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

[Sebastiano Pasqualato]

Dear Structural Biologists,
apologies if I share this communication to the whole community, although the 
services we provide are strictly meant for Italian scientists.
However, I hope it might be of general interest for the community being aware 
of such an initiative.
 
It is with great pleasure that we finally announce the official opening of the 
National Facilities at Human Technopole. The access of external Users 
affiliated to Universities, Istituti di Ricovero e Cura a Carattere Scientifico 
(IRCCS), and Public Research Entities will be supported by open calls for 
access. Access is granted based on the principles of scientific excellence, 
with the aim of supporting high-quality research. The quality of the submitted 
requests is evaluated and approved by an independent panel of experts, the 
Standing Independent Evaluation Committee, that also defines the Access 
Management Plan. Access will come at no costs for the selected projects.
 
The National Facitlity for Structural Biology consists of six Infrastructural 
Units (IU):
 
IU1 – Cryo-Electron Microscopy: This Unit aims at identifying, visualizing, and 
characterizing biological players of interest, both isolated and within their 
cellular compartments.
IU2 – Biomass Production: This Unit provides access to different cell lines for 
protein expression and performs scale-up of bioprocesses for large-scale 
productions.
IU3 – Biophysics: This Unit is a technological platform for biophysical 
characterization of macromolecules and their interactions
IU4 – Structural Proteomics: This Unit relies on crosslinking mass spectrometry 
(XL-MS) to provide topological and structural restraints on protein-protein 
interactions in samples ranging from purified protein complexes to cellular 
fractions.
IU5 – Dynamic Single-molecule: This Unit provides tool to visualise biological 
processes in real-time with single-molecule sensitivity thanks to cutting-edge 
instruments that combine optical tweezers with fluorescence and label-free 
detection modules.
IU6 – Technology Development: This Unit, planned to be operational in 
2026-2028, will be where all other units converge when it comes to pushing 
technological limitations in the field of integrative structural biology.
 
National Facility Main Webpage: 
https://humantechnopole.it/en/national-facilities/
 
National Facility for Structural Biology (Service List + Technical Info): 
https://humantechnopole.it/en/facilities/national-facility-for-structural-biology/
 
For general enquiries about the call: national.facilit...@fht.org 
<mailto:national.facilit...@fht.org>
 
For technical enquiries about the services: nf.structuralbiol...@fht.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.pasqual...@fht.org>
humantechnopole.it <http://www.humantechnopole.it/>



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

[Sebastiano Pasqualato]

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 scientific collaborations, and support internal and external users.
The Biophysics Unit manages equipment and provides service/support to 
researchers for biophysical characterisation of macromolecular samples, and the 
determination/characterisation of interaction affinities.

We are equipped with a state-of-the art equipment for ITC, BLI, MST, Mass 
Photometry, SEC-MALLS, nanoDSF measurements and are embedded in the Centre for 
Structural Biology of HumanTechnopole, lead by Alessandro Vannini and Gaia 
Pigino, and are part of the National Facility for Structural Biology, an 
integrative structural biology Facility comprising Cryo-EM, Biomass Production, 
Biophysics, Structural Proteomics and Single Molecule Dynamics Units.

All details about the job, and how to apply, here: 
https://careers.humantechnopole.it/o/technician-senior-technician-in-biophysics
Further information directly to me: sebastiano.pasqualato (at) fht.org 


Come join us for the ride, and live in Milan, a thriving city which will be 
home of the Winter Olympic Games 2026!

Thanks for sharing,
best,
Sebastiano





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

[Sebastiano Pasqualato]

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 Structural Biology National Facility is a newly established, thriving 
department of the Human Technopole (http://www.humantechnopole.it/en/), a fast 
growing new Life Science institute recently established in Milano.
The National Facility, led by Paolo Swuec, provides world-class cryo-EM 
services 
(https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/) 
for the research groups at Human Technopole and in the Italian Research 
community. The Facility also comprises platforms for Biophysics,  Biomass 
production, single molecule fluorescence and of course structural proteomics, 
for which help is needed. The unit is equipped with a state of the art Orbitrap 
Eclipse Tribrid mass spectrometer coupled to a Vanquish Neo HPLC and High field 
asymmetric waveform ion mobility spectrometry (FAIMS) and the workflows of the 
facility focus on crosslinking mass spectrometry, with the ambition to expand 
to other structural proteomics workflows.
 
We are looking for a young enthusiastic person with experience in proteomics, 
mass spectrometry and/or structural biology who will assist in instrument 
management and training, and will develop small technological projects of 
interest for the whole Facility, working close with other units, Human 
Technopole scientists and external facility users. 
 
More details on the position, and how to apply, can be found here: 
https://careers.humantechnopole.it/o/techniciansenior-technician-in-structural-proteomics
 . You can contact the manager of the unit, Andrea Graziadei, at 
andrea.grazia...@humantechnopole1.recruitee.com for informal inquiries.
 
thanks and ciao,
Andrea


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Re: [ccp4bb] Reg. ITC machine

[Sebastiano Pasqualato]

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, Matthew Whitley 
>  wrote:
> 
> Hello Sivaraman,
> 
> We have a Malvern MicroCal PEAQ-ITC system in our lab that is used regularly. 
>  In general, we are pleased with the machine.  We have experienced no major 
> problems with the instrument, the data quality is good, and replicate 
> measurements yield very similar results.  I have never used the Affinity ITC 
> from TA Instruments, so I cannot comment on that system.
> 
> Matthew
> 
> 
> 
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[ccp4bb] Staff Scientist opportunity in "Single Molecule Biophysics" at Human Technopole in Milan, Italy

[Sebastiano Pasqualato]

Dear all,
another job post from the newly established life science Institute of Milan, 
Italy, Human Technopole (http://www.humantechnopole.it/en/ 
<http://www.humantechnopole.org/>)
We are looking for a Staff Scientist to establish and manage a Single Molecule 
Biophysics Platform as a part of an ongoing collaboration with Lumicks.

We are looking for persons with proven track record in single-molecule studies, 
with specific experience with Lumicks optical tweezers (C-trap and M-trap).

The successful candidate will work in close collaboration with the Scientists 
of the Structural Biology Research Centre of Human Technopole 
(https://humantechnopole.it/en/research-centres/structural-biology/ 
<https://humantechnopole.it/en/research-centres/structural-biology/>), and 
their platform will be part of a larger number of research facilities and 
platforms, such as the Cryo-EM facility 
(https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/ 
<https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/>).

More details, and how to apply can be found at the following link: 
https://careers.humantechnopole.it/o/staff-scientist-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 







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

[Sebastiano Pasqualato]

Dear all,
the newly established Human Technopole Institute, based in Milan, Italy 
(http://www.humantechnopole.it/en/ <http://www.humantechnopole.org/>) is 
looking for a Staff Scientist to manage the Structural Proteomics Facility.

We are looking for persons with proven track record in high-resolution MS-based 
proteomics, with specific experience in cross-linking- (XL) and native- MS.

Structural proteomics technologies will be closely integrated with the Science 
Groups of the Structural Biology Research Centre of Human Technopole 
(https://humantechnopole.it/en/research-centres/structural-biology/ 
<https://humantechnopole.it/en/research-centres/structural-biology/>), and will 
be part of a larger number of research facilities and platforms, such as the 
Cryo-EM facility 
(https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/ 
<https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/>)

More details, and how to apply can be found at the following link: 
https://careers.humantechnopole.it/o/staff-scientist-to-manage-a-structural-proteomics-facility
 
<https://careers.humantechnopole.it/o/staff-scientist-to-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 







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

[Sebastiano Pasqualato]

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/ 
 Twitter: 
@VanniniLab).
The Vannini Lab combines cryo-electron microscopy (both SPA and cryo-ET), X-ray 
crystallography, mass spectrometry, single molecule measurements and various 
biophysical techniques to elucidate the role of multi-subunit macromolecular 
machineries in genome function and organization. In particular, we are 
interested in understanding at the molecular level how non-coding gene 
transcription machineries, auxiliary transcription factors, chromatin 
remodellers, SMC complexes and transposable elements affect gene expression and 
genome structure.

The  HT Centre of Structural Biology has top-notch managed facilities for 
Cryo-EM (Titan Krios, 1 Glacios, 1 Aquilos2, 1 Spectra, 1 Talos 120), 
cryo-CLEM, Light imaging, XL- and native mass -pectrometry and support units 
for Biophysics (mass photometry, SEC-MALLS, ITC, x-ray crystallography etc), 
Biomass production (E,coli, yeast, insect cells, suspension mammalian cells 
with fermenters up to 150 litres) and a dedicated managed platform for single 
molecule experiments on optical tweezers (Lumicks C-trap and M-trap). 

We are looking for highly motivated and creative individuals with a strong 
interest in structural and functional characterization of large multi-subunit 
complexes, using integrative approaches. Previous expertise in structural 
biology or, in alternative, RNA biochemistry is essential.


Additional Information:
HT offers a highly collaborative, international culture. The working language 
at HT is English. HT will foster top quality, interdisciplinary research by 
promoting a vibrant environment consisting of independent research groups with 
access to outstanding graduate students, postdoctoral fellows and core 
facilities.
Please note that researchers coming to Italy for the first time, or returning 
after residing abroad, benefit from very attractive income tax reductions (up 
to 90%).

General enquires concerning the role should be sent to Prof. Alessandro Vannini 
(alessandro.vann...@fht.org >). Applications 
should not be sent to this address.

Deadline for applying 15th October 2021

https://careers.humantechnopole.it/o/postdoctoral-fellows-milan 



Prof. Alessandro Vannini
Head of Structural Biology Research Centre
Human Technopole
Palazzo Italia
Viale Rita Levi‑Montalcini, 1
20157 Milan, Italy

E. alessandro.vann...@fht.org 
 ​

Alessandro Vannini
Head of Structural Biology Research Centre 
+39 02-30247425+39 3451470481 

  




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

[Sebastiano Pasqualato]

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 between PyMOL and other softwares 
> used in structural biology and new mac M1 chips. Being a Linux user, I have 
> no clue. Could mac users share their experience?
> 
> Thanks
> Best regards,
> Claude
> 
> Le 16/09/2021 à 09:40, WENHE ZHONG a écrit :
>> Dear CCP4 community,
>> 
>> The COOT is not running smoothly on my M1 chip Macbook. For example, when 
>> both model and the electron density map are displayed, the moving from one 
>> residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only 
>> happened to my old computer, but I am surprised to find it happens in the 
>> newest macbook.
>> 
>> Anyone have this problem and has a solution? Thanks.
>> 
>> Best regards,
>> Wim
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
>> 
> -- 
> Dr Claude Sauter
> Directeur de Recherche
> Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS)
> Biologie des ARNt et pathogénicité  tel +33 (0)388 417 102
> 2 allée Conrad Roentgen fax +33 (0)388 602 218
> F-67084 Strasbourg - France  http://cj.sauter.free.fr/xtal 
> 
> 
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> 



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

[Sebastiano Pasqualato]

Dear all,
a position is open at the Biochemistry and Structural Biology Unit of the 
European Institute of Oncology in Milan.

The Unit 
(https://www.research.ieo.it/research-and-technology/technological-units/biochemistry-and-structural-biology-unit/
 
<https://www.research.ieo.it/research-and-technology/technological-units/biochemistry-and-structural-biology-unit/>)
 is one of the technological platforms of the Department of Experimental 
Oncology of the European Institute of Oncology (www.research.ieo.it 
<http://www.ieo0researh.it/>), a comprehensive cancer centre located in the 
south area of Milan.

We provide services and support to the department in the fields of Biochemistry 
and Structural Biology and collaborate both with scientific groups of the 
department and external ones to foster the structural biology aspects of their 
projects.

The ideal candidate has a Master/PhD degree in Chemistry, Biotechnology or 
Biology, with strong interest in biochemistry and structural biology. We are 
looking for an enthusiastic, motivated person, with good organisational and 
relational skills, and a good knowledge of English.

She/he will take care of assisting scientists collaborating with the Unit in 
macromolecular samples purification, characterisation and crystallisation, 
managing sample shipment to synchrotrons, supervising instrumentation usage and 
maintenance.
The Unit is setting up a Cryo-EM lab with an in-house VitroBot blotting device 
and external 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 at least one referee 
contact to sebastiano.pasqual...@ieo.it <mailto:sebastiano.pasqual...@ieo.it>.

Best regards,
Sebastiano

-- 
Sebastiano Pasqualato, PhD
Biochemistry and Structural Biology 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: 
https://www.research.ieo.it/research-and-technology/technological-units/biochemistry-and-structural-biology-unit/




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[ccp4bb] Yeast microtubule model

[Sebastiano Pasqualato]

Dear all,
I’m addressing to people working in the microtubule field.

Has someone created, or knows where I could find, a pdb file of the yeast 
microtubule, or a portion of it?
I’m interested in studying the contacts between subunits within the lattice.
I know one could generate that using yeast 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 Structural Biology 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




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[ccp4bb] CHAPS provider

[Sebastiano Pasqualato]

Dear all,
we are considering whether to buy the columns and reagents to purify our own 
Wnt3 protein or to buy it.
Given that the purification requires large amount of column eluents with 1% 
CHAPS, we are looking for the cheapest CHAPS provider to understand if the 
in-house purification is 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
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990





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[ccp4bb] low resolution refinement

[Sebastiano Pasqualato]

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 9437 5167
fax +39 02 9437 5990

Re: [ccp4bb] Introducing Dials User Interface for CCP4

[Sebastiano Pasqualato]

works now!
thanks a lot,
s

> On 07 May 2018, at 17:08, luis.fuentes-mont...@diamond.ac.uk 
>  wrote:
> 
> Try typing the next two commands in your terminal before running "dui":
> 
> 
> export BOOST_ADAPTBX_FPE_DEFAULT=1
> export BOOST_ADAPTBX_SIGNALS_DEFAULT=1
> 
> 
> This hack is NOT supposed to be needed, we should fix it with the next update.
> 
> 
> Thanks,
> 
> 
> Luiso
> 
> 
> From: CCP4 bulletin board  on behalf of Martín 
> Martinez Ripoll 
> Sent: 07 May 2018 14:48:11
> To: ccp4bb
> Subject: Re: [ccp4bb] Introducing Dials User Interface for CCP4
> 
> Hi Luis,
> 
> The same problem reported by Sebastiano (see below) regarding DUI (Dials User 
> Interface) occurs using Mac OSX 10.13.4 and older Quartz 2.7.9.
> 
> Regards,
> Martin
> _
> Dr. Martin Martinez-Ripoll
> Research Professor Emeritus
> xmar...@iqfr.csic.es<mailto:xmar...@iqfr.csic.es>
> Department of Crystallography & Structural Biology
> www.xtal.iqfr.csic.es<http://www.xtal.iqfr.csic.es/>
> www.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 Sebastiano 
> Pasqualato
> Enviado el: lunes, 07 de mayo de 2018 13:43
> Para: CCP4BB@JISCMAIL.AC.UK
> Asunto: 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 with this 
> error message (in red).
> Any hints on what is happening?
> Thanks,
> s
> 
> spasqual@host065:~/Desktop/esrf_05052018/IEO_x2/data> dui
> running Python version of lst_ext C++ Module
> sys_arg.template= None
> sys_arg.directory= None
> str(e) = [Errno 2] No such file or directory: 'dials_files/bkp.pickle'
> e.__doc__ = I/O operation failed.
> e.message =
> creating new DialsCommand (obj)
> 
> Running process on  posix
> 
> 
> creating new DialsCommand (obj)
> 
> Running process on  posix
> 
> 
> root_node.lin_num = 0
> 
> status
> |  lin num
> |   |  command
> |   |   |
> --
> S   0   \___Root
> N   1 \___None<<< here
> ---
> TreeNavWidget(__init__)
> idials_gui_path = 
> /Applications/ccp4-7.0/lib/py2/site-packages/mini_idials_w_GUI
> The " output " set of parameters is automatically handled by idials
> The " output " set of parameters is automatically handled by idials
> The " output " set of parameters is automatically handled by idials
> The " output " set of parameters is automatically handled by idials
> The " output " set of parameters is automatically handled by idials
> sys_arg_in = 
> unable to update data panel
> 
> turning log fonts to GREEN
> 
> QWebSettings.JavascriptEnabled = 1
> No need to load HTML file yet
> 
> 
> no datablock given
> 
> No pickle file given
> Unable to calculate mean and adjust contrast
> test setStyle(QStyleFactory.create())
> 1
> failed to << check_gray_outs() >>
> tmp_curr.lin_num == 1
> templ_text =  ?
> update_pbar_msg = click << Select File(s) >> or edit input line
> libc backtrace (-1 frames, most recent call last):
> Segmentation fault (sorry, call stacks not available)
>This crash may be due to a problem in any imported
>Python module, including modules which are not part
>of the cctbx project. To disable the traps leading
>to this message, define these environment variables
>(e.g. assign the value 1):
>BOOST_ADAPTBX_FPE_DEFAULT
>BOOST_ADAPTBX_SIGNALS_DEFAULT
>This will NOT solve the problem, just mask it, but
>may allow you to proceed in case it is not critical.
> spasqual@host065:~/Desktop/esrf_05052018/IEO_x2/data>
> 
> 
> On 02 May 2018, at 17:37, 
> luis.fuentes-mont...@diamond.ac.uk<mailto:luis.fuentes-mont...@diamond.ac.uk> 
> mailto:luis.fuentes-mont...@diamond.ac.uk>>
>  wrote:
> 
> Dear ccp4bb,
> 
> I am happy to introduce you to the new Dials User Interface (DUI) for CCP4.
> 
> DUI is a graphical user interface t

