Re: [ccp4bb] replacing B-factor column and color accordingly

Hi Yahui, There are definitely some old python scripts floating around online to help with this sort of thing. pdb-tools · PyPI GitHub - harmslab/pdbtools: A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

Re: [ccp4bb] Tools for identifying possible contaminants

I think this may do the contaminant search you are looking for. ContaMiner (kaust.edu.sa) Best, Mike On Wed, Jul 3, 2024 at 12:04 PM Kyle Gregory < 3632

[ccp4bb] Post-doc/staff openings: AAV structure, cell entry & gene therapy

emch...@missouri.edu<mailto:biochemch...@missouri.edu>). Michael S. Chapman, Ph.D. Wurdack Professor<https://cafnr.missouri.edu/person/michael-chapman/> & Chair, Dept. Biochemistry<https://biochem.missouri.edu/>; University of Missouri | Dept. Biochemistry | 503 S. College

Re: [ccp4bb] nearestcell

Hi Kay, http://flops.arcib.org:8084/sauc-1.1.1/ similar to the nearest-cell server, which seems to change its link and is harder to find (or stale link) https://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi HTH, Mike On Wed, Dec 27, 2023 at 1:39 PM Kay Diederichs < kay.diederi...@uni-konsta

Re: [ccp4bb] Problem with ligand identification

Hi Rafal, Did you try oxalic acid? The density being close to His, and with the shape, give it a try! Good luck! Pradeep Pallan From: CCP4 bulletin board on behalf of Rafal Dolot Sent: Wednesday, November 15, 202

Re: [ccp4bb] To Trim or Not to To Trim

-- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsic

[ccp4bb] Workshop on Crystallographic Fragment Screening, March 01-03, 2023

Zoom. If you are interested to listen in, please check out the webpage and register for the stream: hz-b.de/inext Please note, that there is a limited number of available spots in the Zoom session. Tatjana, Jan, Manfred -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2023

: - Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A) - Photon flux: 1.8x10¹¹ Phot/sec x 100 mA at sample position (0.04-1 sec exposure time per frame) - PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max. distance from the sample - Microdiffractometer (MD2) with Mini-kappa

Re: [ccp4bb] binding pockets...

Have you tried P2Rank? It is quite fast, and there is a standalone version that has command line options to run against all coordinate files in a directory using batch mode. https://prankweb.cz/ https://prankweb.cz/about https://github.com/rdk/p2rank You can try the web version to see how it per

[ccp4bb] Copying NCS chain to heteroligomer

protein). Unfortunately, we did not find a way to do that in Coot. Is there any option for this? Thanks a lot in advance, Alessandro -- * * Alessandro S. Nascimento * * Associate Professor

Re: [ccp4bb] outliers

finition of what an outlier is, does not really make sense to me. Best, Manfred Am 09.11.2022 um 09:17 schrieb Dale Tronrud: And now it is time for an "old man story". Back in the early 1990's the Brookhaven PDB started to worry about "validating" the models being deposi

[ccp4bb] Ph.D. position at HZB/BESSY II in Berlin

: https://recruitingapp-5181.de.umantis.com/Vacancies/1860/Description/2?lang=eng -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2022

(wavelength: 0.775-2.25 A) - Photon flux: 1.8x10¹¹ Phot/sec x 100 mA at sample position (0.04-1 sec exposure time per frame) - PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max. distance from the sample - Microdiffractometer (MD2) with Mini-kappa goniometer - Automatic sample

[ccp4bb] Deadline extended, NOW July 25, 2022; Helmholtz Workshop on Integrative Structural Biology

tte and Manfred -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Germany Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Herman

[ccp4bb] Helmholtz Workshop on Integrative Structural Biology

tte and Manfred -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Germany Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmhol

Re: [ccp4bb] Sad demise of Prof. M. Vijayan, MBU, IISc, India

Dear Colleague, My condolences. He was a very generous person and a great scientist. Sincerely, Sukrit Srivastava -- IFFR On Sun, 24 Apr 2022 at 13:38, ASHISH ANILRAO DESHMUKH < 79fffa49db31-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear All, > > With profound sorrow, we are sad to inform th

[ccp4bb] Job opportunity in Berlin - HZB and Humboldt University advertise a postdoc position

. The successful candidate will also be involved in the operation of the BESSY II bio-macromolecular crystallography beamlines (headed by Dr. Manfred S. Weiss) including supporting external users at the beamlines and will take part in graduate student education. Initially, a contract lasting until 31.12

[ccp4bb] REFMAC5 refinement: nucleic acid residues with bad geometry

REFMAC5 refinement: nucleic acid residues with bad geometry Hi All, I am in the final refinement stage of an X-ray structure of a protein-DNA complex, 2.3 A resolution, using Refmac5 (REFMAC 5.8.0267, CCP4Interface 7.1.018, Linux platform). I am confident about the space group, refinement steps,

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2022

to include them if available. Experimental setup: BL14.1: - Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A) - Photon flux: 1.8x10¹¹ Phot/sec x 100 mA at sample position (0.04-1 sec exposure time per frame) - PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max

[ccp4bb] Different conformation of chains

Dear All, I am working with a protein, the structure of which is already published in the PDB (2 chains in asu) The published structure has a break of around 20 residues. I have crystallized the same protein and saw some density near the gap (20 residues break). I could build 3-4 residues in Chai

Re: [ccp4bb] software DS, fconv still available ? contact?

nditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Germany Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitg

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2021

include them if available. Experimental setup: BL14.1: - Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A) - Photon flux: 1.8x10¹¹ Phot/sec x 100 mA at sample position (0.04-1 sec exposure time per frame) - PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max. distance

Re: [ccp4bb] Should Rmerge be reported?

