Re: [ccp4bb] Question about CCP4 monomer dictionaries

Hi Stephen A value of 1.48 A sounds reasonable to me. For H2O2 https://cccbdb.nist.gov/exp2x.asp?casno=7722841&charge=0 Also in the paper below we have the structure of a peroxide derivative pretty much at atomic resolution and the O-O distance refined at 1.47 A Bui et al. Direct evidence for a p

Re: [ccp4bb] Highest resolution of X-ray / neutron / electron crystallography, cryo EM

Just queried the PDB and found 4AR3 for neutron at 1.05A. Best Roberto On 9 Jun 2020, at 14:46, Tobias Beck mailto:tobiasb...@gmail.com>> wrote: Dear all, Thanks for the link to the latest BioRxiv papers! So for cryo EM it is 1.2 now. Any numbers for neutron? Best, Tobias. Tobias Beck mail

Re: [ccp4bb] powdery residue on pucks?

Fully agree with what others have said. When ’the dust’ happened to us we had to replace that particular shipping dewar as T was not holding for very long. Best wishes Roberto On 22 Feb 2020, at 00:33, Emilia C. Arturo (Emily) mailto:ecgart...@gmail.com>> wrote: Hi All, We have been noticing

Re: [ccp4bb] Shipping samples for neutron diffraction

Dear Stephen I guess the first thing to understand is whether you have a RT or cryo NMX planned. In my personal experience the transition from RT to cryo NMX is not necessarily straightforward. If you (and the beam line scientist) are sure that cryocooled xtals will give you an experiment then

Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb

I assume you’re using ccp4i and not i2. If you use the latter the mmcif coords file produced should be ok. I have had the same problem a few days ago. Best wishes Roberto On 25 Sep 2019, at 15:00, stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwe

Re: [ccp4bb] select from a pdb file a sphere of atoms

pymol? example S1 around 12.3 a. Atoms with centers within 12.3 Angstroms of the center of any atom in S1 Best wishes Roberto On 3 Apr 2019, at 15:18, Stephen Cusack mailto:cus...@embl.fr>> wrote: Dear All, I am looking for an accessible programme that allows selection of atoms from a

[ccp4bb] Faculty positions in cryoEM at King's College London

Dear Colleagues I would like to draw your attention on the following Lecturer/Senior Lecturer positions in cryoEM available at King’s College London. Closing date for the application is 11-Apr-2019. https://my.corehr.com/pls/kingrecruit/erq_jobspec_version_4.display_form?p_company=1&p_internal_

Re: [ccp4bb] Crystallization problems using MPD (2-Methyl-2,4-pentanediol)

Hi js It happened to us as well with a 1:1 protein complex with decent affinity (Kd about 1 uM). The MPD-based condition (quite high % MPD if I recall correctly) would break the complex apart and only one of the two components formed a crystal (effectively allowing crystallisation of a sample w

Re: [ccp4bb] Refinement with native and anomalous data

Dear Piotrek You can find some info on the use of prior phase information in refinement with Refmac in Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67. doi: 10.1107/S0907444911001314. Epub 2011 Mar 18. REFMAC5 for the refi

[ccp4bb] PhD opportunity

Dear all An exciting computational PhD position is available to extend the current capabilities of Refmac5, one of the flagship programs of the CCP4 suite, to the field of neutron crystallography. Details for the application can be found at https://www.kcl.ac.uk/health/study/studentships/div-st

Re: [ccp4bb] XQuartz and High Sierra OSX

356%7C0&sdata=EBaOqIeiudEp2d42gZQUOyWuxXEX7VlQ6r5eEWNlDY8%3D&reserved=0> On 2 Dec 2017, at 00:04, Steiner, Roberto mailto:roberto.stei...@kcl.ac.uk>> wrote: Hi all Since my recent upgrade to High Sierra, XQuartz (most recent version 2.7.11 - fresh installation) does not longer behave p

Re: [ccp4bb] XQuartz and High Sierra OSX

Solution: I noticed yesterday that XQuartz was behaving normally when my laptop was not connected to the Apple Thunderbolt Display. Resetting the Thunderbolt Display solved the problem. Roberto On 2 Dec 2017, at 00:04, Steiner, Roberto mailto:roberto.stei...@kcl.ac.uk>> wrote: Hi all