Re: [ccp4bb] Introducing Dials User Interface for CCP4

[Sebastiano Pasqualato]

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 with this error 
message (in red).
Any hints on what is happening?
Thanks,
s

spasqual@host065:~/Desktop/esrf_05052018/IEO_x2/data> dui
running Python version of lst_ext C++ Module
sys_arg.template= None
sys_arg.directory= None
str(e) = [Errno 2] No such file or directory: 'dials_files/bkp.pickle'
e.__doc__ = I/O operation failed.
e.message = 
creating new DialsCommand (obj)

 Running process on  posix 


creating new DialsCommand (obj)

 Running process on  posix 


root_node.lin_num = 0

status 
 |  lin num 
 |   |  command 
 |   |   | 
--
 S   0   \___Root
 N   1 \___None<<< here 
---
TreeNavWidget(__init__)
idials_gui_path = /Applications/ccp4-7.0/lib/py2/site-packages/mini_idials_w_GUI
The " output " set of parameters is automatically handled by idials
The " output " set of parameters is automatically handled by idials
The " output " set of parameters is automatically handled by idials
The " output " set of parameters is automatically handled by idials
The " output " set of parameters is automatically handled by idials
sys_arg_in = 
unable to update data panel

 turning log fonts to GREEN 

 QWebSettings.JavascriptEnabled = 1
No need to load HTML file yet


 no datablock given 

No pickle file given
Unable to calculate mean and adjust contrast
test setStyle(QStyleFactory.create())
1
failed to << check_gray_outs() >>
tmp_curr.lin_num == 1
templ_text =  ? 
update_pbar_msg = click << Select File(s) >> or edit input line 
libc backtrace (-1 frames, most recent call last):
Segmentation fault (sorry, call stacks not available)
This crash may be due to a problem in any imported
Python module, including modules which are not part
of the cctbx project. To disable the traps leading
to this message, define these environment variables
(e.g. assign the value 1):
BOOST_ADAPTBX_FPE_DEFAULT
BOOST_ADAPTBX_SIGNALS_DEFAULT
This will NOT solve the problem, just mask it, but
may allow you to proceed in case it is not critical.
spasqual@host065:~/Desktop/esrf_05052018/IEO_x2/data> 


> On 02 May 2018, at 17:37, luis.fuentes-mont...@diamond.ac.uk 
>  wrote:
> 
> Dear ccp4bb,
> 
> I am happy to introduce you to the new Dials User Interface (DUI) for CCP4.
> 
> DUI is a graphical user interface that is designed to make data processing 
> with DIALS more user-friendly and efficient. A key feature is a full history 
> tree that keeps track of all steps of processing. Every position in the tree 
> represents the execution of a DIALS command line with full record of the 
> user-supplied parameters, and the results, which can be inspected with 
> several visualisation tools. At any step, the user can either fork, proceed 
> to the next command or navigate to another step without loss of information. 
> This ability to keep track of different branches of data processing gives the 
> user freedom to explore different hypotheses, such as the space group of the 
> crystal.
> 
> DUI is intended to be intuitive and immediately useful across a wide range of 
> user expertise. Beginners learning about the integration process with DIALS 
> will benefit from the ease-of-use of the GUI and the visualisation tools. 
> Experts retain full control of the underlying DIALS programs and can use the 
> history tree to test different ideas quickly.
> 
> DUI does not have a launcher from ccp4i2 yet, but you can launch it by just 
> typing dui from your terminal. I would recommend to cd to the directory with 
> your images first. And of course have updated CCP4 to the latest version.
> 
> Enjoy!
> 
> Thanks,
> 
> Luis Fuentes-Montero (Luiso)
> 
> 
> -- 
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the e-mail and do not use, 
> copy, retain, distribute or disclose the information in or attached to the 
> e-mail.
> Any opinions expressed within this e-mail are those of the individual and not 
> necessarily of Diamond Light Source Ltd. 
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
> attachments are free from viruses and we cannot accept liability for any 
> damage which you may sustain as a result of software viruses which may be 
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England and 
> Wales with its registered office at Diamond House, H

Re: [ccp4bb] size exclusion columns

[Sebastiano Pasqualato]

Hi Markus,
just be aware that silica-based SEC columns are very sensitive to alkaline pH 
conditions, so you should not use them at pH higher that 7.5
We found that to be a limitation and thus chose polymer-based columns.
Hth,
ciao,
Sebastiano

> On 26 Apr 2018, at 18:03, Markus Heckmann  wrote:
> 
> Dear all,
> 
> We are looking for a size exclusion chromatography column
> (silica-based) for protein purification prior to a MALS-detector. We
> looked for (www.waters.com BEH-450), Sepax (Unix-C 300) and Phenomex
> (BioZen SEC-3).  Any 'column' tips or recommendations 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?

[Sebastiano Pasqualato]

Hi all,
a group in the department here has a sample with high amount of maltodextrins 
(~40 mg/ml) that they would like to load on a superdex column.
Anyone has advices on whether this is doable / not recommendable / absolutely 
to avoid?
So far, I have just found that people are separating 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
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] crystal imaging system

[Sebastiano Pasqualato]

Dear all,
we are in the process of considering the purchase of a new Crystal Imager.

So far, we have been considering the Formulatrix Rock Imager 182 and the TriTek 
Crystal Pro HT.
I would be extremely grateful to anyone who could provide me:

- feedback and user experience (positive/negative) 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
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990
web http://is.gd/IEOXtalUnit

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

[Sebastiano Pasqualato]

Dear Janet,
thanks for the excellent tip! It worked like charme!
I think the reason why our solution turned milky was that we were adding NaOH 
pellets without controlling the temperature, and possibly its increase caused 
the (seemingly irreversible) transition to the “porridge” state.
Your method allowed to get a solution which remained clear, despite the 
increase in temperature.
Thanks again!
I have also to thank Edward A. Berry, Diana R. Tomchick and Edward E. Pryor for 
the answers to my post and the valuable information.
Have a nice weekend,
ciao,
Sebastiano


> On 9 Jun 2017, at 01:35, Janet Newman  wrote:
> 
> The way I have done it (and it was sort of fun in a mad scientist way) was to 
> mix up solid DL-malic acid and sodium hydroxide in the right amounts and add 
> water as needed.  This generates  of heat, but gets around the 
> solubility minimum which is impossible to get out of:
> 
> I mixed 40.23 g of DL-malic acid powder (MW=134.1) with 24g of NaOH pellets 
> (MW=40) in a large beaker with a stirrer bar.  Put the beaker in a larger 
> container of ice, and put that on a stirrer in the cold room. Add 80 mL H20 
> to the beaker containing the chemicals, stand back - lots of heat evolved.
> when everything has quietened down, make up to 100 mL with water (we filtered 
> through a 0.22 um filter).
> 
> Cheers, Janet
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward 
> A. Berry
> Sent: Friday, 9 June 2017 2:53 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] preparing DL-Malic acid stock solution
> 
> (di)Sodium D,L-malate is available from Sigma-Aldrich (# CDS023113) and
> probably dissolves to give a 3M solution which is slightly alkaline.
> If pK2 is 5.1, then an insignificant amt of malic acid should bring the
> pH down to 7 (If you have to add a significant amount, just add more
> water to dilute to a final conc of 3M Malate + Malic acid)
> 
> 
> On 06/08/2017 12:32 PM, Diana Tomchick wrote:
>> As the pKa1 of malic acid is 3.4, it may be that the partially neutralized 
>> malic acid salt is less soluble than the acid or the fully neutralized salt.
>> 
>> The pKa2 of malic acid is 5.1.
>> 
>> Contact the people at Hampton Research
>> 
>> https://www.hamptonresearch.com/contact_us.aspx
>> 
>> and ask them. They sell it as a 3.0 M solution, pH neutralized to 7.0.
>> 
>> It is possible that you need to fully neutralize it before it turns clear, 
>> or that you may also need to gently heat it.
>> 
>> Diana
>> 
>> **
>> Diana R. Tomchick
>> Professor
>> Departments of Biophysics and Biochemistry
>> University of Texas Southwestern Medical Center
>> 5323 Harry Hines Blvd.
>> Rm. ND10.214A
>> Dallas, TX 75390-8816
>> diana.tomch...@utsouthwestern.edu <mailto:diana.tomch...@utsouthwestern.edu>
>> (214) 645-6383 (phone)
>> (214) 645-6353 (fax)
>> 
>> On Jun 8, 2017, at 9:54 AM, Sebastiano Pasqualato 
>> mailto:sebastiano.pasqual...@gmail.com>> 
>> wrote:
>> 
>> 
>> Dear all,
>> we’ve recently having trouble preparing a 3 M stock solution of DL-Malic 
>> Acid, pH 7 (which we had, so it’s doable!).
>> When we reach pH 3 - 4 the solution turns milky white and does not goes back 
>> to a clear solution even when the pH is raised.
>> Does anybody have any advice on how to get 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 9437 5990
>> web http://is.gd/IEOXtalUnit
>> 
>> 
>> 
>> --
>> 
>> UTSouthwestern
>> 
>> Medical Center
>> 
>> The future of medicine, today.
>> 

[ccp4bb] preparing DL-Malic acid stock solution

[Sebastiano Pasqualato]

Dear all,
we’ve recently having trouble preparing a 3 M stock solution of DL-Malic Acid, 
pH 7 (which we had, so it’s doable!).
When we reach pH 3 - 4 the solution turns milky white and does not goes back to 
a clear solution even when the pH is raised.
Does anybody have any advice on how to get 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 9437 5990
web http://is.gd/IEOXtalUnit

[ccp4bb] Electronic Laboratory Notebook

[Sebastiano Pasqualato]

Dear all,
another enquiry for the great community!

We are considering the idea of moving to electronic laboratory notebooks rather 
than paper ones.

Are you happily using one and would warmly suggest its implementation?
Our department does not only deal with biochemical experiments, but performs a 
lot of genomics (big data analysis) and mouse genetics experiments, so 
experience of Notebooks used in departments that also have those activities 
would be a plus.
We will consider free and paid softwares, if you have information on the costs 
that would be also very much appreciated!

Thanks 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

[Sebastiano Pasqualato]

Dear all,
is anybody using BLI instruments such as the ForteBio Octet in their 
lab/department?

A colleague in a neighbour institute is looking for information on their 
performance, overall and in comparison with SRP instruments.
Any advice with respect to:
- how these instruments really 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 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] SUMMARY: looking for paper describing optimisation of crystals using a screen kit as additive

[Sebastiano Pasqualato]

Dear all,
as usual the bulletin board nails it.
The paper I was vaguely remembering was indeed the following:

Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):646-50
Crystallization of foot-and-mouth disease virus 3C protease: surface 
mutagenesis and a novel crystal-optimization strategy.
Birtley JR, Curry S.

But of course, the bulletin board goes even further, providing other 
interesting hints and food for thoughts:

Structure. 2003 Sep;11(9):1061-70.
Enhancing protein crystallization through precipitant synergy.
Majeed S, Ofek G, Belachew A, Huang CC, Zhou T, Kwong PD.

Acta Crystallogr F Struct Biol Commun. 2014 Sep;70(Pt 9):1117-26
Microseed matrix screening for optimization in protein crystallization: what 
have we learned?
D'Arcy A, Bergfors T, Cowan-Jacob SW, Marsh M

Structure. 2017 Jan 3;25(1):107-120
Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy 
for Isoform-Specific Mechanical Protection.
Pernigo S, Fukuzawa A, Beedle AE, Holt M, Round A, Pandini A, Garcia-Manyes S, 
Gautel M, Steiner RA.

http://www2.mrc-lmb.cam.ac.uk/groups/JYL/WWWrobots/PDF/PresentationsOther/additive-screening.pdf
 
<http://www2.mrc-lmb.cam.ac.uk/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 paper (or was is a talk at a conference?) describing the 
> optimisation of initial hits of crystallisation by using a standard screen 
> kit as additive.
> Something like setting the tray using the initial crystallisation hit 
> condition in the reservoir and mixing 75% of the hit 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 Campus
> via Adamello, 16
> 20139 - Milano
> Italy
> 
> tel +39 02 9437 5167
> fax +39 02 9437 5990
> web http://is.gd/IEOXtalUnit <http://is.gd/IEOXtalUnit>

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

[Sebastiano Pasqualato]

Dear all,
I recall a paper (or was is a talk at a conference?) describing the 
optimisation of initial hits of crystallisation by using a standard screen kit 
as additive.
Something like setting the tray using the initial crystallisation hit condition 
in the reservoir and mixing 75% of the hit 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 Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990
web http://is.gd/IEOXtalUnit

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

[Sebastiano Pasqualato]

Hi all,
sorry for the off-topic question, but I was wondering if any of you bought and 
uses happily a “fill port” for the Akta systems which is not the “fill port, 
INV-907” from GE Healthcare 
(http://www.gelifesciences.com/webapp/wcs/stores/servlet/productById/en/GELifeSciences-it/18112766
 
<http://www.gelifesciences.com/webapp/wcs/stores/servlet/productById/en/GELifeSciences-it/18112766>
 - for which they charge 130 euros), but an alternative from another brand.

It should be usable with standard 0.7 mm “flat end” needles, just like the GE 
one.

Thank you very much in advance,
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

[Sebastiano Pasqualato]

Thanks Mark,
that solved the problem.

Thanks also to Ioan, Engin and Jochen, who replied with similar solutions.

