[ccp4bb] Official Opening of the National Facility for Structural Biology @Human Technopole

ht.org <mailto:nf.structuralbiol...@fht.org> Best, Sebastiano Sebastiano Pasqualato Senior Manager Biophysics National Facility for Structural Biology Human Technopole Palazzo Italia Viale Rita Levi‑Montalcini, 1 20157 Milan, Italy E. sebastiano.pasqual...@fht.org <mailto:sebastiano.pas

[ccp4bb] JOB OPPORTUNITY: Technician/Senior Technician in Biophysics in Milan

Dear all, please advertise this job opportunity. The Biophysics Unit of the National Facility for Structural Biology of Human Technopole, in Milano, Italy, is seeking to recruit a research technician who will actively participate in maintaining instruments and workflows, take part in scientifi

[ccp4bb] NOW HIRING: Structural Proteomics position at Human Technopole, Milano

On behalf of Andrea Graziadei: Dear all, the structural proteomics unit of the National Facility for Structural Biology of Human Technopole is looking for a technician! If you’re interested in proteomics, mass spectrometry and structural (systems) biology, please consider applying! The St

Re: [ccp4bb] Reg. ITC machine

Hello Sivaraman, I completely second Matthew’s message, having had the same experience he had, in two different workplaces and with two different Malvern PEAQ-ITC instruments. I have one anecdotal, and not direct, unpleasant feedback from TA instrument users. Ciao, S > On 9 Aug 2023, at 18:05,

[ccp4bb] Staff Scientist opportunity in "Single Molecule Biophysics" at Human Technopole in Milan, Italy

st-single-molecule-biophysics Please, share this ad to anyone you think might be interested, ciao, Sebastiano PS: sorry for the double posting in different bulletin boards Sebastiano Pasqualato Biophysics Platform Manager ##

[ccp4bb] Staff Scientist opportunity in "Structural Proteomics" at Human Technopole in Milan, Italy

o-manage-a-structural-proteomics-facility> Please, share this ad to anyone you think might be interested, ciao, Sebastiano PS: sorry for the double posting in different bulletin boards Sebastiano Pasqualato Biophysics Platform Manager

[ccp4bb] Post doc positions *CryoEM - Vannin Lab* in the newly established Structural Biology Centre of Human Technopole, MIlan

The Human Technopole (HT) Foundation is looking for Post-doctoral fellows to work in the Structural Biology Research Centre in the laboratory of Prof. Alessandro Vannini (https://humantechnopole.it/en/research-groups/vannini-group/

Re: [ccp4bb] COOT running on Macbook Pro M1 chip

Hi Claude, Pymol 2.4.0 (installed via homebrew) works fine for me in Apple M1 MacBook Pro, 2020. Ciao, S > On 16 Sep 2021, at 12:12, Claude Sauter wrote: > > Dear all, > > to continue on the same theme, a colleague biochemist asked me a couple of > days ago if there is any incompatibility bet

[ccp4bb] Senior Technician Position at the Biochemistry and Structural Biology Unit - IEO Milano

nal Electron Microscopy access, which the candidate is expected to manage. Experience in setting up grids and Cryo-EM data collection will be a distinguishing skill. Potential applicants are encouraged to contact Dr. Sebastiano Pasqualato, sending a brief description of interests, and a CV with

[ccp4bb] Yeast microtubule model

tubulin dimers, but I don’t know exactly how. If someone has already done that and is willing to share it, that would be extremely helpful. Thanks a lot in advance, ciao, S PS: sorry for the cross posting to members of both bulletin boards. -- Sebastiano Pasqualato, PhD Biochemistry and

[ccp4bb] CHAPS provider

worth the cost. Could anybody share their experience with low-cost chemical providers, please? Thank you very much, have a nice weekend, Sebastiano -- Sebastiano Pasqualato, PhD Biochemistry and Structural Biology Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus

[ccp4bb] low resolution refinement

Hi all, just be sure: does Low Resolution Refinement Pipeline in ccp4 always use Free_R_flag=0? Thanks, s -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02

