Re: [ccp4bb] Unidentified blobs

It is most likely to be something in your crystallisation condition, your cryoprotectant, or the buffer you stored your protein in. Could be a detergent carried through several steps of purification Could for example be some part of a PEG molecule that gets ordered round a more hydrophobic bit

Re: [ccp4bb] Table in NSMB

I would have thought that ligands are ligand/ion?. What I have just done with a recent structure and I await the reviewers noticing or not is include the ethylene glycol from the cryo that I can (probably) see in a solvent (rather than water) atom number and bfactor line along with water

Re: [ccp4bb] Table in NSMB

Sorry misread the initial post. Yes a protein ligand should be in the protein but you could give B factor number for each chain- my comments about what goes in ligand and what in solvent may be of general interest/comment Nick -- Prof Nicholas H. Keep Executive Dean of School of Science

[ccp4bb] Britton/Murray Rust plot

I am confused by the Britton/Murray-Rust plots in ctruncate. My reading this morning has indicated that the Britton plot was actually proposed by Fisher and Sweet 1980. Treatment of diffraction data from crystals twinned by merohedry. Acta Crystallogr.A36:755--760 and plots the fraction of

Re: [ccp4bb] Bfactors too high after TLS refinement

TLS in phenix does seem to lead to high B factors in some of our cases. To check whether it was particular to our datasets , we rerefined some similar structures to ours from the PDB and found that their B factors increased to high values similar to our structure when run through the same

[ccp4bb] Loop clashing on symmetry axis

Am refining a structure in P3(1)21 with three copies in the ASU. It is pretty close to completion R/Rfree 18/21 with 2A data. However in one copy a section that is clear in the other two is poor as it meets itself on a two fold. My interpretation is that one copy of the loop is in a visible

Re: [ccp4bb] Loop clashing on symmetry axis

On 10/06/2014 18:48, Nicholas Keep wrote: is set to zero Sorry in my last email this should read is set to a fraction eg 0.5 Nick Am refining a structure in P3(1)21 with three copies in the ASU. It is pretty close to completion R/Rfree 18/21 with 2A data. However in one copy a section

[ccp4bb] Two Molecular Biology Lab Manager Positions

Birkbeck, University of London has two vacancies to mange our Molecular Biology research laboratories. The post holders are responsible for ordering, equipment maintenance and health and safety. They will also be involved in development of teaching laboratory practicals and assisting in

Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore

I think Fred is overstating the problem of compulsory adverts. There are also cases where the expected pre-selected candidate does not get the job as a better candidate appears. There are also cases where there is eventually no job for anyone. Another outcome of an interview is you don't get

Re: [ccp4bb] PEG refinement

I doubt there is a consensus on this. Your PEG solution is a mixture of lengths of polymer and normally you can only see a small fraction of the PEG molecule. PEG400 will be between 8 and 10 ethylene glycols. Bigger PEGS probably vary more. My experience is that you can often only see

[ccp4bb] P212121 and P213

I have a structure which normally crystallises in P213 but one data set the edges became slightly non-equivalent in length by a couple of angstroms and the data process in P212121 P212121 symmetry operators appears to be a subset of P213 http://img.chem.ucl.ac.uk/sgp/large/019az1.htm

Re: [ccp4bb] P212121 and P213

Thanks Eleanor, your tip has got me there. I was attempting the problem the wrong way round. To get it to work I had to reindex the P212121 h=-l k=k l=h Then rigid body refinement of the P213 symmetry generated trimer dropped it to 40% and NCS refinement to around 25% My reasoning for

[ccp4bb] Structural Biologist Central London

*Structural Biologist * *Location: Central London, UK* *12 month fixed-term contract* *Salary dependent on experience* ** Cancer Research Technology (CRT) is a specialist drug discovery, technology transfer and commercialisation company which aims to advance new discoveries to beat cancer.

[ccp4bb] Fwd: [ccp4bb] Structural Biologist Central London_ DEADLINE VERY SOON

*Structural Biologist * *Location: Central London, UK* *12 month fixed-term contract* *Salary dependent on experience* ** Cancer Research Technology (CRT) is a specialist drug discovery, technology transfer and commercialisation company which aims to advance new discoveries to beat cancer.