Best,
ciao,
S


> On 29 Oct 2014, at 15:56, Mark Brooks  wrote:
> 
> Try reinstalling X-quartz.
>  
> IIRC, /usr/X11R6 is deleted during MacOS upgrades.
>  
> Mark
> 
> 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 more.
> Here’s the error message:
> 
> Seba@host041:~> nedit
> dyld: Library not loaded: /usr/X11R6/lib/libXp.6.dylib
>   Referenced from: /Applications/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
> 20139 - Milano
> Italy
> 
> tel +39 02 9437 5167 
> fax +39 02 9437 5990 
> web http://is.gd/IEO_XtalUnit <http://is.gd/IEO_XtalUnit>
> 
> 
> 
> 
> 
> 
> 
> ___
> phenixbb mailing list
> pheni...@phenix-online.org <mailto:pheni...@phenix-online.org>
> http://phenix-online.org/mailman/listinfo/phenixbb 
> <http://phenix-online.org/mailman/listinfo/phenixbb>
> 
> 

-- 
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

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

[Sebastiano Pasqualato]

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 more.
Here’s the error message:

Seba@host041:~> nedit
dyld: Library not loaded: /usr/X11R6/lib/libXp.6.dylib
  Referenced from: /Applications/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
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990
web http://is.gd/IEO_XtalUnit

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

[Sebastiano Pasqualato]

Ooopsss!!!
Of course it should read "experimental and computational cancer biology" but 
with this invasive automatic correctors, one typo can lead to very interesting 
fields of study, I guess…

Ciao,
S

On Apr 4, 2014, at 6:10 PM, "Oganesyan, Vaheh"  wrote:

> It 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 
> Sebastiano Pasqualato
> Sent: Friday, April 04, 2014 12:01 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Tenure track junior Group Leader Positions in Milan, Italy
>  
>  
> Dear all,
> there are open positions for junior Group Leaders in the field of 
> experimental and computational dance biology at the European Institute of 
> Oncology in milan, Italy.
> Please, find enclosed the details.
>  
> To the extent this electronic communication or any of its attachments contain 
> information that is not in the public domain, such information is considered 
> by MedImmune to be confidential and proprietary. This communication is 
> expected to be read and/or used only by the individual(s) for whom it is 
> intended. If you have received this electronic communication in error, please 
> reply to the sender advising of the error in transmission and delete the 
> original message and any accompanying documents from your system immediately, 
> without copying, reviewing or otherwise using them for any purpose. Thank you 
> for your cooperation. To the extent this electronic communication or any of 
> its attachments contain information that is not in the public domain, such 
> information is considered by MedImmune to be confidential and proprietary. 
> This communication is expected to be read and/or used only by the 
> individual(s) for whom it is intended. If you have received this electronic 
> communication in error, please reply to the sender advising of the error in 
> transmission and delete the original message and any accompanying documents 
> from your system immediately, without copying, reviewing or otherwise using 
> them for any purpose. Thank you for your cooperation.

-- 
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

Re: [ccp4bb] PDB structure validation

[Sebastiano Pasqualato]

Hi Debashis,
you have "Density fit analysis" in the "Validate" menu in Coot, if it's just 
that what you're looking for.
Ciao,
S

On Oct 31, 2013, at 4:43 PM, Debasish Chattopadhyay  wrote:

>  
> Yes, there remains many questions beyond Adit. 
> I do want to emphasize that the new scrutiny in PDB is very good since it now 
> includes a density fitting analysis (everything in the structure should be 
> the density, right) etc.   But one has to go through the submission to 
> generate the report and then has to resubmit the coordinates again if 
> corrections are necessary.   
> We know about Molprobity, structures with good Molprobity score and clash 
> score can still have some issues. 
> I just saw the note from Pavel and I need to check the option in Phenix.
>  
> Thanks all.
>  
> Debasish
>  
> From: longingforadmiss...@gmail.com [mailto:longingforadmiss...@gmail.com] On 
> Behalf Of Mahesh Lingaraju
> Sent: Thursday, October 31, 2013 10:32 AM
> To: Debasish Chattopadhyay
> Subject: Re: [ccp4bb] PDB structure validation
>  
> Hi 
>  
> One can do an unofficial validation in Adit server ( one of the pdb 
> deposition services) but i have found that although it is almost the same 
> thing, it does not provide a lot of information that we get from the official 
> report. 
>  
> I found that the apps from the PDB_redo help a lot in ironing out the kinks 
> at the final stages of structure refinement that are otherwise not so 
> obvious. 
>  
> Thanks 
>  
> Mahesh
>  
>  
>  
> 
> On Thu, Oct 31, 2013 at 11:25 AM, Debasish Chattopadhyay  
> wrote:
> I was wondering if there is a way to generate a PDB validation report 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 Alabama at Birmingham
> CBSE-250
> 1025 18th Street South, Birmingham, Al-35294
> USA
> Ph: (205)934-0124; Fax: (205)934-0480
>  

-- 
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_xtalU

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

[Sebastiano Pasqualato]

Dear all,
sorry to bother you with an off-topic request.

Does anybody have a contact for a person or a firm that provides maintenance 
and service for Crystal Farm plate imagers?
They used to be serviced by Bruker, but they don't support them anymore, as far 
as I know.

Any help highly 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?

[Sebastiano Pasqualato]

Check the highly build of xia2:

http://xia2.blogspot.it/2013/06/nightly-build.html

the one of Jun 25th surely works with the new version of XDS, provided you 
install the nightly build of phenix (works with dev-1412).

hth,
ciao,
S


On Jul 3, 2013, at 10:20 AM,   wrote:

> Hi,
> I found 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 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

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

[Sebastiano Pasqualato]

Hi Kay, hi all,

sorry to bother again, but I was wondering if people is experiencing the same 
problem I am.

With the nice new XDS graphical interface, I cannot manage to have the "show 
frame with predicted spots" script to work.

It looks like all the steps are performed correctly, but then XDS-viewer does 
not display the frame (here you can see what happens: 
https://dl.dropboxusercontent.com/u/4914553/Screen%20Shot%202013-06-26%20at%204.44.40%20PM.png).

Is anybody else experiencing this?
Any hint on how to make XDS-viewer to work in  this case?

Thanks in advance,
Sebastiano



On Jun 15, 2013, at 9:49 AM, Kay Diederichs  
wrote:

> Hi everybody,
> 
> I developed a GUI for academic users of XDS which is documented at 
> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSgui . This 
> XDSwiki article also has the links to binaries of xdsGUI (or XDSgui or 
> xds-gui; this has not been decided yet ...), for Linux 32 and 64 bit 
> (compiled on a RHEL 6 clone), and Mac OS X (compiled on 10.7).
> The 'added value' of the GUI is that it produces informative plots which 
> should greatly help to make decisions in data processing.
> The GUI is simple, tries to be self-explanatory and should be straightforward 
> to operate. Noteworthy may be the TOOLS tab which offers a means to run 
> commandline scripts upon a click with the mouse. This tab accepts user 
> modifications which should make it attractive also for expert users - they 
> can run their own scripts.
> This is the first version made publicly available. There are probaby bugs and 
> I would like to learn about these. In particular, Mac experts please tell me 
> how to solve the problems explained at the bottom 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

-- 
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] announcement: (another) GUI for XDS

[Sebastiano Pasqualato]

hi Kay,
thanks a lot for the prompt reply.

Indeed the problem rises from the fact that the program is launched in a 
"non-bash" environment, so one would have to add generate_XDS.INP to the PATH 
of the Mac interface, rather than to the bash PATH.
I took the workaround of launching XDSgui from the command line, rather than by 
clicking on its icon, and everything works fine.

For what concerns ads-viewer, sorry I didn't notice the .dmg file.
installation is just painless with that, adding an alias to the bin in the 
.bashrc file.

The program looks like running nice now.

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.
>> I'm on Mac OSX 10.8.4. The dmg installer and the script work nicely.
>> 
>> However, I have a couple of problems::
>> 
>> 1.
>> I have placed the generate_XDS.INP script in the XDS directory
>> (/Applications/XDS-OSX_64/) and it should be hence added to the PATH by
>> the same lines that add the ads commands to the PATH.
>> 
>> Those are the lines:
>> 
>> export XDSPATH=/Applications/XDS-OSX_64/
>> export PATH=$PATH:$XDSPATH
>> 
>> in my ~/.bashrc
>> 
>> Indeed, the script looks accessible from wherever:
>> 
>> Seba@host053:~> generate_XDS.INP
>> generate_XDS.INP version 0.36 (12-June-2013) . Obtain the latest version
>> from
>> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP
>> Seba@host053:~>
>> 
>> However, when I load a frame in the xds-gui frame tab, and then click
>> onto the "generate XDS.INP" button, I get a message stating:
>> 
>> You have to install generate_XDS.INP in your Path.
>> 
>> Could you tell me what I am missing?
> 
> I don't know much about Macs but this looks more like a bash problem ... it 
> works for me when I use ~/.bash_profile  (i.e. not ~/.bashrc )
> 
> The bash documentation on my Linux says:
> "When  an  interactive  shell  that  is not a login shell is started, bash 
> reads and executes commands from ~/.bashrc, if that file exists."
> 
> The bash is invoked from a _program_ here, not from an interactive shell 
> (console or terminal window), which may result in ~/.bashrc not being 
> executed.
> 
>> 
>> 
>> 2.
>> The wiki page states that XDSgui depends on XDS-viewer.
>> Could you tell me ho to install that on a Mac?
>> 
> 
> XDS-viewer is not my program, so I guess you have to install it like any 
> other program; see also http://xds-viewer.sourceforge.net/
> 
> I just looked it up on my Mac:
> turn34:~ dikay$ ll /usr/local/bin/xds-viewer
> lrwxr-xr-x  1 root  wheel  58 Apr  3 11:27 /usr/local/bin/xds-viewer -> 
> /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin
> 
> so it was probably installed in the usual way (from the DMG), but I do not 
> remember how I did it.
> 
> Please tell me how you solved these problems.
> 
> best,
> 
> Kay
> 
>> 
>> Thanks a lot for the excellent work,
>> ciao,
>> 
>> Sebastiano
>> 
>> 
>> On Jun 15, 2013, at 9:49 AM, Kay Diederichs
>> mailto:kay.diederi...@uni-konstanz.de>>
>> wrote:
>> 
>>> Hi everybody,
>>> 
>>> I developed a GUI for academic users of XDS which is documented at
>>> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSgui .
>>> This XDSwiki article also has the links to binaries of xdsGUI (or
>>> XDSgui or xds-gui; this has not been decided yet ...), for Linux 32
>>> and 64 bit (compiled on a RHEL 6 clone), and Mac OS X (compiled on 10.7).
>>> The 'added value' of the GUI is that it produces informative plots
>>> which should greatly help to make decisions in data processing.
>>> The GUI is simple, tries to be self-explanatory and should be
>>> straightforward to operate. Noteworthy may be the TOOLS tab which
>>> offers a means to run commandline scripts upon a click with the mouse.
>>> This tab accepts user modifications which should make it attractive
>>> also for expert users - they can run their own scripts.
>>> This is the first version made publicly available. There are probaby
>>> bugs and I would like to learn about these. In particular, Mac experts
>>> please tell me how to solve the problems explained at the bottom of
>>> the Wiki article ...
>>> 
>>> thanks,
>>> 
>>>

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

[Sebastiano Pasqualato]

Hi Kay, hi all,

sorry for the -maybe- naive questions, but i'm struggling to get the GUI for 
XDS going.
I'm on Mac OSX 10.8.4. The dmg installer and the script work nicely.

However, I have a couple of problems::

1.
I have placed the generate_XDS.INP script in the XDS directory 
(/Applications/XDS-OSX_64/) and it should be hence added to the PATH by the 
same lines that add the ads commands to the PATH.

Those are the lines:

export XDSPATH=/Applications/XDS-OSX_64/
export PATH=$PATH:$XDSPATH

in my ~/.bashrc

Indeed, the script looks accessible from wherever:

Seba@host053:~> generate_XDS.INP 
generate_XDS.INP version 0.36 (12-June-2013) . Obtain the latest version from
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP
Seba@host053:~> 

However, when I load a frame in the xds-gui frame tab, and then click onto the 
"generate XDS.INP" button, I get a message stating:

You have to install generate_XDS.INP in your Path.

Could you tell me what I am missing?


2.
The wiki page states that XDSgui depends on XDS-viewer.
Could you tell me ho to install that on a Mac?


Thanks a lot for the excellent work,
ciao,

Sebastiano 


On Jun 15, 2013, at 9:49 AM, Kay Diederichs  
wrote:

> Hi everybody,
> 
> I developed a GUI for academic users of XDS which is documented at 
> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSgui . This 
> XDSwiki article also has the links to binaries of xdsGUI (or XDSgui or 
> xds-gui; this has not been decided yet ...), for Linux 32 and 64 bit 
> (compiled on a RHEL 6 clone), and Mac OS X (compiled on 10.7).
> The 'added value' of the GUI is that it produces informative plots which 
> should greatly help to make decisions in data processing.
> The GUI is simple, tries to be self-explanatory and should be straightforward 
> to operate. Noteworthy may be the TOOLS tab which offers a means to run 
> commandline scripts upon a click with the mouse. This tab accepts user 
> modifications which should make it attractive also for expert users - they 
> can run their own scripts.
> This is the first version made publicly available. There are probaby bugs and 
> I would like to learn about these. In particular, Mac experts please tell me 
> how to solve the problems explained at the bottom 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



-- 
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] Glutathione rsin

[Sebastiano Pasqualato]

Hi Mirek, hi all,
I'm also very interested in the topic, so please keep me up with the replies, 
or make sure to post a summary, please.

In addition to the price, the problem we're facing with GSH-beads from GE 
(although we haven't tried others yet) is that we can't manage to deplete our 
lysates.
We are always left with a large amount of unbound GST-tagged protein in the 
flow through, that is eventually captured by a second, third and sometime 
fourth  incubation with fresh beads.
Using larger beads volume won't help.
Has anybody faced and/or overcame this problem?

Thanks a lot in advance,
ciao,

Sebastiano


On Jun 4, 2013, at 8:54 PM, "Cygler, Miroslaw"  wrote:

> Hi,
> I would like to ask the bb faithful for their experience with the glutathione 
> affinity resins. We have been using so far the Glutathione Sepharose fast 
> flow from GE but the price is getting steeper. We found Glutathione Superflow 
> resin from Clontech to be significantly less expensive and Glutathione 
> agarose from Fisher somewhere in-between. We have no experience with the 
> latter two resins and I wonder what is the experience of other 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 Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

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

[Sebastiano Pasqualato]

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 Donghui,
> 
> did you actually check this stretch IS a beta-strand, given how
> distorted it looks? I am asking because in my experience people tend
> to believe what programs like pymol or molscript tell them to believe
> without checking the model e.g. for a hydrogen bonding network
> supporting the secondary structure definition.
> 
> I may also remember incorrectly, but as far as I know pymol does not
> use the DSSP algorithm as e.g. molscript and often comes up with
> different boundaries for the secondary structure elements. I believe
> the dssp algorithm is more accurate, although this may be because I
> like molscript (typing) better than pymol (clicking).
> 
> Regards,
> Tim
> 
> On 05/30/2013 05:29 AM, wu donghui wrote:
>> Dear all,
>> 
>> I found a problem when I use pymol to prepare structure interface.
>> Strand is distorted when residue from the strand is connected to
>> the strand by turning on "side_chain_helper on". However when
>> side_chain_helper is off, the strand turns to normal shape but the
>> residue from it is disconnected to the strand. I attached the
>> picture for your help. I know there must be some tricks for this.
>> Welcome for any input. Thanks a lot.
>> 
>> Best,
>> 
>> Donghui
> 
> - -- 
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
> 
> iD8DBQFRp3/cUxlJ7aRr7hoRAkV+AJ9QkNSlAhSC4VAKe2UHt+YpqSY3SwCfQ+Zw
> ry5vjpLD1hRVZGU7qHnajj4=
> =yxdy
> -END PGP SIGNATURE-

Re: [ccp4bb] a new version of XDS

[Sebastiano Pasqualato]

Hi Folmer,
it's just a matter of time, you know, given the short-living license of XDS. ;-)

Anyway, I second the request,
ciao,
s


On May 30, 2013, at 8:50 AM, Folmer Fredslund  wrote:

> Hi all,
> 
> Nice with a new version (I guess that means improvements :-)
> 
> Before I upgrade, I just have one question:
> 
> Does the change in the XPARM.XDS format mean that software such as xia2 will 
> be broken? 
> 
> Thanks,
> Folmer
> 
> 
> 2013/5/29 Kay Diederichs 
> ... is available for academic users at 
> http://homes.mpimf-heidelberg.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

-- 
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] Diffraction image viewer with display of resolution circles

[Sebastiano Pasqualato]

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 users,
> 
> I'm looking for the diffraction image viewer, which will be able to
> display of resolution circles and export it to new image. I tried use
> idiffdisp, but after choose of the "Show/clear resolution circles", there
> is no action. Images were collected using Rayonics MX-225 detector - maybe
> detector format is a problem?
> 
> Best regards,
> 
> Rafal
> 
> |--|
> |Rafal Dolot, Ph.D.|
> |  |
> |Polish Academy of Sciences|
> |Centre of Molecular and Macromolecular Studies|
> |Department of Bioorganic Chemistry|
> |Sienkiewicza 112  |
> |90-363 Lodz, Poland   |
> |Phone: +48(42)6803215 |
> |Cell:  +48 502897781  |
> |--|

[ccp4bb] SUMMARY: PDB "crawler"

[Sebastiano Pasqualato]

Hi Boaz,
that is definitely what I was looking for.
Thank you very much.