[ccp4bb] XQuartz and High Sierra OSX

Hi all Since my recent upgrade to High Sierra, XQuartz (most recent version 2.7.11 - fresh installation) does not longer behave properly. Essentially, X11 does not seem to understand touchpad actions (for example cannot close X11 windows, cannot drag them around, etc.). This problems also affec

Re: [ccp4bb] A polite reminder to xia2 users

ers when Refmac is used? What's the best practice? > > JPK > > -Original Message- > From: Steiner, Roberto [mailto:roberto.stei...@kcl.ac.uk] > Sent: Thursday, November 05, 2015 11:42 AM > To: Keller, Jacob > Cc: > Subject: Re: [ccp4bb] A polite reminder to

Re: [ccp4bb] A polite reminder to xia2 users

shocking ! it should have been Steiner, RA (not Steiner R or Steiner, RS,) plus the most recent one is missing from the list….! REFMAC5 for the refinement of macromolecular crystal structures. Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. Acta

Re: [ccp4bb] How to fit BioSAXS shape to the Structure

SITUS is another good option. R >From my iPhone On 26 Jun 2015, at 08:20, "Deborah Harrus" wrote: > Dear Weifei, > > You might want to use SUPCOMB from the ATSAS suite. > http://www.embl-hamburg.de/biosaxs/supcomb.html > > Cheers, > > Deborah.

[ccp4bb] I

>From my iPhone

Re: [ccp4bb] Bulk solvent

On 12 Jan 2015, at 10:09, Bernhard Rupp mailto:b...@ruppweb.org>> wrote: What still evades me is, why exactly is the Babinet immune to these effects of excluding/masking-out unmodelled parts? The Babinet correction is also a function of the MODELLED part, just the opposite sign. So an incomplet

[ccp4bb] J

>From my iPhone

Re: [ccp4bb] Classification of Ig-like domains

Dear Thomas There are several Ig-like domains that do not contain S-S bridges . I am not aware of a software tool that does what you'd like. However, two key papers on the Ig-like fold (old but still very relevant) that might be useful to you are: (1) Bork, Holm & Sander - The Immunoglobulin

Re: [ccp4bb] Metal ion differentiation - reg

If you have a access to a synchrotron you can try double difference anomalous DDANO maps see Than et al. Acta Cryst. (2005). D61, 505–512 for an example Best Roberto On 1 Jul 2014, at 16:10, Dhanasekaran Varudharasu mailto:dhana...@gmail.com>> wrote: Dear all, I have solved a s

Re: [ccp4bb] Refining Metal Ion Occupancy

Straightforward in Refmac...(a CCP4 package)... >From my iPhone On 6 May 2014, at 18:02, "Chris Fage" wrote: > Hi Everyone, > > In my 2.5-angstrom structure, there is negative Fo-Fc density > surrounding a metal ion after refining in Phenix. From anomalous > diffraction I am certain of the met

Re: [ccp4bb] Phasing with Many Monomers/AU

In my experience translational NCS also can a part when one has many molecules in the a.u. If MR is an option, modern packages are rather good in dealing with TNCS. We used Molrep + Refmac at 3.x A (still unpublished) for a case with 18 complexes (36 monomers) in the a.u. and things weren't as b

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

Many (more) reviewers - [panic on Roberto's face] Isn't real peer-review just a question of standing the test of time? A piece of work blatantly wrong will sooner or later be picked up by someone (although I acknowledge that wrong papers can have serious consequences on one's ability to g

Re: [ccp4bb] Concerns about statistics

BTW there's a also an earlier paper (properly cited in Karplus & Diederichs 2012) showing the benefit of weak 'high-resolution' reflections. Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):988-1000. doi: 10.1107/S0907444910029938. Epub 2010 Aug 13. Inclusion of weak high-resolution X-ray