[ccp4bb] Crystallisation/Crystallography commercial permenant positions in Central London ONE WEEK TO APPLY

There is just one week left to apply for these jobs Structural Biologists (X-ray Crystallography) Central London (REF. SB0107) Cancer Research Technology (CRT) is a specialist oncology company, which develops discoveries arising from Cancer Research UK and other prestigious oncology focused

[ccp4bb] X-ray lab manager Birkbeck University of London- permenant position

Final reminder of this vacancy applications close in a week's time X-ray Laboratory Manager Research Assistant We are seeking an experienced person to manage our protein X-ray crystallography laboratory and to provide research assistance to the Academic staff using the laboratory. The

Re: [ccp4bb] refmac5

I think you get this problem whether or not you have selected to write a map. I find that you need to open up the dialogue for maps set to temp.map and temp1.map and then the gui remembers that going forward whether or not you deselect the option to generate a map. It also means you cannot

[ccp4bb] Postdoctoral position in X-ray/EM at Birkbeck, University of London

Contact [EMAIL PROTECTED] or [EMAIL PROTECTED] for informal enquiries please do NOT reply to this email. Postdoctoral Research Assistant – Ref: 10082 School of Crystallography, Faculty of Science Full time, fixed term appointment for up to five years The School of Crystallography/Institute of

[ccp4bb] Cis/trans double bonds in refmac/coot

I have a structure with an unsaturated lipid in the active site, which according to the chemists has one cis and one trans double bond. I would expect these to be controlled by the torsion angles in the cif files. However altering torsions between 0 and 180 makes no difference to the

[ccp4bb] Baubles (re imosflm)

I have questions about baubles in general. I find that using firefox (3.0.4 windows) baubles logs do not open directly from ccp4i or imosflm and I get an error i is not a registered protocol (or c) which I think is the drive the file is on. However if I open the file in via open file then it

[ccp4bb] NCS restraints of domains

I am refining a low (3A) resolution structure of a 3 domain protein. There are 4 copies in the ASU. I have been applying tight NCS restraints by domain in refmac and have pulled the weak MR solution down to Rfree below 30 (just). However my question is that in 2 of the 4 copies one of the

[ccp4bb] Processing to detector corners with XDS

Sorry this is off topic. I am trying to push a data set into the corners of the detectors as Mean I/SIGI looks strong for the circle that the XDS integrates to. The resolution appears to be hard coded in the detector header (and is reported back by XDS in the .LP files) which seems to override

[ccp4bb] Thanks for the many responses

Thanks for the many responses. I had been setting the parameters right. The problem was I was not telling xds to go back as far as INIT in the reprocessing. JOB ALL was the answer Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science

[ccp4bb] Permanent X-ray Lab Manager Post London UK

Birkbeck College, University of London, has a long tradition in X-ray crystallography going back to JD Bernal. As part of the Institute of Structural Molecular Biology with UCL we are looking for a permanent X-ray lab manager to be in charge of our new crystallisation facility (including imager

[ccp4bb] Graduate Teaching assistant/Phd Student Birkbeck University of London

Birkbeck is recruiting a graduate teaching assistant to combine some teaching duties with doing a Ph.D. at one of the top centres for Structural biology in the UK. The deadline for applications is 1st September to ideally start this October. Please bring this to the attention of any suitable

[ccp4bb] [Fwd: [ccp4bb] Permanent X-ray Lab Manager Post London UK]

There is just over a week left to apply for this X-Ray Lab Manager job in central London. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological

[ccp4bb] Resolution and distance accuracies

We clearly have confidence in distance measurements in crystal structures of an order of magnitude better than the resolution ie 0.1-0.3 Angstroms, but can anyone point me to a more exact theory of distance accuracy compared to optical resolution, preferably one that would apply to microscopy

[ccp4bb] Liquid nitrogen resistant flooring

Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid nitrogen. Ie you can fill dewars on without cracking. Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick -- Prof Nicholas H. Keep

[ccp4bb] Graduate Teaching Assistants- Birkbeck University of London

There are two graduate teaching assistant available for October 2011 in the Dept of Biological Sciences, Birkbeck University of London. These positions require you to teach and support teaching for up to 50% (17.5 hours a week) of your time during term and to undertake a Ph.D with a member of

[ccp4bb] Prodrug bugs

Dear CCP4 There is a bug in the ccp4i interface to prodrug on both linux and windows. There is a title line that is read in to the command file which means the software does not run Unrecognised keyword. This can be removed using the run and view com file option However on windows I then get the

Re: [ccp4bb] Creating CIF Files and Renaming Ligands

Did you rename the ligand in the CIF file as well? It would be nice if the Prodrg interface allowed you to type in the name of the ligand you want in the CIF and PDB file. Hopefully a global replace in your favourite text editor of DRG with LIG or whatever you want to call your ligand would

[ccp4bb] Merging hi and low res data

We have a high and low res pass on a crystal that is going to around 1.2 A on the pilatus at Diamond. We tried to scale them together using the xds CORRECT files from the xia2 -3dii runs (gives best results as far as we can see comparing xia2.html files) through aimless via ccp4i interface.