Other suggestions, on weekly queries based on "your favourite protein" sequence 
were given by Gerard Kleyvegt 
(http://bip.weizmann.ac.il/noop/NOOP_seqalert.html) and David Briggs 
(http://www.sbg.bio.ic.ac.uk/phyre2/html/help.cgi?id=help/phyrealarm)

Ciao,
Sebastiano

On Mar 20, 2013, at 3:41 PM, Boaz Shaanan  wrote:

> Hi,
> 
> I think that  what you're looking for (or close to it) is available on the 
> pdb site. Through your PDB login you can do a search according to keyword(s) 
> and ask to repeat the search periodically. You'll get an alert in the e-mail. 
> I actually use it for some time.
> 
>   Cheers,
> 
>   Boaz
> 
>  
>  
> Boaz Shaanan, Ph.D. 
> Dept. of Life Sciences  
> Ben-Gurion University of the Negev  
> Beer-Sheva 84105
> Israel  
> 
> 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 [sebastiano.pasqual...@gmail.com]
> Sent: Wednesday, March 20, 2013 2:40 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] PDB "crawler"
> 
> 
> Hi all,
> just wondering if anybody is aware of a service similar to PubCrawler 
> (http://pubcrawler.gen.tcd.ie/), but for PDB structures, released and 
> unreleased.
> Basically a weekly email that would alert you of freshly deposited structures 
> that match some keywords.
> 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 9437 5990


-- 
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

please note the change in email address!
sebastiano.pasqual...@ieo.eu

[ccp4bb] PDB "crawler"

[Sebastiano Pasqualato]

Hi all,
just wondering if anybody is aware of a service similar to PubCrawler 
(http://pubcrawler.gen.tcd.ie/), but for PDB structures, released and 
unreleased.
Basically a weekly email that would alert you of freshly deposited structures 
that match some keywords.
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 9437 5990

Re: [ccp4bb] statistics from a structure factors file

[Sebastiano Pasqualato]

Thanks Graeme.
Long live and prosper to the unmerged files, then.
ciao,
s

On Jan 17, 2013, at 10:37 AM, Graeme Winter  wrote:

> Hi Sebastiano,
> 
> If they hand you an *unmerged* mtz file containing scaled data you can
> do this, by remerging the data with Scala or Aimless. Equivalently the
> unmerged output of scalepack or XSCALE (or XDS CORRECT)
> 
> If however you have merged data then you have lost this information,
> though completeness and Mn(I/sig) are available, but not Rsym / Rpim /
> multiplicity etc. Unmerged files are good :o)
> 
> Cheerio,
> 
> 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 Rsym,
>> Mn(I/sigI), Multiplicity, Completeness, from a structure factors file
>> already containing  merged structure factors?
>> 
>> That is, if somebody 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 Institute of Oncology
>> IFOM-IEO Campus
>> via Adamello, 16
>> 20139 - Milano
>> Italy
>> 
>> tel +39 02 9437 5167
>> fax +39 02 9437 5990
>> 
>> please note the change in email address!
>> sebastiano.pasqual...@ieo.eu
>> 
>> 
>> 
>> 
>> 
>> 


-- 
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

please note the change in email address!
sebastiano.pasqual...@ieo.eu

[ccp4bb] statistics from a structure factors file

[Sebastiano Pasqualato]

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 Rsym, 
Mn(I/sigI), Multiplicity, Completeness, from a structure factors file already 
containing  merged structure factors?

That is, if somebody 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 Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

please note the change in email address!
sebastiano.pasqual...@ieo.eu

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

[Sebastiano Pasqualato]

Excellent.
Thanks a lot for the clarifications.
ciao,
s

On Jan 16, 2013, at 4:14 PM, Kay Diederichs  
wrote:

> Sebastiano,
> 
> CORRECT does scale the data. XSCALE is only needed for two or more datasets, 
> or if other requirements exist - you named one.
> 
> The two varieties 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 refined a structure using the mtz output by the GO.COM automatic 
> reduction routine of SLS beamline PXIII, which does not involve a scaling 
> step (I discovered recently).
> I was willing to have the integration statistics of the reflection file I 
> used in the refinement's high resolution bin.
> I will definitely give xprep a try.
> 
> Another question that raised by looking deeper into their automatic procedure 
> (thanks Meitian for the help) is that when integrating with XDS CORRECT 
> keeping the FRIEDEL'S_LAW=TRUE or =FALSE I get a different number of 
> reflections in the final mtz.
> 
> In my case, if I run the same XDS.INP script and change only the 
> FRIEDEL'S_LAW flag, I obtain:
> 
> 
> =TRUE: 11551 reflections
> 
>  *  Resolution Range :
> 
> 0.000430.11138 ( 48.225 -  2.996 A )
> 
>  * Sort Order :
> 
>   1 2 3 0 0
> 
>  * Space group = 'P 3 2 1' (number 150)
> 
> 
> 
>  OVERALL FILE STATISTICS for resolution range   0.000 -   0.111
>  === 
> 
> 
>  Col SortMinMaxNum  % Mean Mean   Resolution   Type 
> Column
>  num order   Missing complete  abs.   LowHigh   
> label 
> 
>1 ASC  0  29  0  100.00 13.7 13.7  48.22   3.00   H  H
>2 NONE 0  16  0  100.00  4.7  4.7  48.22   3.00   H  K
>3 NONE   -32  32  0  100.00  0.5 12.2  48.22   3.00   H  L
>4 NONE1.4   292.0 0  100.0019.4019.40  48.22   3.00   F  FP
>5 NONE0.1 4.3 0  100.00 0.70 0.70  48.22   3.00   Q  
> SIGFP
>6 NONE0.0 1.0 0  100.00 0.95 0.95  48.22   3.00   I  
> FreeRflag
> 
> 
>  No. of reflections used in FILE STATISTICS11551
> 
> 
> =FALSE: 11643 reflections
> 
>  * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
> 
>   100.5450  100.5450   96.4500   90.   90.  120. 
> 
>  *  Resolution Range :
> 
> 0.000430.11138 ( 48.225 -  2.996 A )
> 
>  * Sort Order :
> 
>   1 2 3 0 0
> 
>  * Space group = 'P 3 2 1' (number 150)
> 
> 
> 
>  OVERALL FILE STATISTICS for resolution range   0.000 -   0.111
>  === 
> 
> 
>  Col SortMinMaxNum  % Mean Mean   Resolution   Type 
> Column
>  num order   Missing complete  abs.   LowHigh   
> label 
> 
>1 ASC  0  29  0  100.00 13.7 13.7  48.22   3.00   H  H
>2 NONE 0  16  0  100.00  4.7  4.7  48.22   3.00   H  K
>3 NONE   -32  32  0  100.00  0.5 12.2  48.22   3.00   H  L
>4 NONE1.4   291.9 0  100.0019.4019.40  48.22   3.00   F  FP
>5 NONE0.1 4.3 0  100.00 0.67 0.67  48.22   3.00   Q  
> SIGFP
>6 NONE  -13.613.269   99.41-0.01 0.69  48.22   3.00   D  
> DANO
>7 NONE0.0 5.769   99.41 1.13 1.13  48.22   3.00   Q  
> SIGDANO
>8 NONE 0   2  0  100.00  0.0  0.0  48.22   3.00   Y  
> ISYM
>9 NONE0.0 1.0 0  100.00 0.95 0.95  48.22   3.00   I  
> FreeRflag
> 
> 
>  No. of reflections used in FILE STATISTICS11643
> 
> 
> Aren't they supposed to be the exact same number?
> 
> Thanks,
> ciao,
> s
> 
> 
> On Jan 16, 2013, at 1:12 PM, Tim Gruene  wrote:
> 
>> -----BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>> 
>> Dear Sebastiano,
>> 
>> you could use xprep to get the statistics in user defined resolution
>> shells.
>> 
>> Out of curiosity: Would you mind sharing why you want 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 allows to change the number of
&

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

[Sebastiano Pasqualato]

On Jan 16, 2013, at 2:19 PM, Tim Gruene  wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear Sebastiano,
> 
> if the output of GO.COM produces an mtz-file you can use for phasing
> or refinement, I am very confident there is a scaling step involved.

Sorry, my bad.
I meant there's no XSCALE nor scala that has been run. CORRECT does the scaling.

> This might also be an explanation for the discrepancy you point out:
> With FRIEDEL'S_LAW=TRUE the statistics which affects the rejection of
> outliers would have more reflections within each group of symmetry
> related reflections and hence a greater spread which might lead to the
> rejection of some of the classes. But this is a mere guess.

The way I performed the two runs was by running CORRECT step of XDS followed by 
XDSCONV, f2mtz and cad.

When working with the FRIEDEL'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:
>> 
>> 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 refined a structure using the mtz output by the
>> GO.COM automatic reduction routine of SLS beamline PXIII, which
>> does not involve a scaling step (I discovered recently). I was
>> willing to have the integration statistics of the reflection file I
>> used in the refinement's high resolution bin. I will definitely
>> give xprep a try.
>> 
>> Another question that raised by looking deeper into their automatic
>> procedure (thanks Meitian for the help) is that when integrating
>> with XDS CORRECT keeping the FRIEDEL'S_LAW=TRUE or =FALSE I get a
>> different number of reflections in the final mtz.
>> 
>> In my case, if I run the same XDS.INP script and change only the
>> FRIEDEL'S_LAW flag, I obtain:
>> 
>> 
>> =TRUE: 11551 reflections
>> 
>> *  Resolution Range :
>> 
>> 0.000430.11138 ( 48.225 -  2.996 A )
>> 
>> * Sort Order :
>> 
>> 1 2 3 0 0
>> 
>> * Space group = 'P 3 2 1' (number 150)
>> 
>> 
>> 
>> OVERALL FILE STATISTICS for resolution range   0.000 -   0.111 
>> ===
>> 
>> 
>> Col SortMinMaxNum  % Mean Mean   Resolution
>> Type Column num order   Missing complete  abs.
>> LowHigh   label
>> 
>> 1 ASC  0  29  0  100.00 13.7 13.7  48.22   3.00
>> H  H 2 NONE 0  16  0  100.00  4.7  4.7  48.22
>> 3.00   H  K 3 NONE   -32  32  0  100.00  0.5 12.2
>> 48.22   3.00   H  L 4 NONE1.4   292.0 0  100.0019.40
>> 19.40  48.22   3.00   F  FP 5 NONE0.1 4.3 0  100.00
>> 0.70 0.70  48.22   3.00   Q  SIGFP 6 NONE0.0 1.0 0
>> 100.00 0.95 0.95  48.22   3.00   I  FreeRflag
>> 
>> 
>> No. of reflections used in FILE STATISTICS11551
>> 
>> 
>> =FALSE: 11643 reflections
>> 
>> * Cell Dimensions : (obsolete - refer to dataset cell dimensions
>> above)
>> 
>> 100.5450  100.5450   96.4500   90.   90.  120.
>> 
>> *  Resolution Range :
>> 
>> 0.000430.11138 ( 48.225 -  2.996 A )
>> 
>> * Sort Order :
>> 
>> 1 2 3 0 0
>> 
>> * Space group = 'P 3 2 1' (number 150)
>> 
>> 
>> 
>> OVERALL FILE STATISTICS for resolution range   0.000 -   0.111 
>> ===
>> 
>> 
>> Col SortMinMaxNum  % Mean Mean   Resolution
>> Type Column num order   Missing complete  abs.
>> LowHigh   label
>> 
>> 1 ASC  0  29  0  100.00 13.7 13.7  48.22   3.00
>> H  H 2 NONE 0  16  0  100.00  4.7  4.7  48.22
>> 3.00   H  K 3 NONE   -32  32  0  100.00  0.5 12.2
>> 48.22   3.00   H  L 4 NONE1.4   291.9 0  100.0019.40
>> 19.40  48.22   3.00   F  FP 5 NONE0.1 4.3 0  100.00
>> 0.67 0.67  48.22   3.00   Q  SIGFP 6 NONE  -13.613.269
>> 99.41-0.01 0.69  48.22   3.00   D  DANO 7 NONE0.0
>> 5.769   99.41 1.13 1.13  48.22   3.00   Q  SIGDANO 8
>> NONE 0   2  0  100.00  0.0  0.0  48.22   3.00
>> Y  ISYM 9 NONE0.0 1.0     0  100.00

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

[Sebastiano Pasqualato]

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 refined a structure using the mtz output by the GO.COM automatic reduction 
routine of SLS beamline PXIII, which does not involve a scaling step (I 
discovered recently).
I was willing to have the integration statistics of the reflection file I used 
in the refinement's high resolution bin.
I will definitely give xprep a try.

Another question that raised by looking deeper into their automatic procedure 
(thanks Meitian for the help) is that when integrating with XDS CORRECT keeping 
the FRIEDEL'S_LAW=TRUE or =FALSE I get a different number of reflections in the 
final mtz.

In my case, if I run the same XDS.INP script and change only the FRIEDEL'S_LAW 
flag, I obtain:


=TRUE: 11551 reflections

 *  Resolution Range :

0.000430.11138 ( 48.225 -  2.996 A )

 * Sort Order :

  1 2 3 0 0

 * Space group = 'P 3 2 1' (number 150)



 OVERALL FILE STATISTICS for resolution range   0.000 -   0.111
 === 


 Col SortMinMaxNum  % Mean Mean   Resolution   Type 
Column
 num order   Missing complete  abs.   LowHigh   
label 

   1 ASC  0  29  0  100.00 13.7 13.7  48.22   3.00   H  H
   2 NONE 0  16  0  100.00  4.7  4.7  48.22   3.00   H  K
   3 NONE   -32  32  0  100.00  0.5 12.2  48.22   3.00   H  L
   4 NONE1.4   292.0 0  100.0019.4019.40  48.22   3.00   F  FP
   5 NONE0.1 4.3 0  100.00 0.70 0.70  48.22   3.00   Q  
SIGFP
   6 NONE0.0 1.0 0  100.00 0.95 0.95  48.22   3.00   I  
FreeRflag


 No. of reflections used in FILE STATISTICS11551


=FALSE: 11643 reflections

 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)

  100.5450  100.5450   96.4500   90.   90.  120. 

 *  Resolution Range :

0.000430.11138 ( 48.225 -  2.996 A )

 * Sort Order :

  1 2 3 0 0

 * Space group = 'P 3 2 1' (number 150)



 OVERALL FILE STATISTICS for resolution range   0.000 -   0.111
 === 


 Col SortMinMaxNum  % Mean Mean   Resolution   Type 
Column
 num order   Missing complete  abs.   LowHigh   
label 

   1 ASC  0  29  0  100.00 13.7 13.7  48.22   3.00   H  H
   2 NONE 0  16  0  100.00  4.7  4.7  48.22   3.00   H  K
   3 NONE   -32  32  0  100.00  0.5 12.2  48.22   3.00   H  L
   4 NONE1.4   291.9 0  100.0019.4019.40  48.22   3.00   F  FP
   5 NONE0.1 4.3 0  100.00 0.67 0.67  48.22   3.00   Q  
SIGFP
   6 NONE  -13.613.269   99.41-0.01 0.69  48.22   3.00   D  DANO
   7 NONE0.0 5.769   99.41 1.13 1.13  48.22   3.00   Q  
SIGDANO
   8 NONE 0   2  0  100.00  0.0  0.0  48.22   3.00   Y  ISYM
   9 NONE0.0 1.0 0  100.00 0.95 0.95  48.22   3.00   I  
FreeRflag


 No. of reflections used in FILE STATISTICS11643


Aren't they supposed to be the exact same number?