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

So there is a CCP4 GUI Just prepare a txt file with the relevant occupancykeywords and use it in the GUI under 'Refmac keyword file' Best R >From my iPhone On 12 Apr 2013, at 19:50, "Kavyashree Manjunath" wrote: > Respected Sir, > > I saw this option in refmac5 - 5.6.0037, (I use > refm

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

Dear Kavya What about using occupancy refinement in refmac? link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy refinement. R On 12 Apr 2013, at 17:12, Kavyashree Manjunath wrote: > Dear users, > > Is it advisable to refine the occupancy of > a ligand for a 2.0Ang data by

Re: [ccp4bb] delete subject

I fully agree that questions should keep coming. In addition it might be worth pointing out that CCP4 (and others) organise great crystallographic schools which are ideal for this sort of problem. Most of the schools ask you to bring your own data (!) and you can sit down with developers and exp

Re: [ccp4bb] refinement protein structure

we should all chip in a water molecule or two and the second author becomes "the CCP4 community"…. On 27 Mar 2013, at 17:22, Antony Oliver wrote: > At the risk of being somewhat cheeky - perhaps I could claim second author? > I too have successfully solved the structure - and I totally concur

Re: [ccp4bb] first use of synchrotron radiation in PX

Nice account on the subject J Synchrotron Radiat. 2010 July 1; 17(Pt 4): 433–444. Published online 2010 May 14. doi: 10.1107/S0909049510011611 Impact of synchrotron radiation on macromolecular crystallography: a personal view Zbigniew Dauter,a,* Mariusz Jaskolski,b,* and Alexander Wlodawer,c,*

Re: [ccp4bb] CCP4 Update 014

I can only echo Kay's comments. The CCP4 update system is just great. Together with a few others I was one of the initial beta testers of the update system. Beta-testing could not have not been easier. The thing just worked! Congratulations on an brilliant and extremely useful piece of software

Re: [ccp4bb] Pisa application

Maybe Nat Protoc. 2011 Aug 11;6(9):1341-54. doi: 10.1038/nprot.2011.367. Predic

Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry

My understanding is that ML functions in the presence of pseudo-translational symmetry are suboptimal (see a very short discussion in Acta Cryst. (2011). D67, 355–367. Acta Cryst. (2008). D64, 99–107 is also a good reading). Having said that if your crystal/dataset exhibits twinning on top of ps

Re: [ccp4bb] Alternative conformation of Phe and Tyr?

Or refine the occupancies with Refmac... Roberto >From my iPhone On 27 Jul 2012, at 11:04, "Tim Gruene" wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Ngo Duc Tri, > > I would manually set the occupancy of chain A to about 30% and chain > B's to 70% and try again.There is

Re: [ccp4bb] Does anyone have used DelPhi to calculate the Electrostatic potentials of DNA ？

Dear Eleanor I (capital!) believe the original poster means http://compbio.clemson.edu/delphi.php Best wishes Roberto On 11 Jul 2012, at 09:54, Eleanor Dodson wrote: On 11 Jul 2012, at 03:36, dengzq1987 don't understand the question really. What DELPHI do you mean? Many programs output DEL

Re: [ccp4bb] Phaser Fatal runtime error.

Don't know where the exact problem is. However, it is definitely possible to use a Crysalis-Scala-Truncate-Phaser pipeline without runtime errors. I have done a few times. I am sure you will be able to get help from Agilent people. If not, feel free to get back to me. Best Roberto On 26 Jun 2

Re: [ccp4bb] Suggestions for solving a structure with 8-10 copies per asymmetric unit

We solved recently a structure with 18 dimers in the a.u. related by translational symmetry. Molrep did a great job at quickly placing all molecules but few. The missing ones were found later by map inspection. We found rather important to play with the resolution cutoff. I understand new versio

Re: [ccp4bb] Anaerobic glovebox crystal cryo-cooling

Hi David I was using a very similar Belle Technology setup during my PhD. One thing we did was to modify the receiving dewar in the microscope chamber by screwing in small metal clips to the inside wall such that standard Hampton magic wands could be clipped immediately after plunging. That allo