Re: [ccp4bb] Introducing Dials User Interface for CCP4

ww.xtal.iqfr.csic.es/Cristalografia/<http://www.xtal.iqfr.csic.es/Cristalografia/> > Telf.: +34 917459550 > Consejo Superior de Investigaciones Científicas > Spanish National Research Council > [cid:image002.jpg@01D3E61A.CD4118D0] > > De: CCP4 bulletin board En nombre de Sebastian

Re: [ccp4bb] Introducing Dials User Interface for CCP4

Hi Luis, I’m trying to run the Dials user Interface on a Mac (OSX version 10.11.6, Quartz 2.7.11). i go into the directory where the images are, launch the dui and the graphical user interface appears, without any image displayed. When I click on the “select images” button, the program crashes w

Re: [ccp4bb] size exclusion columns

ndations when dealing > with large proteins (MDa)? > > Many thanks > Markus -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

[ccp4bb] maltodextrins on superdex columns?

dextrans on superdex columns, but their elution buffer is supplemented with 5% ethanol. Is that added to avoid specific binding of the sugars to the column matrix? Is that necessary or can it be excluded? Thanks a lot in advance for any hint, ciao, Sebastiano -- Sebastiano Pasqualato, PhD

[ccp4bb] crystal imaging system

) on those instruments; - information on other instruments you would suggest. Thank you very much in advance, wishing you a pleasant weekend, best regards, ciao, S -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus

Re: [ccp4bb] preparing DL-Malic acid stock solution

t;> >> Diana >> >> ** >> Diana R. Tomchick >> Professor >> Departments of Biophysics and Biochemistry >> University of Texas Southwestern Medical Center >> 5323 Harry Hines Blvd. >

[ccp4bb] preparing DL-Malic acid stock solution

a clear solution? Has anyone gone through the same? Thanks in advance, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02

[ccp4bb] Electronic Laboratory Notebook

a lot, ciao Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEOXtalUnit

[ccp4bb] info on BLI instrumentation

perform; - easy of use; - cost of performing experiments; - biological/biochemical problems that can addressed will be highly appreciated! thanks a lot in advance, best, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of

[ccp4bb] SUMMARY: looking for paper describing optimisation of crystals using a screen kit as additive

k/groups/JYL/WWWrobots/PDF/PresentationsOther/additive-screening.pdf> Thanks everyone for the feedback and help! May the crystals grow happily and diffract nicely, ciao, Sebastiano > On 8 May 2017, at 15:18, Sebastiano Pasqualato > wrote: > > > Dear all, > I recall a

[ccp4bb] looking for paper describing optimisation of crystals using a screen kit as additive

condition with 25% of a commercial sparse matrix screen kit with the protein in the drop. I can’t find the reference, can anybody help me? Thanks a lot, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO

[ccp4bb] [OT]: Akta system "fill port INV-907" alternative

dvance, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit <http://is.gd/IEO_XtalUnit>

Re: [ccp4bb] [phenixbb] [ot]: nedit on Mac 10.10 yosemite

rk > > On 29 October 2014 14:45, Sebastiano Pasqualato > mailto:sebastiano.pasqual...@gmail.com>> > wrote: > > Hi folks, > sorry for the off-topic and slightly ‘demodée’ question, but, since I updated > to Yosemite on my Mac, "nedit" does not work any

[ccp4bb] [ot]: nedit on Mac 10.10 yosemite

s/nedit/nedit Reason: image not found Trace/BPT trap: 5 Seba@host041:~> Anybody knows if there is a fix for that? Thanks in advance, S -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 2013

Re: [ccp4bb] Tenure track junior Group Leader Positions in Milan, Italy

sounds very interesting: “experimental and computational dance biology”. > Any type of computational dance or there are style limitations? > > Regards, > > Vaheh Oganesyan > www.medimmune.com > > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >

Re: [ccp4bb] PDB structure validation

eport before > depositing the coordinates so that one can go back and make necessary > corrections to the file before deposition. It will save a lot time and > perhaps would improve the quality of deposited structures. > > Debasish Chattopadhyay > > University of Alaba

[ccp4bb] [ot] looking for Crystal Farm 400 service & maintenance

ighly appreciated, best regards, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

Re: [ccp4bb] is there any version of xia2 or XDSME compatible with new XDS?

nd the current release of xia2 or XDSME is not compatible with latest > XDS. > Is there any similar software available? > Thanks! -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Mi

Re: [ccp4bb] announcement: (another) GUI for XDS

tom of the Wiki article ... > > thanks, > > Kay > -- > Kay Diederichs > http://strucbio.biologie.uni-konstanz.de > email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 > Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz -- Seba

Re: [ccp4bb] announcement: (another) GUI for XDS

. Thanks again, ciao, Sebastiano On Jun 20, 2013, at 11:18 AM, Kay Diederichs wrote: > On 06/20/2013 11:07 AM, Sebastiano Pasqualato wrote: >> >> Hi Kay, hi all, >> >> sorry for the -maybe- naive questions, but i'm struggling to get the GUI >> for XDS going

Re: [ccp4bb] announcement: (another) GUI for XDS

icle ... > > thanks, > > Kay > -- > Kay Diederichs > http://strucbio.biologie.uni-konstanz.de > email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 > Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz -- Sebastian

Re: [ccp4bb] Glutathione rsin

people with > these resins? Do they have decent binding capacity? Can they be efficiently > regenerated or are they a single use only? > Thanks for your help, > > Mirek > > > -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

Tim, if I'm not wrong, if you judo type "dss" on the pymol command line you will apply dssp to your pdb and have your model checked for secondary structure elements. Ciao, S -- Sebastiano On 30/mag/2013, at 18:35, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear

Re: [ccp4bb] a new version of XDS

mpg.de/~kabsch/xds/ > Please note that there are some incompatibilities; most notably, the new > format of XPARM.XDS is different so that the new INTEGRATE does not work with > an old XPARM.XDS. > > best, > > Kay > > > > > -- > Folmer Fredslund --

Re: [ccp4bb] Diffraction image viewer with display of resolution circles

Phenix has a diffraction viewer, too. You may want to try that. Ciao, Sebastiano -- Sebastiano Pasqualato Crystallography Unit Department of Experimental Oncology European Institute of Oncology via Adamello, 16 Milan, Italy On 23/mag/2013, at 10:16, Rafal Dolot wrote: > Dear CCP4 us

[ccp4bb] SUMMARY: PDB "crawler"

> E-mail: bshaa...@bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sebastiano > Pasqualato [sebastia

[ccp4bb] PDB "crawler"

Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

Re: [ccp4bb] statistics from a structure factors file

; > Graeme > > > > On 17 January 2013 09:18, Sebastiano Pasqualato > wrote: >> >> Hi all, >> maybe a silly question, but I can't figure this out. >> >> Is there a piece of software to calculate "Table I statistics" such as R

[ccp4bb] statistics from a structure factors file

hands me an mtz file he used to solve a structure, how can I determine the overall quality of the collected data, without having access to the processing logs? Thanks in advance, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Instit

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

s of FRIEDEL'S_LAW differ in their rejections! > > HTH, > > Kay > > > > Sebastiano Pasqualato schrieb: > > Thanks to Kay and Tim or the feedback. > > The reason I wanted to get statistics from the CORRECT step of XDS is that I > have re

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

'S_LAW flag on, CORRECT outputs F(+), F(-) but also merged F. I was expecting those were merged identically to the case in which FRIEDEL'S_LAW is off. But maybe your point is correct. Thanks, s > Cheers, > Tim > > On 01/16/2013 02:03 PM, Sebastiano Pasqualato wrote: >>

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

nt to do this and > why you don't want to use the XSCALE statistics instead? The > statistics are probably more meaningful after scaling, I guess. > > Best, > Tim > > On 01/15/2013 04:22 PM, Sebastiano Pasqualato wrote: >> >> Hi all, I was wondering if XDS