Thanks,
ciao,
s


On Jan 16, 2013, at 1:12 PM, Tim Gruene  wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear Sebastiano,
> 
> you could use xprep to get the statistics in user defined resolution
> shells.
> 
> Out of curiosity: Would you mind sharing why you want 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 allows to change the number of
>> resolution bins appearing in the table:
>> 
>> SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF
>> RESOLUTION
>> 
>> of CORRECT.LP.
>> 
>> Please, note that I am not referring to the table output by XSCALE,
>> in which you can change the resolution bins with the keyword
>> RESOLUTION_SHELLS=, but rather the table output by the CORRECT job
>> of XDS.
>> 
>> Thanks in advance, ciao, Sebastiano
>> 
>> 
> 
> - -- 
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> 
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
> 
> iD8DBQFQ9pk/UxlJ7aRr7hoRAqreAJ9/aKSHyXWahBc96/3x0U5iriZk4gCg2fWC
> GVLgXUEN+10M9IpCDRENGF0=
> =SK0P
> -END PGP SIGNATURE-


-- 
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

please note the change in email address!
sebastiano.pasqual...@ieo.eu

[ccp4bb] changing resolution bins statistics in CORRECT.LP

[Sebastiano Pasqualato]

Hi all,
I was wondering if XDS allows to change the number of resolution bins appearing 
in the table:

SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION

of CORRECT.LP.

Please, note that I am not referring to the table output by XSCALE, in which 
you can change 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, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

sebastiano.pasqual...@ieo.eu

Re: [ccp4bb] vitrification vs freezing

[Sebastiano Pasqualato]

Dear all,

I surely was not hoping in such a huge response to my original question.
I think we all have read excellent contributions, and pleasant posts.
Although, as often happens, a unique consensus has not emerged, I have for sure 
a clearer idea of what I should use in the future, and have 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
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

please note the change in email address!
sebastiano.pasqual...@ieo.eu

Re: [ccp4bb] vitrification vs freezing

[Sebastiano Pasqualato]

Oui bon d'accord, mais il faudra tout de même décider si utiliser "vitrifiés" 
ou bien "congelés"...

sorry couldn't resist ;-)

s

On Nov 16, 2012, at 10:54 AM, Tim Gruene wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Hi James,
> 
> I once heard that in (European) law French is the language of choice
> because it were the most precise one (which I find easy to believe).
> Maybe we should try and convince journals to only accept articles
> written in French - not sure, this will improve their quality, though,
> comparing my level of French with my level of English ;-)
> 
> Lovely discussion,
> Tim
> 
> On 11/15/2012 09:15 PM, James Stroud wrote:
>> On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote:
>>> I have heard this discussion before and reminds me of people
>>> claiming strawberries were nuts - which botanically may be
>>> correct, but would still not make me complain about strawberries
>>> in a fruit cake I ordered at a restaurant.
>>> 
>>> My Pengiun English Dictionary states (amongst other
>>> explanations) freeze: "to make extremely cold",
>> 
>> 
>> Tim's comment strikes at the heart of the problem.
>> 
>> I think the scientific community should decide a few points.
>> 
>> 1. What is the approved language and dialect for science? 2. Within
>> this dialect, what should be the authoritative dictionary? 3. Will
>> we allow use of definitions that are not the primary definition
>> (second, third, fourth). 4. Will we allow the use of homonyms? 5.
>> If not, which homonyms should prevail?
>> 
>> These are all very 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
> 
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
> 
> iD8DBQFQpg1XUxlJ7aRr7hoRAl33AKCbSYXQmD2YyVug5s3i+2CYDVDzqQCfZ7Qz
> 4IiEP5B5NrB+D0s+r/tIa6o=
> =nN9O
> -END PGP SIGNATURE-

-- 
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

please note the change in email address!
sebastiano.pasqual...@ieo.eu

Re: [ccp4bb] vitrification vs freezing

[Sebastiano Pasqualato]

Hi Tim.

Well, I surely get your point, but I have to say, that really was the last in 
the "minor points" addressed by the (again excellent!) referee.
That did not bother me at all, I really appreciate a referee that reads 
thoroughly my paper.

Also, it is true we do write in English, but we do also write of science, and 
that implies being as precise as we can be.

Many have confirmed (thanks Roberto, Mark, Mischa, Henry, Harry, Mathews) that 
"vitrified" is the correct wording, and "cryocooled" could be used as well, 
without being imprecise.

So I just guess I will stick to the new words, happy to have learned something 
new about scientific English.

Thank you too,
ciao,
s

On Nov 15, 2012, at 6:59 PM, Tim Gruene wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear s,
> 
> I have heard this discussion before and reminds me of people claiming
> strawberries were nuts - which botanically may be correct, but would
> still not make me complain about strawberries in a fruit cake I
> ordered at a restaurant.
> 
> My Pengiun English Dictionary states (amongst other explanations)
> freeze: "to make extremely cold", so as long as you think your article
> is written in English, you did not say anything wrong, assuming your
> readers are intelligent enough to understand what you are trying to
> say - and in a crystallographic article, the process of 'freezing'
> your 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 referee, btw!) commented like this:
>> 
>> "crystals were vitrified rather than frozen."
>> 
>> These were crystals grew in ca. 2.5 M sodium malonate, directly dip
>> in liquid nitrogen prior to data collection at 100 K. We stated in
>> the methods section that crystals were "frozen in liquid nitrogen",
>> as I always did.
>> 
>> After a little googling it looks like I've always been wrong, and
>> what we are always doing is doing is actually vitrifying the
>> crystals. Should I always use this statement, from now on, or are
>> there english/physics subtleties that I'm not grasping?
>> 
>> Thanks a lot, ciao, s
>> 
>> 
> 
> - -- 
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
> 
> iD8DBQFQpS17UxlJ7aRr7hoRAvX0AJ9b3YYQ4kXu5J0wJdEYudPclTmKtQCg8HSx
> R4wgkmbp2l7Q/ns/HfJkqgY=
> =R9Wp
> -END PGP SIGNATURE-

-- 
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

please note the change in email address!
sebastiano.pasqual...@ieo.eu

[ccp4bb] vitrification vs freezing

[Sebastiano Pasqualato]

Hi folks,
I have recently received a comment on a paper, in which referee #1 (excellent 
referee, btw!) commented like this:

"crystals were vitrified rather than frozen."

These were crystals grew in ca. 2.5 M sodium malonate, directly dip in liquid 
nitrogen prior to data collection at 100 K.
We stated in the methods section that crystals were "frozen in liquid 
nitrogen", as I always did.

After a little googling it looks like I've always been wrong, and what we are 
always doing is doing is actually vitrifying the crystals.
Should I always use this statement, 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 5167
fax +39 02 9437 5990

please note the change in email address!
sebastiano.pasqual...@ieo.eu

Re: [ccp4bb] Space group R32 and H32

[Sebastiano Pasqualato]

That is perfectly clear.
What was confusing me was indeed (mostly) the PDB CRYST1 record.
I guess I will go for R32:h.
Thanks a lot,
ciao,
s

On Jul 30, 2012, at 6:36 PM, Ian Tickle wrote:

> Hi Sebastiano
> 
> How programs refer to it is irrelevant for the purposes of
> publication!  If you want to be precise and stick to the ITC
> convention on nomenclature it's "space group R32 in the setting
> R32:h", since as I explained it's only the standard symbol R32 which
> is generally shown in the main ITC table of space groups; the setting
> symbols 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 it up.
> 
> -- Ian
> 
> On 30 July 2012 17:20, Sebastiano Pasqualato
>  wrote:
>> 
>> Hi there,
>> at this point I'm confused, at least with respect to one thing.
>> If I have a solved a structure in spacegroup #155, with a=b and different
>> from c, and alpha=beta=90, gamma=120, this would be reported as R32 in the
>> international tables. However programs refers to it as H32.
>> What should I report in the (in)famous  "table 1" ?
>> Thanks in advance,
>> ciao,
>> s
>> 
>> On Jul 30, 2012, at 5:23 PM, Ian Tickle wrote:
>> 
>> Without wishing to re-ignite previous discussions on this topic
>> (perhaps  ...  tags would be in order!), I would point
>> out that this and similar confusion with other space groups has arisen
>> largely from a failure of some programmers (and users!) to fully
>> comprehend the important difference between a 'standard symbol' and a
>> 'setting symbol' for a space group, no doubt because in many cases
>> these are superficially identical, or a least very similar.  This
>> point is also made in the Computational Crystallography Newsletter
>> article on H3 and H32 that I referenced earlier.
>> 
>> The Hermann-Mauguin symbol (aka 'standard symbol') is unique to a
>> space group and crucially is designed to be independent of the setting
>> (orientation and/or origin).  It is used to identify a space group
>> without reference to the setting, and therefore its main use is to
>> provide page headings and index entries in ITC. There exist exactly
>> 230 H-M standard symbols for the 230 unique 3D space groups.  The H-M
>> standard symbol is the same for all settings of a particular space
>> group and therefore cannot be used to define the setting: for that you
>> obviously need additional information.
>> 
>> The standard symbol is thus of little or no relevance to practical
>> crystallography: for that you must use a setting symbol.  However for
>> the majority of space groups only one setting is accepted as
>> 'conventional' so in those cases the standard and setting symbols are
>> identical; it's only where there are multiple settings that problems
>> arise.
>> 
>> A simple analogy might be to say that an object is called 'building'
>> and that is also its standard symbol.  It describes the object without
>> reference to its orientation or position and so is not relevant to the
>> practical problem of defining the view of the building: for that you
>> need extra symbols.  For example you might need to specify one of the
>> setting symbols 'building (front elevation)', 'building (side
>> elevation)' or 'building (plan)'.
>> 
>> So R32 is a H-M standard symbol which corresponds to the 2 alternate
>> setting symbols R32:r and R32:h as described in the article.  Plainly
>> you can't use the H-M symbol R32 to uniquely specify the setting since
>> it is the standard symbol for both the R32:r and R32:h settings.  The
>> latter are _not_ H-M symbols: they are ITC extensions of the H-M
>> symbol.
>> 
>> For other space groups further confusion has arisen because ITC often
>> uses the exact same character string for both the standard symbol and
>> one of the corresponding alternate setting symbols.  An obvious
>> example is P21212: this is the H-M standard symbol for SG #18 but is
>> also one of the 3 ITC setting symbols for P21212, the other two being
>> P22121 and P21221.  Perhaps the intention would have been clearer if
>> the ITC setting symbols had all been made different from the standard
>> symbol, as they are in the R32 case.  For example P21212a, P21212b and
>> P21212c would have been equally valid choices for t

Re: [ccp4bb] Space group R32 and H32

[Sebastiano Pasqualato]

> 
>> 
>> Ian Tickle wrote:
>>> 
>>> If we're all agreed that ITC(A) is taken as the authority on all
>>> matters of space group symbology (and I for one certainly agree that
>>> it should be), then SG symbol H32 (SG #145:
>>> http://img.chem.ucl.ac.uk/sgp/medium/145bz1.htm) has nothing to do
>>> with R32 (SG #155: http://img.chem.ucl.ac.uk/sgp/medium/155az1.htm)!
>>> According to the Hermann-Mauguin system of nomenclature H32 (more
>>> correctly written as H3_2 where the '_' indicates a subscripted screw
>>> axis) would be the hexagonal-centred (H) lattice setting of P32 (P3_2
>>> in H-M).  H32 as an alternate setting symbol for R32 is a very recent
>>> PDB invention which conflicts with the well-established H-M convention
>>> used throughout ITC.  The ITC symbols for the rhombohedral&  hexagonal
>>> 
>>> axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious
>>> extensions of the H-M symbols without introducing any conflict with
>>> the existing convention, as the PDB symbol does.  The confusion has
>>> arisen from the failure to distinguish the lattice type (the first
>>> letter of the symbol) from the symbol for the basis system of the
>>> setting (the final letter after the ':').
>>> 
>>> See http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_H3_H32.pdf for an
>>> excellent explanation of all this and of the confusion that arises
>>> when programmers ignore established conventions and 're-invent the
>>> wheel' (e.g. SCALEPACK apparently swaps the meaning of the PDB symbols
>>> R32&  H32 and uses R32 for PDB H32 and vice-versa!).
>>> 
>>> 
>>> Cheers
>>> 
>>> -- Ian
>>> 
>>> On 27 July 2012 21:09, Bernhard Rupp  wrote:
>>>> 
>>>> H32 indicates the hexagonal obverse setting (as you list) for a R
>>>> centered trigonal cell, which is 3x larger than the primitive R32 cell
>>>> indexed a=b=c, al=be=ga<>  90. Standard imho is the H32 setting, for which 
>>>> I
>>>> will probably get flamed.
>>>> The relation between H and R cells is depicted here:
>>>> 
>>>> http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm
>>>> 
>>>> This has been discussed and is explained in the ccp4 tutorials and doc
>>>> afaik, where you can find more detailed info.
>>>> 
>>>> For proper format in a journal, I would suggest to adhere to the format
>>>> given in the ITC (International tables for Crystallography), I.e. Bravais
>>>> Italic, subscripted screw symbols. Note that this is not the format you put
>>>> it into most programs - their docs help.
>>>> 
>>>> 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
>>>> 
>>>> -Original Message-
>>>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>>>> Theresa Hsu
>>>> Sent: Friday, July 27, 2012 12:54 PM
>>>> To: CCP4BB@JISCMAIL.AC.UK
>>>> Subject: [ccp4bb] Space group R32 and H32
>>>> 
>>>> Dear all
>>>> 
>>>> I have a confusion on the space group R32 and H32. For a cell parameter
>>>> of a = b not equal to c, alpha=beta, not equal to gamma, is it considered 
>>>> as
>>>> R32 or H32?
>>>> 
>>>> I tried searching the mail list archives but it does not help a beginner
>>>> crystallographer like me.
>>>> 
>>>> I also have another basic question. What is the correct way for writing
>>>> space groups? Is the Bravais lattice in italic and is there space after
>>>> that? Or it does not matter because both are used in literature?
>>>> 
>>>> Thank you.
>>> 
>>> 
>> 

-- 
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

please note the change in email address!
sebastiano.pasqual...@ieo.eu

Re: [ccp4bb] modeling thioester bond

[Sebastiano Pasqualato]

Thanks Manish.
With the help of Paul and using JLigand, which is nicely connected to coot in 
version 0.7-pre1, I managed to create the bond and have the correct library CIF 
file.

Still, I can't manage to "regularize" the bond and residues close to it. It 
looks like I have to go through refcmac via "structure idealisation".

Unlike in the case of "sphere refinement", when you have a density map, in my 
case I don't know how to "regularize" a zone which is comprised between two 
different chains.

Thanks for the tip,
ciao,
s


On Jul 26, 2012, at 2:19 PM, Manish Chandra Pathak wrote:

> 
> 
> Just defining LINK in your pdb file should work. Try this format.
> LINK NZ  LYS A 233 C4A PLP A 400 
> 
> 
> OR
> 
> You need a dictionary file to tell the COOT that the two residues are 
> 
> connected. If an instance already exist in PDB, then you can download 
> 
> the refmac dictionary from  http://xray.bmc.uu.se/hicup/
> Otherwise, use PRODRG Dundee server with coordinates of both 
> 
> residues (Cys-X) to create a new residue dictionary. 
> 
> all the best
> 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
> 
> 
> 
> 
>> 
>> From: Sebastiano Pasqualato 
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Sent: Wednesday, July 25, 2012 9:48 PM
>> Subject: [ccp4bb] modeling thioester bond
>> 
>> 
>> 
>> 
>> No answers yet from the COOTbb (yet), so I'm cross posting this to the 
>> ccp4bb.
>> Sorry for the double post.
>> 
>> 
>> 
>> 
>> 
>> 
>> Hi there,
>> I'd like to model a thioester bond, starting from protein A with an exposed 
>> Cys, and having juxtaposed the carboxyl group of a C-terminal residue of 
>> protein B.
>> 
>> 
>> The way I would like to proceed is by:
>> 
>> 
>> 1) telling coot that there's a bond between the S atom and the C atom of the 
>> two groups;
>> 2) regularize that zone in order to have something that makes chemical sense.
>> 
>> 
>> Could you advice me on how to proceed for the two steps?
>> That is, how do I tell coot that 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 OncologyIFOM-IEO Campusvia Adamello, 1620139 - Milano
>> Italy
>> 
>> tel +39 02 9437 5167
>> fax +39 02 9437 5990
>> 
>> please note the change in email address!sebastiano.pasqual...@ieo.eu
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 

-- 
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

please note the change in email address!
sebastiano.pasqual...@ieo.eu

[ccp4bb] modeling thioester bond

[Sebastiano Pasqualato]

No answers yet from the COOTbb (yet), so I'm cross posting this to the ccp4bb.
Sorry for the double post.