[ccp4bb] Bucanneer and molecular replacement

I have been trying to get my head around using bucanneer for molecular replacement. I am not sure that I have understood the specify a heavy atom or MR model and what this does or the model to be extended options. I am not sure of the difference between the two, and bucanneer will only run on

[ccp4bb] Postdoc Position in Electron Microscopy Birkbeck University of London

PLEASE EMAIL h.sai...@mail.cryst.bbk.ac.uk NOT message poster Dear Colleagues, Two postdoctoral positions are available in the group of Professor Helen Saibil, in the EM lab, Crystallography Department, Birkbeck College, London. The posts are funded by a Wellcome Trust Programme grant in the

[ccp4bb] Group B factors in refmac

We have been solving a protein complex at 3.1 A by molecular replacement. One copy of two chains in the asymmetric unit. The two chains have fairly different average B factors. As would be expected isotropic B factors in refmac overfits the data and leaves a large gap between R and Rfree. TLS

[ccp4bb] Proportion of MR in the PDB

Does anyone have a good estimate of the proportion of molecular replacement structures in the PDB? I tried using the search tools at RCSB and PDBe. The PDBe gives 55.1% but apparently only 3411 structures have phase determination information recorded, so this does not look to be terribly

[ccp4bb] comparing coordinates- SUMMARY

Thanks for the many emails I have received. Particularly to Ed who wrote and posted a script to the board and other people who offered to do it over the weekend. I have achieved what I want with the unsupported ccp4 program compar (Plea to CCP4 support- increase the array sizes by an order of

[ccp4bb] Career Development Fellow Birkbeck University of London

Birkbeck, University of London has a long tradition in structural biology going back to JD Bernal. As part of the institute for Structural Molecular Biology http://www.ismb.lon.ac.uk/ under Prof Gabriel Waksman FRS, it remains a leading centre in the UK for structural biology. The college

[ccp4bb] Graphic for rotation about axis

Where can you get hold of a graphic that indicates a rotation around the horizontal or vertical axis These occur in a lot of papers to indicate the relation between two views but I don't seem to easily be able to google how to get hold of them best wishes Nick -- Prof Nicholas H. Keep

Re: [ccp4bb] How many is too many free reflections?

I agree with Gerard. It would be much better in many ways to generate a separate file of Free R flags for each crystal form of a project to some high resolution that is unlikely to ever be exceeded eg 0.4 A that is a separate input file to refinement rather than in the mtz. The generation

[ccp4bb] Career Development Fellows in the ISMB, Birkbeck University of London

Birkbeck, University of London has three vacancies for Career Development Fellows for up to three years funded by Wellcome ISSF funding. These posts may be held part-time or full-time.

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

I must also credit Robbie with the easiest (most elegant?) solution to my question. You run 0 cycles of refmac with the mixed B factor model. Thanks all for your inputs. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science

[ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

It would be nice to be able to run zero cycles of refmac to get a map etc direct from a PDB file. However due the PDB requiring the TLS component of B factor to be included this does not work. Is there software to remove the TLS component so a zero cycle of refmac can be run. Best wishes

[ccp4bb] Fwd: X-ray Lab Manger Birbeck University of London- Permanent Post

A reminder this vacancy closes on Sunday. There is a vacancy for an X-Ray Laboratory Manager at the Institute for Structural and Molecular Biology at Birkbeck/UCL based at Birkbeck, University of London. see https://tinyurl.com/y7jgfmr5 This is a permanent University Funded post. A brief

[ccp4bb] X-ray Lab Manger Birbeck University of London- Permanent Post

There is a vacancy for an X-Ray Laboratory Manager at the Institute for Structural and Molecular Biology at Birkbeck/UCL based at Birkbeck, University of London. see https://tinyurl.com/y7jgfmr5 This is a permanent University Funded post.  A brief description of the role is below and

[ccp4bb] Director of Institute for Structural and Molecular Biology at UCL/Birkbeck

Biosciences and Chair of the Search Committee (f.brod...@ucl.ac.uk <mailto:f.brod...@ucl.ac.uk>) or, for enquiries about Birkbeck, Professor Nicholas Keep (n.k...@bbk.ac.uk <mailto:n.k...@bbk.ac.uk>). Closing Date 31st July 2018 -- Prof Nicholas H. Keep Executive Dean of Schoo

[ccp4bb] Support for Mosquito Robots

Does anyone (particularly in the UK) have their Mosquito robot maintained by anyone other than TTP labtech the manufacturers? Our procurement people want to see if there are any other providers. Thanks Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of

