenue des Martyrs

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

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 pdbse

Re: [ccp4bb] 3D stereo and pymol

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,

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

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

Re: [ccp4bb] 3D stereo and pymol

e 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 Bio

Re: [ccp4bb] ITC data clarification.

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

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

"Monitor0"     DefaultDepth    24     Option "AllowGLXWithComposite" "True"     Option "Stereo" "10"     Option         "nvidiaXineramaInfoOrder" "DFP-6"     Option "metamodes" "

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

imera work straight without problems in hardware stereo mode. The experience is absolutely great. Best Wim -- Wim Burmeister Professeur Institut de Biologie Struct

[ccp4bb] GRAL MASTER 2 RESEARCH SCHOLARSHIPS in Grenoble/France - Launch of the call for application 2016

in case if you are in contact with Master students: for this list the most relevant speciality is the Master 2 of  "Integrative Structural Biology (ISB)". Wim Burmeister   Dear

Re: [ccp4bb] Temperature factor discrepancy

ideal bond angles (°) 2.0 1.9 Average B-factor [Å2] 39 46 Values for the highest resolution bin are given in brackets. Cheers Wim Wim Burmeister a écrit : Dear all

[ccp4bb] Temperature factor discrepancy

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 FRA

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

rds 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

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

ction. 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

Re: [ccp4bb] Negative density around C of COO-

. Could some body enlighten me on this feature? The other original reference for the radiation damage effect on carboxyls is actually: Burmeister, W. P. Structural changes in cryo-cooled protein crystals owed to radiation damage. Acta Cryst. D 56, 328-341 (2000). Greetings Wim Burmeister

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

Dear Yanming My previous message only holds if there is no sign of twinning. Alternatively, you may have a near perfect-twinning with a twin operation corresponding to an rotation around the xy-diagonal and a crystallographic or non-crystallographic 2-fold axis around x and y. Wim Burmeister

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

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

Re: [ccp4bb] question

mand file using the gui before running it. 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 ru

Re: [ccp4bb] packing

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'Ins

Re: [ccp4bb] His-His H-bond

e 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 Burme

Re: [ccp4bb] Refinement of data from twinned crystals

ddle of the two values obtained by the different techniques. Greetings Wim Burmeister -- ******* Wim Burmeister Professeur, Membre de l'Institut Universitaire de France Unit of Virus Host Cell Interactions (UVHCI) UMR5233