Hi there,
I'd like to model a thioester bond, starting from protein A with an exposed 
Cys, and having juxtaposed the carboxyl group of a C-terminal residue of 
protein B.

The way I would like to proceed is by:

1) telling coot that there's a bond between the S atom and the C atom of the 
two groups;
2) regularize that zone in order to have something that makes chemical sense.

Could you advice me on how to proceed for the two steps?
That is, how do I tell coot that 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 5990

please note the change in email address!
sebastiano.pasqual...@ieo.eu

[ccp4bb] advice on spectrometric instruments choice

[Sebastiano Pasqualato]

Dear all,
I'm looking for some advices on the choice of some spectroscopic equipment for 
our lab.

What we would like to have is the possibility of measuring Circular Dichroism 
spectra, and perform kinetic analysis in fluorescence, possibly also with a 
stopped-flow set up, for pre-steady state kinetics.

Would you reckon a single instrument would be capable of fulfilling these 
tasks, or would you rather advice the investment on two instruments?

Could you guys please give me suggestions on piece of instruments that you're 
happy (or unhappy) with?
I've been currently 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
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

please note the change in email address!
sebastiano.pasqual...@ieo.eu

[ccp4bb] selective protection of C-terminal carboxylate

[Sebastiano Pasqualato]

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 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] pymol question

[Sebastiano Pasqualato]

Hi all,

is there a way in Pymol to have a loop/tube representation of the protein 
backbone that would pass through the N-CA-C-N(+1)-CA(+1)-C(+1) atoms rather 
than CA-CA(+1) atoms?
I remember something like this (a loop vs turn representation) in Molscript or 
Ribbons, but can't find 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

[Sebastiano Pasqualato]

Dear Imre, dear Katya,
thanks a lot for the prompt and insightful replies.

@Imre: well, I don't think it is a matter of linker of lack of Met/presence of 
stop codon after GST.
We use the exact same linker in bacteria and that works just nice, while wrt to 
the Met, we have cases in which we have kept the original Met (gene starting 
from aa 1) or in which we didn't include it (N-term deletion mutants) and we 
experience the same problem.
I tend to second rather Katya's opinion that what we purify in massive amounts 
are indeed native GSH-binding proteins (I dind't think at that at all!).

@Katya: I will have a look at the paper you sent me. However, the trouble is 
that the high amount of GHS binding protein is lowering the amount of 
GST-fusion protein we manage to recover from beads. So even being able to 
purify it form native GSH-binding proteins will not be ideal.

I think I will carefully consider the option of expressing MBP-fusion proteins, 
and move away from GST, as you both suggest.

Thanks a zillion for the tips,
best,
Sebastiano

On Mar 16, 2012, at 2:40 PM, Imre Berger wrote:

> Dear Sebastiano -
> 
> I have actually no experience at all with GST in insect cells since I do not 
> use this tag (mainly because I do not like the dimerization propensity of 
> this tag and the glutathione elution step).
> 
> However, I do not think what you observe should be related to  insect 
> cells...but I have no data on my own for GST fusions in insect cells.
> 
> May I ask: Do you have a starting methionine in your construction AFTER the 
> GST (i.e. did you keep for example the native ATG start codon when you cloned 
> your gene?). And: Did you verify the reading frame (basically an huge excess 
> of GST would mean that there is no readthrough resp. a stop codon somewhere 
> close to the fusion tag, that is very unlikely.
> 
> Is there a long unstructured linker between GST and your protein resp. doyou 
> suspect there is a long unstructured region in the N-term of your proteins?
> 
> I am soprry that I can';t help you much, but as said, Idon;t like GST - I 
> used it as an undergaduate many years ago and totally disliked it (i had a 
> protein that dimerized and with the GST tag which also dimerized it became an 
> agregating mess), kept this aversion until now.
> 
> How about MBP? That's EXCELLENT.
> 

On Mar 16, 2012, at 2:13 PM, Katya Heldwein wrote:

> Dear Sebastiano,
> 
> what you see is not your cleaved GST tag but rather native insect 
> glutathione-binding proteins that are produced in relatively large amounts (a 
> few mgs per L). I am attaching a paper where recombinant GST-tagged proteins 
> were successfully separated from these pesky insect GlutBPs under specific 
> elution conditions. This has not worked for us, though. So, we simply do not 
> express GST-tagged proteins 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,
>> 
>> we have an accumulating series of GST-fusion proteins here that are all 
>> displaying the same behavior when expressed in Hi5 insect cells with the 
>> MultiBac system.
>> 
>> What we are experiencing is a massive production of free GST and only a 
>> limited amount of fusion protein.
>> 
>> Since the linker we have engineered between GST and our protein is the one 
>> that exists in the pGEX-6p vector series, with the preScission protease 
>> site, I was wondering if any of you had experience of this cleavage site 
>> being processed within these insect cells.
>> 
>> Thanks in advance for the help,
>> 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

[ccp4bb] GST-fusion protein production in insect cells

[Sebastiano Pasqualato]

Dear CCP4ers, Dr. Berger,

we have an accumulating series of GST-fusion proteins here that are all 
displaying the same behavior when expressed in Hi5 insect cells with the 
MultiBac system.

What we are experiencing is a massive production of free GST and only a limited 
amount of fusion protein.

Since the linker we have engineered between GST and our protein is the one that 
exists in the pGEX-6p vector series, with the preScission protease site, I was 
wondering if any of you had experience of this cleavage site being processed 
within these insect cells.

Thanks in advance for the help,
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

[Sebastiano Pasqualato]

Dear Wenhe,
have you looked at http://www.jalview.org/ ?
is this what you are looking for? http://www.jalview.org/examples/examples3.html
ciao,
Sebastiano

On Feb 3, 2012, at 6:32 AM, WENHE ZHONG wrote:

> Dear members,
> 
> Apologize for this off-topic question. I am looking for a protein sequence 
> alignment tool which is capable to generate a particular output file similar 
> to the attached format (please see the attached picture). I have been looking 
> at some popular programs but none of them can show the conserved amino acids 
> by colored blocks as shown 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 - Milano
Italy

tel +39 02 9437 5172
fax +39 02 9437 5990

Re: [ccp4bb] Crystallization robot and trypsin

[Sebastiano Pasqualato]

Hi Horacio,
we have a Cartesian Honeybee and perform trypsin-containing trials by setting 
up drops with a dedicated protein+trypsin tip, which we then wash extensively 
with water, 6 M guanidinium hydrochloride, then water, isopropanol and again 
water.
hth,
ciao,
Sebastiano

On Jan 24, 2012, at 1:12 PM, Horacio Botti wrote:

> Dear all
> 
> We may use a Honeybee 963 robot to screen crystallization conditions for 
> trypsin-containing protein samples and we are worried about robot 
> contamination by residual protease. 
> How do you normally clean robots when using this kind of sample? Your 
> suggestions/recommendations will be appreciated. Thks!!
> 
> Horacio Botti
> Unit of Protein Crystallography, 
> Institut Pasteur of Montevideo, Uruguay.
> 
> 
> PS: below you have an old short CCP4 discussion:
> [ccp4bb]: Crystallization robots and protease.
> 
> To: ccp...@dl.ac.uk
> Subject: [ccp4bb]: Crystallization robots and protease.
> From: Marc Graille 
> Date: Mon, 19 Dec 2005 13:21:36 +0100
> Sender: owner-ccp...@dlmail1.dl.ac.uk
> User-agent: Debian Thunderbird 1.0.2 (X11/20050602)
> ***  For details on how to be removed from this list visit the  ***
> ***  CCP4 home page http://www.ccp4.ac.uk ***
> 
> Dear all,
> 
> I have a question regarding the use of robotics to screen for crystallization 
> conditions for proteases.
> Does anyone have already used robots on proteases? If yes, have you 
> experienced any protease "contaminant" in the robot pipes, which could have 
> affected the results on other projects performed during the next few days ??
> I mean that we cannot exclude that a "contaminant" could digest the protein 
> we are working on and yield crystals of a fragment of the studied protein.
> 
> We are hesitating in using our crystallization robots on proteases as we are 
> afraid to have some contaminant in the pipes that will disturb all our future 
> experiments!!!
> Any advice about how to clean the robot syringes after use of proteases are 
> welcome!!!
> 
> 
> Regards,
> 
> Marc
> 
> --
> Marc Graille, PhD
> Equipe de Genomique Structurale
> Institut de Biochimie et de Biophysique Moleculaire et Cellulaire (IBBMC)
> CNRS UMR8619 Bat 430 Universite Paris Sud
> 91405 Orsay Cedex
> Tel: 0169155047
> 
> 
> ***  For details on how to be removed from this list visit the  ***
> ***  CCP4 home page http://www.ccp4.ac.uk ***
> 
> 
> 
> Dear Marc
> 
> We recommend cleaning dispensing tips with Hellmanex II from the German
> company Hellma.  It's for cleaning cuvettes.  You can buy it from VWR
> and others.
> 
> Hellmanex is a mildly alkaline solution with surfactants etc.  It has no
> enzymes in it, but you do need to flush with buffer to get rid of the
> alkali.
> 
> Previously, users reported that cleaning with methanol mixed with
> concentrated HCl worked very well in extreme cases.
> 
> Our robot, the Oryx, uses only one tip for protein.  This is
> semi-disposable.  Using one tip and touching off the drops has the great
> advantage that virtually no protein is wasted, and drops as low as 20 nl
> can be dispensed, even containing 50% glycerol!
> 
> We recommend that users keep tips that have been used for proteases
> separately, and clean them after use.  (The system comes with 8 tips and
> replacements cost 45 USD.)  Also 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, Berkshire, RG177HD, UK
> Directors: Peter Baldock, Patrick Shaw Stewart, James Smith
> http://douglas.co.uk or http://www.douglasinstruments.com
> Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
> 
> 


-- 
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 5172
fax +39 02 9437 5990

Re: [ccp4bb] Linux vs MacOS for crystallographic software

[Sebastiano Pasqualato]

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:
>> 
>> 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 - Consortium for Genomic Technologies
>> via Adamello, 16
>> 20139 - Milano
>> Italy
>> 
>> tel +39 02 9437 5172
>> fax +39 02 9437 5990
>> 
>> 
>> 
>> 
>> 
>> 
> 
> -- 
> 
> ***
> Dirk Kostrewa
> Gene Center Munich, A5.07
> Department of Biochemistry
> Ludwig-Maximilians-Universität München
> Feodor-Lynen-Str. 25
> D-81377 Munich
> Germany
> Phone:+49-89-2180-76845
> Fax:  +49-89-2180-76999
> E-mail:   kostr...@genzentrum.lmu.de
> WWW:  www.genzentrum.lmu.de
> ***


-- 
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

Re: [ccp4bb] Linux vs MacOS for crystallographic software

[Sebastiano Pasqualato]

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 - Consortium for Genomic Technologies
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5172
fax +39 02 9437 5990

Re: [ccp4bb] hkl2map on Mac OSX 10.6

[Sebastiano Pasqualato]

thanks Joachim.
thanks Luca,

the path hint was successful.

I have added the lines :

export SHELXPATH=~/xtal/shelx_intelmac
export PATH=$PATH:$SHELXPATH

to my .bashrc, rather than adding the aliases, and now hkl2map find the shelx 
executables.
(it does complain that I don't have xfit, 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:
>> 
>> 
>> 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 aliased in 
>> my .bashrc, and will run from the command line.
>> I also have downloaded and aliased the 'wish hkl2map-0.2-dist' command, that 
>> does open hkl2map windows.
>> 
>> However, when type hkl2map, I get this:
>> 
>> ...
>> 
>> 
>> Any ideas on how to solve the problem?
>> Thanks a lot in advance,
>> best,
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
> 
> -- 
> Joachim
> 
> Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
> Braunschweig | www.helmholtz-hzi.de
> 
> Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
> Bundesministerium für Bildung und Forschung
> Stellvertreter: MinDirig Heiko Gevers, Niedersächsisches Ministerium für 
> Wissenschaft und Kultur
> Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA
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-- 
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] Technician Position available in Milan

[Sebastiano Pasqualato]

Dear all,
a technical position is available to work in the Crystallography Unit of the 
IFOM-IEO-Campus in Milan.
(http://www.ifom-ieo-campus.it/joinus/detail_jobs.php?docuID=1566)

The position is available immediately, and will be granted until March 2012.
We are looking for a person who will be involved in the general management of 
the Unit's instrumentation, and who will take care of gathering samples from 
the Unit users, set up crystallization trials and perform biophysical 
experiments.
Hence, we look for a person capable of independently organizing her/his work 
and with a 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, 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

Re: [ccp4bb] ccp4 on Mac Intel

[Sebastiano Pasqualato]

Charles and Guillermo, thanks a zillion.
Shame on me, I could't find the scripts!
Well, it'll be good to have already v. 6.2 ...
ciao,
s




On May 3, 2011, at 11:26 AM, Charles Ballard wrote:

> Hi Sebastiano
> 
> you open an X11 windows, then source 
> /Applications/ccp4-6.2.0/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 
>> nicely in the Application folder, and I can get ccp4i working just by 
>> launching from the ccp4 icon.
>> However, I would also like to have the commands working from a X11 terminal, 
>> to get it working for, say xia2.
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
> 
> 
> -- 
> Scanned by iCritical.
> 
> 


-- 
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

Re: [ccp4bb] ccp4 on Mac Intel

[Sebastiano Pasqualato]

Hi Klaus,
that's pretty much the point.
With the .dmg install, there are no "setup" files coming.
I know I could use fink and Bill Scott's way to install the package, and have 
everything running, but was wondering if it would have been possible with the 
.dmg installation, much faster and intuitive.