[ccp4bb] Molprobity "Feature" in ccp4i2 refmac

I have found a 'feature' in molprobity.  if there are two atoms on top of each other (not hard to do by mistake when adding waters in coot), then molprobity does not work or at least does not give the outputs required to then give the coot molprobity checklist file our of the ccp4i2 refmac

[ccp4bb] Java based structural database websites

This is slightly off topic but I suspect people from PDBe etc read this bulletin board. Quite a number of very useful structural biology web sites (Olderado, Vivaldi, EMDB to name but a few) require java based viewers and hence no longer have full (or in the case of vivaldi any) functionality

Re: [ccp4bb] Unknown density

There is no blue (2fo-fc) density at least at the current contour level in your difference density.  That probably indicates what you are seeing is noise rather than a real feature. I am also seeing more intense (above 7 sigma in some cases) positive difference density without actual density

[ccp4bb] Cif deposition from CCP4i2

I am not quite sure if this is a bug report, or advice for other people or what. Essentially I wanted an mmCIF of a refmac refined structure for deposition.  The CCp4i2 "prepare files for deposition" gives an mmcif with a Rfree several % higher than my best refinement. Essentially this

[ccp4bb] CCP4i2 London Road Show

Reminder CCP4i2 London Road show  TOMORROW.  Places still available. *CCP4 i2 Road Show, London* There will be a CCP4 Road Show for use of the i2 interface on Tuesday 12th November, at Birkbeck College. *Time:* 14:00 - 16:00 for the main workshop with about an hour afterwards for those with

[ccp4bb] Fwd: CCP4i2 London Road Show

Reminder One week to London CCP4i2 Road show.  Places still available. *CCP4 i2 Road Show, London* There will be a CCP4 Road Show for use of the i2 interface on Tuesday 12th November, at Birkbeck College. *Time:* 14:00 - 16:00 for the main workshop with about an hour afterwards for those

[ccp4bb] Fwd: [Labmanagers] CCP4i2 London Road Show

Reminder Two weeks to London CCP4i2 Road show.  Places still available. *CCP4 i2 Road Show, London* There will be a CCP4 Road Show for use of the i2 interface on Tuesday 12th November, at Birkbeck College. *Time:* 14:00 - 16:00 for the main workshop with about an hour afterwards for those

[ccp4bb] CCP4i2 London Road Show

*CCP4 i2 Road Show, London* There will be a CCP4 Road Show for use of the i2 interface on Tuesday 12th November, at Birkbeck College. *Time:* 14:00 - 16:00 for the main workshop with about an hour afterwards for those with additional questions. *Place:* Room 416 in the main Birkbeck Malet St

[ccp4bb] Average B factors with TLS

I am at the point of depositing a low resolution (3.15 A) structure refined with REFMAC.  The average B factors were 31 before I added the TLS contribution as required for deposition which raised them to 157- this is flagged as a problem with the deposition, although this did not stop

[ccp4bb] Question about P3, H3 and R3 space groups

I have an answer from Jeremy Cockcroft the author of the 'Birkbeck' Tables. Actually Jeremy has been at UCL for a decade or so and they are hosted from their Nick In answer to the question regarding the use of R and H for trigonal space groups, the letters refer to two distinct types of

[ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

We are going to be doing a data collection for an MRes student at Diamond in the next couple of weeks.  These are his first crystals.  It would be good if he could be involved in watching it. I was wondering if anyone had tried sharing screen and voice via moodle collaborate or Microsoft

Re: [ccp4bb] A "funny" thing related to AlphaFold2 ....

Has anyone made use of an Alpha Fold PDB as opposed to CIF.  On the half dozen or so I have tried to read into CCP4mg or coot the PDB has always failed but the CIF is fine.  I can then write out a PDB if I want. I could add to the conspiracy theories that this is EBI trying to normalise use

[ccp4bb] Distance Learning Structural Biology Modules

The taught modules of the Birkbeck, University of London MSc in Structural Molecular Biology are now available as single modules for Continuous Professional Development (CPD). The modules are in Protein Crystallography

[ccp4bb] Online EM Course

Please pass on to students/colleagues who may be interested. The Department of Biological Sciences at Birkbeck, University of London is offering an on line, postgraduate course module on Macromolecular and Cellular Electron Microscopy, in the spring term January-March 2022. It will cover the

[ccp4bb] Refmac automatically handles twinning?

Just double checking that Refmac automatically handles twinning without the need for a keyword or a box click in i2.  I have a crystal in P32 21 that gives poor Rfactors and maps (Rfree mid 40s) from what should be an excellent model. I have reprocessed in P32, P1 and C2 but all give similar