Re: [ccp4bb] problem transferring ccp4i2 projects from one computer to another

Dear Stuart Thank you for your reply Yes, you are right. The reports are not displayed for any project (not just the imported ones). What should I look at to solve the problem ? Stefano - Mail original - > De: "Stuart McNicholas" > À: "Stefano Trapani" &

[ccp4bb] two year call for a research assistant

specificity (university of Bolzano). The project “DAMaSCo” brings together in a multidisciplinary collaborative effort Dr Stefano Benini and Sanja Baric (Free University of Bolzano, UNIBZ), Prof. Benedetto Ruperti (University of Padua, UNIPD), Prof. Francesco Musiani (University of Bologna, UNIBO

[ccp4bb] REMINDER ! 24 months position for a postdoc c/o Free University of Bolzano deadline 19/11/2021 REMINDER!

their reaction mechanisms and substrate specificity (university of Bolzano). The project “DAMaSCo” brings together in a multidisciplinary collaborative effort Dr Stefano Benini (Free University of Bozen-Bolzano, UNIBZ), Prof. Benedetto Ruperti (University of Padua, UNIPD), Prof. Francesco Musiani

[ccp4bb] two years (24 months) position for a postdoc c/o Free University of Bolzano

(university of Bolzano). The project “DAMaSCo” brings together in a multidisciplinary collaborative effort Dr Stefano Benini (Free University of Bozen-Bolzano, UNIBZ), Prof. Benedetto Ruperti (University of Padua, UNIPD), Prof. Francesco Musiani (University of Bologna, UNIBO) The salary is

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

the possibility of easily performing steps 1-4 (i.e. changing the origin and orientation of a crystal with respect to the orthogonal reference frame) would be a valuable tool in CCP4MG (or any other graphics crystallographic software). Best regards. Stefano Trapani Le 2021-06-03 01:49, Jon

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

Hi Boaz Thank you. That works in Chimera (first superpose, then symmetry expand) but not in CCP4MG (independently of the order of the operations). It would be nice to have an equivalent option implemented in CCP4MG. Best regards Stefano Trapani Le 2021-06-02 16:20, Boaz Shaanan a

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

ranslated version of the "whole" crystal, but a new (different) crystal packing. Stefano Le 2021-06-02 15:14, Stuart McNicholas a écrit : > Dear Stefano, > It might be possible to do what you want in a roundabout way: > > i) Apply matrix to molecule: Molecule Icon -> Tr

Re: [ccp4bb] {Disarmed} AW: [ccp4bb] superpose crystal objects in CCP4MG or other software

Yes, that is the way I usually do, but it can be cumbersome. It would be easier if I could first superpose two molecules from the two crystals, and then decide in which directions to expand by crystal symmetry (I want to compare layers and rows of molecules). Best regards Stefano Le

[ccp4bb] superpose crystal objects in CCP4MG or other software

stent with the new origin/orientation ? * If yes: can the transformation be defined by a least-squares superposition between molecules from the two crystal objects ? Best regards -- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano

[ccp4bb] REMINDER: two years postdoctoral fellowship, deadline for sending the application 22/01/2020

the plant pathogen. interested candidates can contact me for more information on the project and for informal enquiries to apply please follow the link: https://www.unibz.it/en/home/position-calls/positions-for-academic-staff/4468-chimica-organica-dr-benini?group=18 best regards Stefano P.S

[ccp4bb] two years postdoctoral fellowship, deadline for sending the application 22/01/2020

the plant pathogen. interested candidates can contact me for more information on the project and for informal enquiries to apply please follow the link: https://www.unibz.it/en/home/position-calls/positions-for-academic-staff/4468-chimica-organica-dr-benini?group=18 best regards Stefano P.S

[ccp4bb] (off-topic) fundraising campaign - EMERGENCY VENICE

ture means a lot! Kindest regards, Elisa Moretti Stefano Benini, Ph.D. Assistant Professor Guest editor of "Carbohydrate-Active Enzymes: Structure, Activity and Reaction Products" A special issue of International Journal of Molecular Sciences<https://www.mdpi.com/journal