I also have this suggestion from Louis Vanpraet (thank you)

Add the following line to the ".profile" file in your home folder

alias ccp4i='/Applications/ccp4-6.1.13/bin/./ccp4i'

Then you can launch it in any terminal window by executing "ccp4i"

but I was more looking in something like the source of the 'setup' files, so 
that I can have all the commands and not only ccp4i available from the X11 
prompt.
Thanks,
ciao,
s

On May 3, 2011, at 11:06 AM, Klaus Fütterer wrote:

> Dear Sebastiano,
> 
> locate the setup scripts (e.g. ccp4.setup, ccp4.setup-sh) on your system 
> (must be somewhere in the ccp4 directories),
> and source it in your .cshrc or .bshrc files (so that every time you open a 
> c-shell or bash, the necessary aliases are established).
> 
> For instance in my case the line in .cshrc (I"m using C-shell):
> source /sw/share/xtal/ccp4-6.0.2/include/ccp4.setup
> 
> Best,
> 
> Klaus
> 
> ===
> 
>Klaus Fütterer, Ph.D.
>Reader in Structural Biology
>  Undergraduate Admissions
> 
> School of Biosciences   P: +44-(0)-121-414 5895
> University of BirminghamF: +44-(0)-121-414 5925
> Edgbaston E: k.futte...@bham.ac.uk
> Birmingham, B15 2TT, UK   W: http://tinyurl.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 installed 
>> nicely in the Application folder, and I can get ccp4i working just by 
>> launching from the ccp4 icon.
>> However, I would also like to have the commands working from a X11 terminal, 
>> to get it working for, say xia2.
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
> 


-- 
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] ccp4 on Mac Intel

[Sebastiano Pasqualato]

Dear all,
I have installed ccp4 with the dmg package, and everything is installed nicely 
in the Application folder, and I can get ccp4i working just by launching from 
the ccp4 icon.
However, I would also like to have the commands working from a X11 terminal, to 
get it working for, say xia2.
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

[Sebastiano Pasqualato]

Dear all,
thanks for the wealth of replies.
I'll try to summarize and give some answers and clarification.
Here the original post:

Dear all,
I was wondering if somebody could help me out by suggesting the "best" column 
to be used in a Static Light Scattering (I guess it would be the same for a 
Multi Angle Light Scattering) instrument.
We were suggested using a silica-based column, with very high separation 
properties, but it seems that these columns are highly sensitive to (even 
slightly) basic pH's. Even running the column in PBS, it looks like injecting 
samples at pH 8.0 ruins the column resin, making it unusable.
On the other hand, GE Healthcare columns would require a huge amount of 
material to be loaded.
What are you guys using in your instruments? 
Thanks a lot in advance for the feedback,
best,
ciao
Sebastiano

Here's replies and comments:

Laurent Terradot wrote:

> Dea Sebastiano,
> I encountered a similar problem and lost one of these columns. (We use 
> Dawn-Treos/OptiReX in my lab with an akata purifier)
> I am now using GE superdex columns (S200 and S75) and load around 100ul of 
> protein at 10mg/ml. That' s a lot but I fractionate and recover it. The 
> results are good.
> 
> If money is not a problem, Wyatt make their own columns, which might be 
> better for you. I have heard good things about it.
> I 'll be happy to have info if you have some feed back later.
> Best regards,
> 
> Laurent


Well that's one of our problems. We are using a Viscotek SLS instrument on 
their own HPLC machine, and don't have a fractionation unit in line, since we 
thought we could be using analytical amounts, without recovering.
In this respect, 100 ul at 10 mg/ml are way to much.
However, protein amount can be much lower, it seems:

Nikos Pinotsis wrote:

> Hi Sebastiano,
> 
> we have used both silica based and superdex columns and we found the second 
> as a better option for general usage.
> Most of our proteins are on basic buffer and about 50% of them stick 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 prefer to have.
> 
> cheers
> Nikos


 Engin Özkan wrote:

> On 3/8/11 5:03 AM, Sebastiano Pasqualato wrote:
>> On the other hand, GE Healthcare columns would require a huge amount of 
>> material to be loaded.
>> 
> What do you mean by a huge amount of material? You would not be using a 16/60 
> column (125 ml column volume) for an analytical experiment. How about a 
> Superdex 10/300 (used to be called 10/30) or a 5/150 column. These have 
> column volumes at 25 ml and 3 ml, respectively, have great resolution, and 
> probably already compatible with your proteins and buffers.
> 
> We used to use HPLC columns, but some proteins would never elute from these 
> columns. Then we switched to good old Superdex 200 10/300, and it works like 
> a charm every time. We inject <100 ul material at concentrations around 1 
> mg/ml (depending on the molecular weight of the protein in question). The 
> only issue is we have to run these columns at 0.35 ml/min flow rates (instead 
> of the default 0.5 ml/min), since our HPLC has a lot of back pressure for 
> FPLC columns.
> 
> Best,
> Engin

Engin Özkan wrote:

> And as others have said shedding of dextran is a problem with GE columns 
> (this was confirmed to me by GE people), but after extensive system 
> equilibration, we do not see a problem significant enough to ever hurt our 
> light scattering measurements.


With respect to the choice of which GE Column to use, it looks there's a 
consensus for Superdex/Superose 10/300 columns. Some have suggested Superdex 
5/150 columns, which would allow much less material to be loaded (they have a 
diameter of ~5 mm, as the suggested silica column), but others have pointed out 
that the resolution power is way less than those of the 30 cm columns, and this 
is indeed our experience, too, and the reason we dropped those columns.

Sally Pham Thanh Van wrote:

> But I doubt if GE 5/150 column has the same resolution with
> the 10/30 one. When I had mixture of several species, the 10/30 always
> gave better resolution for me, and this is crucial in obtaining
> accurate information about oligomerization state and/or absolute
> molecular weight of the protein. So I think if choosing GE columns for
> light scattering experiment, I would go for 10/30.
> 
> Best wishes,
> Sally.

M T wrote:

> Dear Sebastiano,
> 
> In our case we don't have magical column... We are using small silica columns 
> from shodex or wyatt and for proteins that cannot be

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

[Sebastiano Pasqualato]

Dear all,
I was wondering if somebody could help me out by suggesting the "best" column 
to be used in a Static Light Scattering (I guess it would be the same for a 
Multi Angle Light Scattering) instrument.
We were suggested using a silica-based column, with very high separation 
properties, but it seems that these columns are highly sensitive to (even 
slightly) basic pH's. Even running the column in PBS, it looks like injecting 
samples at pH 8.0 ruins the column resin, making it unusable.
On the other hand, GE Healthcare columns would require a huge amount of 
material to 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
fax +39 02 9437 5990

[ccp4bb] hydrohyapatite column

[Sebastiano Pasqualato]

Hi all,
I read/heard that hydroxyapatite column can be used to purify proteins, getting 
separation results orthogonal to ion exchange and size exclusion chromatography.
I was wondering if any of you would be kind enough to share her/his experience 
with me, and would suggest vendors and models 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

[Sebastiano Pasqualato]

Hi all,
I have a crystallographical/biochemical problem, and maybe some of you guys can 
help me out.

We have recently crystallized a protein:protein complex, whose Kd has been 
measured being ca. 10 uM (both by fluorescence polarization and surface plasmon 
resonance).
Despite the 'decent' affinity, we couldn't purify an homogeneous complex in 
size exclusion chromatography, even mixing the protein at concentrations up to 
80-100 uM each.
We explained this behavior by assuming that extremely high Kon/Koff values 
combine to give this 10 uM affinity, and the high Koff value would account for 
the dissociation going on during size exclusion chromatography. We have partial 
evidence for this from the SPR curves, although we haven't actually measured 
the Kon/Koff values.

We eventually managed to solve the crystal structure of the complex by mixing 
the two proteins (we had to add an excess of one of them to get good 
diffraction data).
Once solved the structure (which makes perfect biological sense and has been 
validated), we get mean B factors for one of the component (the larger) much 
lower than those of the other component (the smaller one, which we had in 
excess). We're talking about 48 Å^2 vs. 75 Å^2.

I was wondering if anybody has had some similar cases, or has any hint on the 
possible relationship it might (or might not) exist between high a Koff value 
and high B factors (a relationship we are tempted to draw).

Thanks in advance,
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

[Sebastiano Pasqualato]

Mario,
beside what you were mentioning, I would definitely try a quick soak (10-30 
seconds) of the crystals in cryo conditions supplemented with halides such as 
NaBr, or NaI, at pretty high concentrations (say 0.5 M), then directly freezing 
without backsoak.
If the crystals survive the treatment, with that amount of mols per unit cells 
and surely some good NCS, you should be able to phase pretty easily.
Well, of course SeMet would be the other option...
ciao,
s

On Sep 30, 2010, at 1:54 PM, Mario Milani wrote:

> Dear all,
> i have a 30 kDa protein that crystallize so far in three different conditions 
> but with the same space group. It initially looks like tetragonal (I4, a=141, 
> b=141, c=208) and then results triclinic (P1, a=141, b=141 c=144, alpha=119, 
> beta=119, gamma=90), hosting about 24 mol. in the unit cell. Other data: self 
> rotation shows the presence of 4 peaks with chi=180; molecular replacement 
> shows the presence of a pseudo-translation peak; DLS made at protein 
> concentration close to crystal growth conditions shows a Rh compatible with 
> something like a tetramer with low polydispersity (about 15%). Do you have 
> any experience with similar ‘asymmetric’ associations? Do you have any 
> suggestions, beside the addition of ligands to the crystal growth conditions, 
> in order to get a ‘simpler’ crystallographic assembly? I have some models 
> (with sequence identity less than 25%) in order to try MR but 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
20139 - Milano
Italy

tel +39 02 9437 5094
fax +39 02 9437 5990

Re: [ccp4bb] Alignment software

[Sebastiano Pasqualato]

Thanks Roger,
that worked perfectly!
I'll try and have fun with aline now.
ciao,
s

On May 25, 2010, at 7:56 PM, Roger Dodd wrote:

> Hi there,
> 
> I just got this working a couple of days ago under Mac OS X 10.6.3. I 
> manually compiled and installed Perl-Tk from CPAN. Steps taken:
> 
> 1. Download and ungzip / untar: 
> http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-804.028_501.tar.gz (the 
> newer -503 version didn't work)
> 2. Change into the directory
> 3. Execute perl Makefile.PL
> 4. make
> 5. make test
> 6. sudo make install
> 
> 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 MacBook Pro (Mac OS X 10.6.3).
> With respect to the instruction I found on the website, I had to change the 
> export lines to be added to the .bashrc in order not to get error messages.
> That's how I added the path info:
> 
> export ALINEHOME='/sw64/share/xtal/aline_011208'
> export PATH=$PATH:$ALINEHOME/bin
> 
> however, I still get an error while trying to run aline:
> 
> s...@host005:~> aline
> Can't locate Tk.pm in @INC (@INC contains: /sw64/lib/perl5 
> /sw64/lib/perl5/darwin /Library/Perl/Updates/5.10.0 
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level 
> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level 
> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level 
> /Network/Library/Perl/5.10.0 /Network/Library/Perl 
> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level 
> /System/Library/Perl/Extras/5.10.0 .) at 
> /sw64/share/xtal/aline_011208/bin/aline line 37.
> BEGIN failed--compilation aborted at /sw64/share/xtal/aline_011208/bin/aline 
> line 37.
> s...@host005:~>
> 
> I even tried with the
> 
> perl -MCPAN -e 'install Tk'
> 
> command, as suggested by the website, but nothing changed.
> 
> Any idea of what's wrong here?
> Thanks a lot for the tips,
> ciao
> s
> 
> On May 25, 2010, at 5:47 AM, Charlie Bond wrote:
> 
> > Hi Victor,
> > Thanks for recommending ALINE.
> >
> > It is not exactly true that development has stopped. It is just glacially 
> > slow as funding for such utilities is not easily obtained!
> >
> > Recommendations for improvements (to improve that potential) are 
> > well-received and a keen user can write their own plug-ins to achieve new 
> > functionality.
> >
> > Cheers,
> > Charlie
> >
> > Victor Alves wrote:
> >> Hi Mohd
> >> You can also check: ALINE (An Extensible WYSIWYG Protein Sequence 
> >> Alignment Editor for Publication Quality Figures)
> >> http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/
> >> It’s quite nice and has a lot of potential, although unfortunately it 
> >> seems that development of the software as stopped  :-(
> >> Cheers
> >> Victor Alves
> >>   *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of 
> >> *Salameh, Mohd A., Ph.D.
> >> *Sent:* sexta-feira, 21 de Maio de 2010 16:11
> >> *To:* CCP4BB@JISCMAIL.AC.UK
> >> *Subject:* [ccp4bb] Alignment software
> >> Dear All,
> >> I’m trying to prepare an alignment figure of 2 proteins that highlight 
> >> conserved and similar residues and probably secondary structures; I will 
> >> 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
> > Crawley WA 6009
> > Australia
> > charles.b...@uwa.edu.au
> > +61 8 6488 4406
> 
> 
> --
> 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
> 
> 
> 
> -- 
> Roger B. Dodd, PhD.
> Cambridge Institute for Medical Research
> Wellcome Trust/MRC Building
> Hills Road
> Cambridge
> CB2 0XY
> UK


-- 
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] Alignment software

[Sebastiano Pasqualato]

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 MacBook Pro (Mac OS X 10.6.3).
With respect to the instruction I found on the website, I had to change the 
export lines to be added to the .bashrc in order not to get error messages.
That's how I added the path info:

export ALINEHOME='/sw64/share/xtal/aline_011208'
export PATH=$PATH:$ALINEHOME/bin

however, I still get an error while trying to run aline:

s...@host005:~> aline
Can't locate Tk.pm in @INC (@INC contains: /sw64/lib/perl5 
/sw64/lib/perl5/darwin /Library/Perl/Updates/5.10.0 
/System/Library/Perl/5.10.0/darwin-thread-multi-2level 
/System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level 
/Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level 
/Network/Library/Perl/5.10.0 /Network/Library/Perl 
/System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level 
/System/Library/Perl/Extras/5.10.0 .) at 
/sw64/share/xtal/aline_011208/bin/aline line 37.
BEGIN failed--compilation aborted at /sw64/share/xtal/aline_011208/bin/aline 
line 37.
s...@host005:~>

I even tried with the 

perl -MCPAN -e 'install Tk'

command, as suggested by the website, but nothing changed.

Any idea of what's wrong here?
Thanks a lot for the tips,
ciao
s

On May 25, 2010, at 5:47 AM, Charlie Bond wrote:

> Hi Victor,
> Thanks for recommending ALINE.
> 
> It is not exactly true that development has stopped. It is just glacially 
> slow as funding for such utilities is not easily obtained!
> 
> Recommendations for improvements (to improve that potential) are 
> well-received and a keen user can write their own plug-ins to achieve new 
> functionality.
> 
> Cheers,
> Charlie
> 
> Victor Alves wrote:
>> Hi Mohd
>> You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment 
>> Editor for Publication Quality Figures)
>> http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/
>> It’s quite nice and has a lot of potential, although unfortunately it seems 
>> that development of the software as stopped  :-(
>> Cheers
>> Victor Alves
>>   *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of 
>> *Salameh, Mohd A., Ph.D.
>> *Sent:* sexta-feira, 21 de Maio de 2010 16:11
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] Alignment software
>> Dear All,
>> I’m trying to prepare an alignment figure of 2 proteins that highlight 
>> conserved and similar residues and probably secondary structures; I will 
>> 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
> Crawley WA 6009
> Australia
> charles.b...@uwa.edu.au
> +61 8 6488 4406


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

[Sebastiano Pasqualato]

Posted on behalf of Prof. Francesco Blasi, who might be directly  
contacted if interested

(check http://www.ifom-ieo-campus.it/research/blasi.php for contacts)

Post doctoral position available from January 2010.

Laboratory: Prof. Francesco Blasi, IFOM (Foundation FIRC Institute of  
Molecular Oncology), at the IFOM-IEO Campus, Milano, Italy. http://www.ifom-ieo-campus.it/


Project. Crystallization and structural analysis of the Prep1-Pbx1-DNA  
complex.


	Prep1 and Pbx1 are homeodomain proteins that interact to bind DNA and  
affect developmental processes by regulating the expression of Hox  
genes. Biochemical analysis has established the presence of N-terminal  
regions in both proteins required for the interaction. On the other  
hand at the C-termini of both proteins contain the homeodomain that is  
the actual DNA-binding region.
	The interest in solving the structure of the Prep1-Pbx1-DNA complex,  
in addition, lies in the novelty of the domains involved for which no  
X-ray structure is available. Moreover, since both Prep1 and Pbx1  
belong to a family of proteins, the involved domains are conserved in  
the other members and therefore modeling will allow to re-construct a  
series of structures, with potential impact also in terms of drug  
targets.