[ccp4bb] changing resolution bins statistics in CORRECT.LP

the resolution bins with the keyword RESOLUTION_SHELLS=, but rather the table output by the CORRECT job of XDS. Thanks in advance, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello,

Re: [ccp4bb] vitrification vs freezing

learnt a few interesting things. Thank you all for that. It's maybe time to step forward from this thread. Thank you all, once again, ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16

Re: [ccp4bb] vitrification vs freezing

important questions if we completely disregard >> context in writing. >> >> James >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -

Re: [ccp4bb] vitrification vs freezing

ur crystal is most likely not your main point where you need to be > 100% unambiguous. > > Cheers, > Tim > > On 11/15/2012 06:13 PM, Sebastiano Pasqualato wrote: >> >> Hi folks, I have recently received a comment on a paper, in which >> referee #1 (excellent

[ccp4bb] vitrification vs freezing

from now on, or are there english/physics subtleties that I'm not grasping? Thanks a lot, ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 516

Re: [ccp4bb] Space group R32 and H32

are not shown in all cases. However simply calling it 'R32:h' > is also completely unambiguous and acceptable (but calling it 'R32' > most definitely is not!). For the PDB CRYST1 record you have > (unfortunately) to call it 'H32'. > > Hope this clears

Re: [ccp4bb] Space group R32 and H32

gt;> You can also try my old space croup decoding program to see general >>>> positions, operators, matrices and other useful stuff. >>>> >>>> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm >>>> >>>> HTH, BR >>>>

Re: [ccp4bb] modeling thioester bond

st > Manish > > > > Manish Chandra Pathak, Ph.D. > Indian Institute of Science Education and Research > ITI (Gas Rahat) Building > Govindpura, Bhopal 462023 India > tel: +91-750-4092340 > > > > >>

[ccp4bb] modeling thioester bond

the bond exists and it has to be taken into account? Thanks in advance, ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 59

[ccp4bb] advice on spectrometric instruments choice

considering the Chirascan from Applied Photophysics, or the Jasco J-815, so far. Any comment on those? Thanks a lot in advance, best regards, ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16

[ccp4bb] selective protection of C-terminal carboxylate

Dear all, is anyone aware of a way to selectively protect the carboxylate at a protein C-terminus, while leaving unaffected those of Asp and Glu side chains? Thanks a lot in advance, have a nice weekend, ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental

[ccp4bb] pymol question

it in Pymol. I'm using Pymol 0.99rc6 Thanks all in advance, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

Re: [ccp4bb] GST-fusion protein production in insect cells

Good luck, > > Katya > > > Ekaterina Heldwein, Ph.D. > Department of Molecular Biology and Microbiology > Tufts University School of Medicine > 136 Harrison Ave > Boston, MA 02111 > Sebastiano Pasqualato wrote: >> >> Dear CCP4ers, Dr. Berger

[ccp4bb] GST-fusion protein production in insect cells

, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

Re: [ccp4bb] off-topic: "special" format for multiple sequence (protein) alignment

in the attached file. > > Maybe some of you have seen some programs can do this? Thank you. > > King regards, > Wenhe > -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 -

Re: [ccp4bb] Crystallization robot and trypsin

we recommend that tips are thoroughly > cleaned once a fortnight for average use in any case. > > I hope this is helpful. > > Sincerely > > Patrick > > > -- > patr...@douglas.co.ukDouglas Instruments Ltd. > DouglasHouse, EastGarston, Hungerford, Ber

Re: [ccp4bb] Linux vs MacOS for crystallographic software

Thanks Dirk, that's good news. I'll take a look at it, then. thanks, ciao, s On Sep 29, 2011, at 9:51 AM, Dirk Kostrewa wrote: > Yes, SHARP and BUSTER both work on a Mac. > > Cheers, > > Dirk. > > Am 29.09.11 09:45, schrieb Sebastiano Pasqualato: >>