[ccp4bb] 3 years research assistant position for masters or junior postdocs

Italy) for informal enquiries (and scientific questions!) do not hesitate to contact me some background information on one of the system to study could be found in this publication: https://doi.org/10.1016/j.jsb.2018.02.002 deadline for application is 09/09/2019 have a nice day S. Stefano Benini,

[ccp4bb] matrix decomposition problem

wondering if : * further solutions may exist * there is a criterion to establish the existence /number of these solutions * there is a practical way of calculating them -- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano

[ccp4bb] 3 years Research assistant position deadline approaching 04/06/2019

ion: https://doi.org/10.1016/j.jsb.2018.02.002 deadline for application is 04/06/2019 have a nice day Stefano Stefano Benini, Ph.D. Assistant Professor Guest editor of "Carbohydrate-Active Enzymes: Structure, Activity and Reaction Products" A special issue of International Journal of Molec

[ccp4bb] PhD position available at Free University of Bolzano, Italy

include hiking, climbing, skiing Not far from Trento, Garda Lake and Verona Best regards Stefano Benini, Ph.D. Assistant Professor https://sbenini.people.unibz.it/ Guest editor of "Carbohydrate-Active Enzymes: Structure, Activity and Reaction Products" A special issue of International

[ccp4bb] 3 years Research assistant position at the Free University of Bolzano (Italy)

nini?group=18 for informal enquiries (and scientific questions!) do not hesitate to contact me some background information on one of the system to study could be found in this publication: https://doi.org/10.1016/j.jsb.2018.02.002 deadline for application is 04/06/2019 have a nice day Stefan

[ccp4bb] Open position structural biology at University of Milan

Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity. Nat Comm 2018 - Oberti et al Concurrent structural and biophysical traits link with immunoglobulin light chains amyloid propensity. SciRep 2017 Best regards SR Stefano Ricagno, PhD Associate

Re: [ccp4bb] OT: Terminal Command-P

Le 2019-04-01 08:53, Paul Emsley a écrit : > Dear All, Sometime I use a Mac. A niggling issue I have is that, in a > Terminal, Command-P doesn't act like Alt-P in (say) a gnome-terminal try ESC-p (not simultaneously) --- Stefano Trapani Maître de Conférences http://www.

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

Sorry, I did not realised that. (I should have changed subject of the original post) Yes, we are not saying different things. Stefano Le 2018-09-19 17:06, Frank von Delft a écrit : > Okay. The original poster asked about hydrogen bonds and electrostatic > interactions. That&#x

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

the entropy loss." Best Stefano Le 2018-09-19 14:41, Frank von Delft a écrit : > Hi Stefano - could you elaborate? > > Certainly the medicinal chemists go on a great deal about how deltaH balances > deltaS and how it's bloody hard to know what is what even when you try to

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

ducation 1998 _75_ (1), 116 DOI: 10.1021/ed075p116 https://pubs.acs.org/doi/abs/10.1021/ed075p116 [6] Stefano > On 19/09/2018 10:40, Stefano Trapani wrote: > > Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : > > (where hydrophobic interactions result from v

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

] Being mainly of an entropic nature, hydrophobic "contacts" are not the direct result of real microscopic "forces" that act between apolar groups. The terms "forces" and "interactions" in widely used expressions like "hydrophobic forces" and "

[ccp4bb] PhD call at the Free University of Bolzano deadline July 9th 2018

ct me... @ stefano.ben...@unibz.it<mailto:stefano.ben...@unibz.it> Best regards S. Stefano Benini, Ph.D. Assistant Professor https://sbenini.people.unibz.it/ "I don't like anything that's fake and I hate pretenders!" * Bioorganic ch

[ccp4bb] Open postdoc position at University of Milan

already defended their PhD thesis. Any interested candidate may contact me and send a short CV (two pages max) with a summary of previous research interests and two references to this email ciciu...@hotmail.com Best regards Stefano For info about the Dept. of Bioscience: www.bioscienze.bio<h

Re: [ccp4bb] definition of "apo" and alternatives?