State of advancement of the project. The project will capitalize on  
previous work in which a large number of constructs and vectors has  
been analyzed, as well as several purification procedures. We are now  
at a stage in which several different constructs expressing at high  
level soluble protein complexes have been produced and reliable  
purification procedures have been established. The work to be done  
will be to search for suitable crystallization procedures and to solve  
the X-ray 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 Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5094

[ccp4bb] heavy atom derivative choice

[Sebastiano Pasqualato]

Hi all,
I've got crystals of a protein of ca 200 residues, with 2 free  
cysteines, 5 histidines, 2 methionines.
We have nice diffraction for the native crystals, that grow in 150 mM  
KSCN, 17% PEG 3350, bis tris propane pH 8.8.
We are crystallising the SeMet derivative, but I'm not completely sure  
I will be able to have nice crystals by saturday, when we have tunable  
time at the ESRF.
I was thinking of trying with some heavy atom soaks, but only have  
like 30 crystals, so limited trials allowed!
Which compound would you advice as more likely to work, and thus worth  
testing?

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

[Sebastiano Pasqualato]

Dear all,
sorry for the off-topic question.
We would to start using fluorescence polarization anisotropy to study  
protein-protein interaction.
We'd like to gather information about the experimental setup, in  
particular:
1. best  fluorescent dye according to the molecular weights of 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
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5094

[ccp4bb] error in ccp4i

[Sebastiano Pasqualato]

hi there,
I'm using ccp4 installed via fink on my macbook pro, and suddenly the  
program complains that it cannot connect to the database server and  
won't let me run a combat job with the following error:


Using CCP4 programs from /sw/share/xtal/ccp4-6.1.1/bin
CCP4i failed to connect to database server after 1 attempt(s)
Accessing the project database directly for this session
ERROR opening socket connection in NotifyDatabase:
Arguments: 159 hect UpdateStatus RUNNING -pid 916
SERVER_HOST: localhost
SERVER_PORT: 4441
Error  : "couldn't open socket: host is unreachable"
ERROR opening socket connection in NotifyDatabase:
Arguments: 159 hect UpdateStatus FINISHED
SERVER_HOST: localhost
SERVER_PORT: 4441
Error  : "couldn't open socket: host is unreachable"

Any clue?
thanks a lot,
ciao
s

PS: I'm right now at the ESRF, is there a 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

[Sebastiano Pasqualato]

Hi Darren,
much much "easier" than VectorNTI is ApE (http://www.biology.utah.edu/jorgensen/wayned/ape/ 
), which is multi-platform and very easy to use for simple tasks.

Please, could you post a summary of the answers?
Thanks,
ciao
Sebastiano



On Jan 28, 2009, at 9:47 AM, Darren Hart wrote:


Hello,
After several years of offering the molecular biology software  
VectorNTI
free to the academic community (their "open access program") and  
building
up a huge user base, Invitrogen have suddenly announced that they  
will no

longer renew these free licences and the existing ones will be left to
expire within the year. There are heavy renewal fees for anyone  
wishing to

continue use of this software.

Can anyone recommend decent alternative PC compatible alternatives?  
Main

uses are construct and primer design, plus simple quick alignments,
sequence data analysis etc. The database structure for storing  
sequences

was pretty useful also.

Ideally free, otherwise reasonably priced. I've seen CLCbio and  
Geneious

have products, both free and paid. Any experience?

Thanks,
Darren
EMBL Grenoble

ps anyone using VNTI might consider a backup of their 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
20139 - Milano
Italy

tel +39 02 9437 5094

[ccp4bb] hydrophobic surface representation

[Sebastiano Pasqualato]

Hi all,
I'd love to have a surface representation of my structure in which I
plot the hydrophobic exposed residues.
A bit like an electrostatic potential plotted onto the surface, but
rather than hydrophilic, an hydrophobic one.
Is there a nice web server or a program that does that or you 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?

[Sebastiano Pasqualato]

Dear all,
thanks a lot for the many replies suggesting me what to put in my
"misterious" density.
Molecules that have been suggested are: acetate, Mg ion with waters,
bicarbonate or nitrate, sulphate, borate, glycerol, tris, alternative
conformation of the Arg side chain, waters.
I have to say that, as you've noticed, the resolution is only 2.6, so
it'll be hard to conclude something beyond reasonable doubts.
What I'm doing is, as Roger Rowlett and David Borhani suggested,
calculating the maps by omitting the waters, and deciding upon the
shape of the density I see there, trying than to fit different molecules.

In doubt, it'd seem reasonable to me to place one of the molecule of
the crystallization conditions. At the moment, it seems that glycerol
could fit nicely.

I also have to apologize for the large attachment. I'm sorry I didn't
notice 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 Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5094
fax +39 02 574 303 310

Re: [ccp4bb] pointless and HKL2000

[Sebastiano Pasqualato]

just use the "no merge original index" command, which you can add
during scaling using a macro. Just type "no merge original index" in
the macro field during scaling.
Then you'll have to import unmerged data to an mtz file using combat,
if I remember correctly.
hth,
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 ? 

> Thanks,

> Simon


>   


-- 
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] chain IDs and residue numbering in depositing chimeras PDB

[Sebastiano Pasqualato]

Dear all,
I'm going to deposit to the PDB a structure in which a polypetidic chain 
is made up by the fusion of two portions of proteins.
That is, it is a chimera of two proteins (say aa 1-100 of protein X 
fused to aa 50-150 of protein Y)
Currently, this polypetidic chain has got a single chain ID and I've 
kept residue numbers growing without caring about the original residue 
numbers of the second protein (i.e. the chain A goes from residue 1 to 
100, then 101 to 201 correspond to residues 50-150 of protein Y)


Now, I've always found it nice to have the correct numbering on the 
residues, when I download a pdb, and was wondering if any of you could 
suggest me a way to have this in my structure.
I wouldn't like to change the chain ID, a) beacuse what's crystallized 
was a single polypeptidic chain b) because many programs will not put a 
link between residues with different chain IDs
A solution would be adding something like "1000" to the numbers of the 
residues of the second protein, but then again the residues numbers will 
jump from 100 to 1050 and there will be no link created by some programs 
(isn't it?)...


How could I do? Any 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

[Sebastiano Pasqualato]

Hi there!
here's my original post:


Hi all,
I'm starting using pymol to generate movies to show my structure.
While its seems fairly easy to generate simple movies with rocking 
or rotating molecules, I have been finding some difficulties 
understanding how to generate more complex movies.
For instance, I'd love to generate a movie in which the molecule 
rotate along the x axis, then along the y axis, while the surface 
slowly shows up... or even more complicated scenarios, involving 
changes in colors of the objects (of course not sudden ones!)...
Does anybody have some scripts to share with me, or can point me to 
some web pages that would explain me how to do that?

Thanks a lot in advance,
best,
Sebastiano


I received several answers
- script examples (thanks Tassos, Enrico), suggestions on how to use 
POVray (thanks Jens).
- Eugene Wu and Fabrizio Villa pointed out this website 
(<http://davapc1.bioch.dundee.ac.uk/teach/pymol/index.htm>http://davapc1.bioch.dundee.ac.uk/teach/pymol/index.htm)

- Roger Rowlett suggested SLERPY (www.pymolwiki.org)

But I finally installed and are now using successfully the very nice 
eMovie indicated by Roberto Steiner 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 9437 5094
fax +39 02 574 303 310



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11:53 AM

[ccp4bb] pymol movies scripts

[Sebastiano Pasqualato]

Hi all,
I'm starting using pymol to generate movies to show my structure.
While its seems fairly easy to generate simple movies with rocking or 
rotating molecules, I have been finding some difficulties 
understanding how to generate more complex movies.
For instance, I'd love to generate a movie in which the molecule 
rotate along the x axis, then along the y axis, while the surface 
slowly shows up... or even more complicated scenarios, involving 
changes in colors of the objects (of course not sudden ones!)...
Does anybody have some scripts to share with me, or can point me to 
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



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1:29 PM

[ccp4bb] apbs parse error

[Sebastiano Pasqualato]

Hi all,
despite using the latest version of pdb2pqr 
(http://agave.wustl.edu/pdb2pqr/server.html) and having downloaded 
the latest version of the apbs plugin for pymol, I still do not 
manage having it work with all the pdbs, most of the time getting an 
error while using the apbs plugin inparsing the pqr file:


Valist_readPQR:  Error parsing atom 2235!
Error reading molecules!

Interestingly, while a pdb works, if you just move it to another 
place (e.g by superposing it to another structure) and then 
recalculate the pqr file, this time the new pqr will give the parsing error!


Does 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
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



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[ccp4bb] SUMMARY: questions about hydrophobic core

[Sebastiano Pasqualato]

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 googling 
around revealed that such a program might not exist.

So it seems I have to define my hydrophobic core residues by hand...
So now my question would be: how to define the hydrophobic core residues?
I would tend to say that those that bury more than ## % (say 70%, 
80% ??) of their otherwise solvent accessible surface area could be 
defined as such, but how can I get such a per residue percentage? 
(NB: this is not the asa buried upon interaction, so I don't know 
how to get the asa of the "free" amino acid)
Alternatively, are there other simple and defined rules to state 
which are the hydrophobic core residues?

Any help appreciated,
thanks in advance,
ciao
s


I received several answers, and wish to thank all of those who took 
their time to help me out on this issue.
I finally used naccess, which is very nice and gives you a percentage 
of buried accessible surface area with respect to the asa of the 
amino acid in an extended conformation (calculated in an Ala-X-Ala peptide).
I found that a nice definition of the hydrophobic core amino acid 
corresponds to those that bury more than 90% of their asa.

Here's a quick summary of the most relevant replies.
thanks again,
ciao
s



[EMAIL PROTECTED]:
>free amino acid: ASA gly/ala-X-gly/ala, and program: naccess. mind you
>residues close to surface residues mihgt easily have 70% buried... i would
>be more conservative. check first with 95%.
>
>hth,
>tommi


mmerckel <[EMAIL PROTECTED]>:
>Hi Sebastiano,
>
>You might try NACCESS for obtaining atom and residue exposed surface areas.
>It returns absolute area and percent area relative to that residue in the
>middle position of a tripeptide. You should also look at Merk Gerstein's
>CODE_MBG programs for some information on buried residue calculations.
>Also look for DPX, residue depth calculation, there is a server and
>free standing C code.
>
>I also have an old reference to hydrophobic core calculations,
>perhaps PEDS or Protein Science, but I haven't (re)found it yet.
>Someone also sent me code for this, if I can find it I'll forward.

Liz Potterton <[EMAIL PROTECTED]>:
>Sebastiano,
>
>I can suggests one approach to finding core residues..
>
>CCP4mg will calculate the total asa buried per residue and residues can be
>selected by the criteria of their buried area.  One way to define 
the protein

>core would be to select residues with, say,  <5.0A*2 asa. You can easily see
>what has been selected in the molecular graphics and try varying 
the criteria

>if necessary.
>If you need to do this for many structures we could write a script.
>
>Liz

"Judith Murray-Rust" <[EMAIL PROTECTED]>:
>Sebastiano
>
>Naccess will calculate acessibility relative to the same residue in an
>extended peptide, which sounds  pretty much what you want. It's not very
>automatic, however. YOu have to install it
>http://wolf.bms.umist.ac.uk/naccess/
>
>and either human-read or parse the output.
>
>J

"Nadir T. Mrabet" <[EMAIL PROTECTED]>:
>Hi,
>
>There exists a formal analytical way in doing this using the 
"survol" command in BRUGEL package.
>In short, this command define the accessible surface (external and 
cavities) to the probe you choose and creates

>separate masks (ensembles) of all atoms/residues that define these surfaces.
>The way to go, then, would be to create a collection mask of all 
accessible atoms/residues and subtract this
>from your protein mask to be left with the mask that contains the 
core residues.
>You could also use a cutoff of 5-10% ASA max (there are different 
ways of calculating these !).
>On the other hand, taking away even residues that display very 
little ASA (< 5%) would certainly leave you with

>genuine core residues.
>Hope this helps.
>
>Greetings,
>
>Pr. Nadir T. Mrabet

"Shabir Najmudin" <[EMAIL PROTECTED]>:
>Dear Sebastian,
 >
>Have you looked at Simon Hubbard's NACCESS program? I think this is 
what yo uare looking for. It does analysis per aa residue if you want.

>
>People at UCL-Biochemistry department - particularly Chrisitne 
Orengo and Janet Thornton's group have done a vast amount analyses on 
protein structures and have a lot of analysis >tools on their website.

>
>Hope this helps
>
>Cheers
>
>Shabir

Juergen Bosch <[EMAIL PROTECTED]>:
>Hi Sebastiano,
>
>you can misuse the Maestro suite from Schroedinger to define your 
hydrophobic core. But I guess it would be an overkill to explain this 
here. You have to fool the >program by indicating a faked ligand in 
the region which you are looking for the core, then when you define 
the constraints you can click on the hydrophobic >constraints tab and 
it will show you the regions it things are hydrophobic in the closer 
region where your faked 

[ccp4bb] questions about hydrophobic core

[Sebastiano Pasqualato]

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 googling 
around revealed that such a program might not exist.

So it seems I have to define my hydrophobic core residues by hand...
So now my question would be: how to define the hydrophobic core residues?
I would tend to say that those that bury more than ## % (say 70%, 80% 
??) of their otherwise solvent accessible surface area could be 
defined as such, but how can I get such a per residue percentage? 
(NB: this is not the asa buried upon interaction, so I don't know how 
to get the asa of the "free" amino acid)
Alternatively, are there other simple and defined rules to state 
which are the hydrophobic core residues?

Any help appreciated,
thanks in 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



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[ccp4bb] automatic hydrophobic core (buried residues) determination

[Sebastiano Pasqualato]

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 Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 Milano
Italy

tel +39 02 9437 5094
fax +39 02 574 303 310



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Re: [ccp4bb] heavy metal labelled GTP derivatives

[Sebastiano Pasqualato]

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 derivatives
and if so where to get them?
thanks
Stephen

--

**
Dr. Stephen Cusack,
Head of Grenoble Outstation of EMBL
Group leader in structural biology of protein-RNA complexes and viral proteins
Joint appointment in EMBL Gene Expression Programme
**

Email:  [EMAIL PROTECTED]
Website: http://www.embl-grenoble.fr
Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 
7306
Fax:(33) 4 76 20 7786 or (33) 4 76 20 
7199

Postal address:   EMBL c/o ILL, BP181, 38042 Grenoble Cedex 9, France
Delivery address: EMBL c/o ILL, Polygone 
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**



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

[Sebastiano Pasqualato]

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.
The option of changing the "principal component" into a virus does 
not seems to work (at least with version 0.97.686).

Thanks again,
cheers
Sebastiano


At 08:30 AM 2/21/2007 -0600, you wrote:


hello Sebastiano-
depending on what version of HKL2000 you are using this could be a 
problem due to a bug. one of the older versions wouldn't default out 
of the scalepack and use one of the larger versions. if this is the 
case, you can just run it from the command line. you have a 
scale.in(scl.in) in your processing directory. just type:


scalepack8m < scale.in > scale.log &

or use

scalepack16m
these are for 8 (or 16) million.

Lastly, if you are doing global refinement, this could also cause 
the process died prompt. if this is the case. just turn it off.


hope this helps-
todd

[ccp4bb] HKL2000 with more that 2 million observations

[Sebastiano Pasqualato]

Hi there,
does anyone know how to use HKL2000 with more than 2 million 
observations (that would be the "scalepackbig" version of scalepack)?
At the moment, the scaling ends with "process died" when it reaches 
the 200th observation read from the .x files.

thanks in 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

[Sebastiano Pasqualato]

Hi all,
I'm looking for some advices on some "general hints" on how to carry 
out a MAD/SAD data collection.
We had SeMet crystals that diffracted to ca. 3.5 Angs, with anomalous 
signal only at ca. 5-5.5 Angs, with diffraction decaying on brilliant 
beamlines (ID29 or ID23 at the ESRF) in a matter of ca. 300 
degrees... Needless to say, that was not sufficient to solve the structure...
We do have improved the crystals that look now nicer and bigger, and 
have some beamtime next weeks both at BM16 and ID29 at the ESRF.
Assumed that we do see diffraction higher that 3 Angs, what would 
people suggest?
Collecting first at the high energy remote for a SAD experiment and 
then going for peak and inflection point, or rather going for the 
peak first, then remote and ip?
I personally would avoid the continuous switch of wavelengths, but I 
know there are some fans of this technique, 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