Re: [ccp4bb] Linux vs MacOS for crystallographic software

On Sep 29, 2011, at 2:48 AM, Nat Echols wrote: > I don't know of any macromolecular crystallography programs that don't run on > Mac - Hey there, does this mean that SHARP works on a Mac? ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech

Re: [ccp4bb] hkl2map on Mac OSX 10.6

but I guess that's not a big deal) Thanks again, ciao, s On Jul 15, 2011, at 11:44 AM, Joachim Reichelt wrote: > Just a hint: > Subshels do not always use aliases, so put shelx etc. in your path e.g. in > /usr/local/bin > > Am 15.07.11 11:40, schrieb Sebastiano Pasqualato:

[ccp4bb] Technician Position available in Milan

great attitude to relate with people and work in a team. To apply, please send your CV, together with the name of at least one referee. Informal inquiries are welcome. cheers, Sebastiano PS: sorry for the double posting to those subscribed to both mailing lists. -- Sebastiano Pasqualato

Re: [ccp4bb] ccp4 on Mac Intel

.2.0/bin/ccp4.setup-sh . All the paths should then be > set. > > Charles Ballard > CCP4 > > On 3 May 2011, at 09:30, Sebastiano Pasqualato wrote: > >> >> Dear all, >> I have installed ccp4 with the dmg package, and everything is installed >> ni

Re: [ccp4bb] ccp4 on Mac Intel

nyurl.com/futterer-lab > === > > > > > > On 3 May 2011, at 09:30, Sebastiano Pasqualato wrote: > >> >> Dear all, >> I have installed ccp4 with the dmg package, and everything is installe

[ccp4bb] ccp4 on Mac Intel

. How do I source this ccp4 installation? Thanks a lot in advance, ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

[ccp4bb] SUMMARY -until now- [OT] which column to use in SLS/MALS instruments

ck on the > silica based column. On the other side a superdex 200 10/30 from GE performed > quite well, we got quite accurate results for both a ~250kDa hexameric enzyme > as also for a 0.3 mg/ml injection of an insulin sample. > Eventually I think depends on the applications you pre

[ccp4bb] [OT] which column to use in SLS/MALS instruments

be loaded. What are you guys using in your instruments? Thanks a lot in advance for the feedback, best, ciao Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172

[ccp4bb] hydrohyapatite column

for such columns. Thanks in advance, best, s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

[ccp4bb] relationship between B factors and Koff

nce, best regards, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

Re: [ccp4bb] difficult P1 crystal

all trials so > far did not solve the structure (using balbes, molrep, phaser and epmr). Any > suggestion is welcome. > Thank you, > > Mario Milani -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16

Re: [ccp4bb] Alignment software

all > > Hopefully that should get things working. > > Cheers, > > Roger > > On 25 May 2010 17:50, Sebastiano Pasqualato > wrote: > Hi there, > I remember a friend of mine showing me Aline, and it looked very nice. > However, I can't make it work on my MacB

Re: [ccp4bb] Alignment software

gt;> greatly appreciate it if anybody can recommend a software that I can use. >> Thanks, Mohd > > -- > Charlie Bond > Professorial Fellow > University of Western Australia > School of Biomedical, Biomolecular and Chemical Sciences > M310 > 35 Stirling Highway >

[ccp4bb] Post-doctoral position, IFOM-IEO-CAMPUS, Milan

structure. Conservatively, we feel that this can be certainly achieved within two years Salary. At the IFOM-IEO Campus, post-doctoral salaries ranges within 24000-36000€/yr. Further information as to fringe benefits etc can be found at the Campus web Site. -- Sebastiano Pasqualato, PhD IFOM-IEO

[ccp4bb] heavy atom derivative choice

g? Thanks in advance for the suggestions, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094

[ccp4bb] [ot] protein-protein interaction via fluorescence polarization anisotropy

f the interacting partners (exc/em wavelength difference, fluorescence lifetime); 2. preferrable conjugating methods (cys, amino derivatization, else?); 3. any other comment and suggestion. Thanks in advance, best regards, Sebastiano and Marina -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimen

[ccp4bb] error in ccp4i

kind of synchrotron-related issue (when you desperately need a software, that's when it goes down!) -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094

Re: [ccp4bb] OT: VectorNTI alternatives

work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16

[ccp4bb] hydrophobic surface representation

guys just color hydrophobic amino acids and show the surface? Thanks in advance, s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310

[ccp4bb] summary: tricoordinate ion?

it was so large (I have to admit, I just sent what Wincoot wrote out! ;-)). Next time I'll be surely posting the image to some website. Thanks again, all the best, S -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adame

Re: [ccp4bb] pointless and HKL2000

, ciao sebastiano Monday, October 6, 2008, 5:04:05 PM, Yue Li wrote: > Hi everyone, > I would like to us pointless in CCP4 to check the laue group of a > crystal. Since pointless needs unmerged data, my question is how to > generate the unmerged data for pointless from HKL2000 ? > Than

[ccp4bb] chain IDs and residue numbering in depositing chimeras PDB

y suggestion is warmly welcomed! Thanks in advance for the help, Sebastiano -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310

[ccp4bb] Summary: pymol movies scripts

ner and Robin Stamler: http://www.weizmann.ac.il/ISPC/eMovie_download.html Thanks all for the useful advices, all the best, Sebastiano -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 Milano Italy tel +39 02

[ccp4bb] pymol movies scripts

some web pages that would explain me how to do that? Thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310

[ccp4bb] apbs parse error

anyone know what is the problem here, or else how to calculate an electrostatic potential map (to be open in pymol) with another program? (I know I can switch to ccp4mg, and that's most likely what I'll do...) thanks in advance, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipar

[ccp4bb] SUMMARY: questions about hydrophobic core

Hi all, here's the original post: At 10:55 AM 6/19/2007 +0200, you wrote: Hi all, a few days ago I sent a post in which I was asking if anybody knew a program to automatically define the hydrophobic core of a protein, given the pdb. Unfortunately I got no answers, and indeed a more thorough

[ccp4bb] questions about hydrophobic core

n advance, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310 No virus found in this outgoing message. Checked by AVG Free Edition. Version:

[ccp4bb] automatic hydrophobic core (buried residues) determination

Hi all, does anyone know if there's a (ccp4 or not) program able to list the hydrophobic core residues of a structure? a quick google for it didn't provide any useful hint... thanks in advance, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sp

Re: [ccp4bb] heavy metal labelled GTP derivatives

Hi Stephen, you can get Iodinated or Brominated nucleotide derivatives from jena bioscience (http://www.jenabioscience.com/cms/en/1/browse/106_nucleotides_and_their_analogs.html) hth, Sebastiano At 02:44 PM 5/7/2007 +0200, Stephen Cusack wrote: Does anyone know of any heavy metal labelled GTP d

Re: [ccp4bb] HKL2000 with more that 2 million observations

Todd, Markus, Misha, Robi, Fabrizio, thanks for the answers. Indeed I'm scaling the data at the command line, now (good ol' way!). The scalepackBig command does not exist anymore, but the ones you've suggested work fine. I was just wondering if there's a way to tell HKL2000 which command to use.

[ccp4bb] HKL2000 with more that 2 million observations

advance, Sebastiano -- Sebastiano Pasqualato, PhD IFOM Istituto FIRC di Oncologia Molecolare via Adamello, 16 20139 Milano Italy tel +39 02 574 303 325 fax +39 02 574 303 310

[ccp4bb] MAD/SAD data collection strategy

chnique, either... Let the gurus talk! Any advice is obviously highly appreciated! Thanks in advance, Sebastiano and Claudio -- Sebastiano Pasqualato, PhD IFOM Istituto FIRC di Oncologia Molecolare via Adamello, 16 20139 Milano Italy tel +39 02 574 303 325 fax +39 02 574 303 310