See also the IUPAC reccomandations : https://goldbook.iupac.org/html/A/A00417.html https://goldbook.iupac.org/html/H/H02836.html --- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani - Centre de

[ccp4bb] Post-doc position at the University of Milan

CV (two pages max) and two references to this address ciciu...@hotmail.com best Stefano Ricagno Stefano Ricagno, PhD Associate Professor Dept. of Bioscience University of Milano Via Celoria, 26. I-20133 Milano (Italy) Tel. +39 02 5031 4914 http://users.unimi.it/stericagno/default.html

[ccp4bb] Some TLS issues in REFMAC5

/refine.2d.pdb:ATOM 3 CB ALA A 1 19.748 -5.555 8.682 1.00 11.10 C ./refine.2d.pdb:ATOM 4 C ALA A 1 18.905 -4.806 6.397 1.00 10.36 C ./refine.2d.pdb:ATOM 5 O ALA A 1 17.698 -4.380 6.390 1.00 11.19 O -- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20T

Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction

Dear Pascal have a look at : https://doi.org/10.1107/S0907444910002763 Acta Cryst. (2010). D66, 514-521 Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions S. Trapani, G. Schoehn, J. Navaza and C. Abergel Best, --- Stefano Trapani Maître de

[ccp4bb] PhD call at the Free University of Bolzano, Faculty of Science and Technology

http://www.unibz.it/SiteCollectionDocuments/Research%20Office/PhD/BANDI/2015_16_Ausschreibung%20PhD_en%2031%20Zyklus_def.pdf Best regards Dr Stefano Benini, Ph.D. Assistant Professor Laboratory homepage: http://pro.unibz.it/staff2/sbenini/B2Cl.htm Personal homepage http://pro.unibz.it/staff2/sbe

[ccp4bb] off-topic: protein losing FAD during purification

Stefano (part-time wetlab person) Dr Stefano Benini, Ph.D. Assistant Professor First International workshop: "Molecular Basis of Fire Blight", Bolzano 15.10.2014 Laboratory homepage: http://pro.unibz.it/staff2/sbenini/B2Cl.htm Personal homepage http://pro.unibz.it/staff2/sbenini/

Re: [ccp4bb] video of crystal pick-up through microscope?

And when handling liquid nitrogen don't forget to get protections against frost bite (goggles, cryogloves) S. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Swastik Phulera Sent: Friday, 13 September, 2013 15:08 To: CCP4BB@JISCMAIL.AC.UK Sub

[ccp4bb] PhD program at the Free University of Bolzano (Italy)

Dolomites with some of the best hiking paths and slopes for skiing. http://whc.unesco.org/en/list/1237/ http://www.obereggen.com/en/winter_activities/ with my best regards Dr Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ "I don't like anythi

[ccp4bb] Reminder: PhD position in structural biology at the Free University of Bolzano

more information on the project and for informal enquiries please contact: stefano.ben...@unibz.it For information on how to apply please contact our secretary: stefania.falc...@unibz.it Best regards Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini

[ccp4bb] PhD position in Bolzano (Italy)

our secretary: stefania.falc...@unibz.it Best regards Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ * Laboratory of Bioorganic Chemistry and Crystallography Faculty of Science and Technology Free University of Bolzano

[ccp4bb] postdoc position at the Univ of Milan

ry in case someone is interested in a chat... Regards Stefano

Re: [ccp4bb] Distinguish NH4 from Na?

Dear Jacob, You may find useful this web site by Marjorie Harding about metal coordination sites in proteins http://tanna.bch.ed.ac.uk/ best regards Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ Bio-organic Chemistry Laboratory

[ccp4bb] PhD position in structural biology at the Free University of Bolzano

bz.it/en/sciencetechnology/progs/phd/phdmountainenvironment/default.html http://www.unibz.it/en/public/research/phd/prospectivePhdstudents.html With my best regards Stefano Benini Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ Bio-or

[ccp4bb] Enterokinase cleavage of His-tagged proteins

reasonable price enterokinase to cleave mgs of his-tagged proteins for crystallization? Thank you very much and best regards Stefano Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ <http://pro.unibz.it/staff2/sben