[ccp4bb] X-ray equipment available

Full Rigaku R-axis IIC Image Plate X-ray diffraction system We would like to offer a complete macromolecular diffraction system free of charge to anyone prepared to pay (up-front) the shipping costs from our laboratory to theirs. The system consists of a R-axis IIC area detector, Rigaku RU-200BH

Re: [ccp4bb] twin refinement in refmac

On 2 Mar 2012, at 08:01, arka chakraborty wrote: Hi all, I will like to know, as a follow up of what Prof. Randy Read said, what should be done to do the refinement against the measured data and not the detwinned F( which refmac outputs in the mtz after twin refinement), during subsequent refi

Re: [ccp4bb] Movements of domains

I believe ESCET was designed to answer your kind of question Best Roberto On 21 Nov 2011, at 22:03, "Filip Van Petegem" mailto:filip.vanpete...@gmail.com>> wrote: Dear crystallographers, I have a general question concerning the comparison of different structures. Suppose you have a crystal

Re: [ccp4bb] Distinguish NH4 from Na?

Bond valence sum Muller et al. Acta Cryst. (2003). D59, 32-37 if the resolution is good (better than 1.8 A) R On 16 Nov 2011, at 18:20, Jacob Keller wrote: > Dear Crystallographers, > > I have crystals containing 666mM NH4 and 540mM Na, and there appears > to be a "water" which is only about

[ccp4bb] Postdoctoral Position at King's College London

A three-year postdoctoral position in the field of mechanistic enzymology is immediately available in the Steiner Laboratory of King’s College London. The salary is £33,193 per annum inclusive of London allowance. The project aims at studying the intriguing biological process of cofactor-indepen

Re: [ccp4bb] hkl2map on Mac OSX 10.6

...and in zsh for me r On 15 Jul 2011, at 14:56, Harry Powell wrote: and in tcsh for me... On 15 Jul 2011, at 14:48, Bosch, Juergen wrote: works fine in bash for me On Jul 15, 2011, at 5:51 AM, Steiner, Roberto wrote: I only managed to get it working using zsh. All other shells were

Re: [ccp4bb] hkl2map on Mac OSX 10.6

I only managed to get it working using zsh. All other shells were giving me errors. Ciao R. On 15 Jul 2011, at 10:40, Sebastiano Pasqualato wrote: Hi all, has anybody managed to have hkl2map running on an intel-based Mac? I have downloaded and installed the shelx programs, which I have alias

Re: [ccp4bb] low resolution refinement

Dear CAI Qixu Refmac does an excellent job at low resolution. Many of the features available in version 5.6.x are described in a very recent Refmac paper Murshudov et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr (2011) vol. 67 (Pt 4) p

[ccp4bb] Postdoctoral Position Available in London

Dear CCP4-ers, _ Postdoctoral position in reactive oxygen species (ROS) biology A postdoctoral position supported by the King’s College London British Heart Foundation Centre of Excellence is available at King’s College London in the field of R

Re: [ccp4bb] disulfide bridge in red density

Hi Sadaf It is also possible that the features you observe are also due to anisotropy of the ADPs. At 1.3A resolution you can perform anisotropic refinement. Give it a go and se if it helps. Best Roberto On 6 Mar 2011, at 18:57, sadaf iqbal wrote: Hello everyone, Recently, i have solved a pr

Re: [ccp4bb] I/sigmaI of >3.0 rule

Ciao Roberto B. You might want to cite: Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):988-1000. Epub 2010 Aug 13. Inclusion of weak high-resolution X-ray data for improvement of a group II intron structure. Wang J. Department of Molecular Biophysics and Biochemistry, Yale University,

Re: [ccp4bb] Micromatrix seeding using the mosquito

Dear Maria In our hands Mosquito MMS worked by adding 2x protein solution + 1x seed solution + 1x reservoir. The reason for doing this was two-fold: I) ratio protein/reservoir is similar to the condition that generated the seed stock II) a deliberate bias toward the initial condition is given

Re: [ccp4bb] Phenix version 1.6.1 released

Dear Dirk > For REFMAC, I > haven't seen anything similar, yet. The external restraints in Refmac should allow you to do this. http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html Best Roberto >