[ccp4bb] PhD student position at Univ. of Milan

ct me directly Any interested candidate should send a short CV and two references to this address ciciu...@hotmail.com all the best Stefano Ricagno Dept. of Biomolecular Sciences & Biotechnology University of Milano Via Celoria, 26. I-20133 Milano (Italy) Tel. +39 02 5031 4894 Fax. +3

Re: [ccp4bb] AMoRe fails to use model coordinates

You could try the stand-alone version of AMoRe from Jorge Navaza's web site. http://mem.ibs.fr/JORGE/index.html Stefano TRAPANI Maître de Conférences Centre de Biochimie Structurale (CBS) CNRS UMR 5048; UM1; UM2; INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex - France Tel

[ccp4bb] which Linux workstation for crystallography to buy?

that I really want to be up to date not to be already late! Thank you very much in advance Stefano Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ Bio-organic Chemistry Laboratory Faculty of Science and Technology

[ccp4bb] Off topic: multidisciplinary international PhD program in Bolzano, Italy

ulty of Science and Technology piazza Università, 5 39100 Bolzano Italy T: +39 0471 017000 F: +39 0471 017009 With my best regards Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ <http://pro.unibz.it/staff2/sbenini/> **

[ccp4bb] theta

(the angle between the incident or diffracted ray and the reflecting crystal planes). However, I hear sometimes calling theta the scattering angle. Is this just a misuse of the term ? Stefano TRAPANI Centre de Biochimie Structurale (CBS) CNRS UMR 5048; UM1; UM2; INSERM UMR 554 29 rue de Navacell

Re: [ccp4bb] heavy atom derivative choice

Dear All, I never tried it myself but could it be a sulphur SAD/MAD a possible alternative? In my experience with heavy atoms (luckily just 2 proteins!) you may waste all of your crystals without finding any heavy metal bound! Or may be the first one you try works Ciao Stefano

Re: [ccp4bb] too good R/Rfree with resolve

over-refinement?), or in this case better say tautology. stefano > Date: Mon, 31 Mar 2008 16:50:13 +0100 > From: [EMAIL PROTECTED] > Subject: Re: [ccp4bb] too good R/Rfree with resolve > To: CCP4BB@JISCMAIL.AC.UK > > On Sun, Mar 30,

[ccp4bb] too good R/Rfree with resolve

too good. Checking refmac log file it looked to me that refmac uses all the reflections in the .mtz file (that is as many reflections as before the resolve run). Ideas? thanks Stefano ps this is my last refmac: 2 mol in the AU, no NCS used, weighting term 0.01, no tls. NcycRfact

[ccp4bb] Alternative origin list in CCP4 documentation

--- Stefano TRAPANI Centre de Biochimie Structurale (CBS) CNRS UMR 5048; UM 1; UM 2; INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13

Re: [ccp4bb] "Dry" structures

for!! please let me know what happens next! ciao ciao Stefano *** Stefano Benini PhD Structural Biology - DECS Mereside 50S38 Alderley Park Phone:+44-1625-518293 (ext.: 28293) http://structuralbiology-ap.rd.astrazeneca.net/people/Stefano-Benini/Stefano

[ccp4bb] small-protein EM models for crystal structure solution

you -- -- Stefano Trapani, PhD Laboratoire de Microscopie Électronique Structurale Institut de Biologie Structurale (IBS) J.P. Ebel UMR 5075, CNRS 41, rue Jules Horowitz F-38027 GRENOBLE Cedex 1 phones: (from France: replace ++33 with 0) ++33 4 3878.9262 FAX: ++3

Re: [ccp4bb] Help with reducing crystal mosaicity

es did not make any difference then my contract finished and so did the project! I hope you still have a lot of time available to try different things but I would not waste time trying to change your cryo ciao Stefano Stefano Benini PhD AstraZeneca UK Structural Biology Mereside 50S38 Ald

Re: [ccp4bb] How to remove nucleic acid contamination for crystallizing zinc finger protein

protein HU from the hyperthermophilic eubacterium Thermotoga maritima may be it works on zinc finger proteins as well ciao Stefano -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: 05 July 2007 15:43 To: CCP4BB@JISCMAIL.AC.UK Subject

[ccp4bb] oxidised cys

refmac couldn't care less... thanks in advance Stefano _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/