___ From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of Manfred S. Weiss <mailto:manfred.we...@helmholtz-berlin.de> Sent: 10 June 2021 13:30 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb]

Re: [ccp4bb] Should Rmerge be reported?

/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwiigtb19uHwAhWS3YUKHSB1AdkQFjABegQIAxAD&url=https%3A%2F%2Fwww.nature.com%2Fdocuments%2Fnr-tables-xray.doc&usg=AOvVaw1RbfYvNeiEM07FBEOohMig>) and even IUCr Journals (https://journals.iucr.org/f/services/structuralc

Re: [ccp4bb] Analysis of NMR ensembles

Hi Harry, The superpose/overlay of all the structures in PyMol should inform you the rigid part of the protein as well as the flexible part. The rigid part would have very low backbone RMSD or overlay tightly and the flexible part (loops, N-term and C-term etc.) would not superpose tightly. If y

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

benefits-of-covid-19-lockdowns/?sh=2f2e73046f63 A few companies tried to sell pandemic insurance prior to 2019, but no one thought it was worth the cost. https://www.insurancejournal.com/news/national/2020/04/03/563224.htm Sorry to reduce the S/N ratio on CCP4BB - I blame pandemic fatigue. Best, Mike

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2021

¹¹ Phot/sec x 100 mA at sample position (0.04-1 sec exposure time per frame) - PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max. distance from the sample - Microdiffractometer (MD2) with Mini-kappa goniometer - Automatic sample changer (CATS), 90 sample storage capacity

[ccp4bb] Position available: Protein biochemist at Civetta Therapeutics

https://careers-civetta.icims.com/jobs/1395/job Overview Civetta Therapeutics (Cambridge, MA) is recruiting a Scientist to Senior Scientist level position in Protein Sciences. Civetta is a cutting-edge biotechnology company, backed by Deerfield Management, and recently launched from the Broad Ins

Re: [ccp4bb] when does non-isomorphism become a habit?

in/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- Dr. Manfred S. Weiss Macr

[ccp4bb] Fwd: Call for MX beamtime proposals at HZB, BESSY II, deadline extended to September 06, 2020

per frame) - PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max. distance from the sample - Microdiffractometer (MD2) with Mini-kappa goniometer - Automatic sample changer (CATS), 90 sample storage capacity (SPINE-Pin & EMBL sample magazine compatibility) IMPORTANT: this

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2020

) - PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max. distance from the sample - Microdiffractometer (MD2) with Mini-kappa goniometer - Automatic sample changer (CATS), 90 sample storage capacity (SPINE-Pin & EMBL sample magazine compatibility) IMPORTANT: this wil

Re: [ccp4bb] protein oligomer

Keep the protein concentration low during purification steps along with using other anti-aggregation agent/s. Make sure that the pH at which you are purifying is not close to the pI of the protein. Until completely purified, all purification steps should be performed in a cold room if it is a

[ccp4bb] Molecular replacement problem

DELTA -3.5403 #RMSD 2.08 #VRMS 0.89 With LLG = 994 and TFZ = 20.1, isn't this a real solution? Robert S. Phillips Professor of Chemistry and of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602 Phone: (706) 542-1996 Fax: (706) 542-9454 E-mail: rsphill...@chem.uga.edu W

[ccp4bb] CCP4 7.1 problems

error with args ("memoization" "In file ~S, line ~S: ~A ~S." ("/home/rob/CCP4/cc p4-7.1/share/guile/1.8/ice-9/boot-9.scm" 103 "Bad define placement" (define (syntax) (error "syntax error in eval-case"))) #f) I upgraded the system to Ubuntu 20.0

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2020

from previous research activities. Please make sure to include them if available. Experimental setup: BL14.1: - Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A) - Photon flux: 1.8x10¹¹ Phot/sec x 100 mA at sample position (0.04-1 sec exposure time per frame) - PILATUS3 S 6M detector with

[ccp4bb] difficult molecular replacement solution

possible space groups, and P212121 was the best solution. These are the results. N LLG TFZ 4 104.97.5 5 137.57.7 6 166.28.3 Am I correct to conclude that there are 6 chains in the asymmetric unit? Rob Robert S. Phillips

[ccp4bb] Rfree too high

9.6% 757.7%997.8% 25440.03 1071.6% 0.4 00.000 0 total 529608 184831277921 66.5% 10.2% 10.6% 5090674.36 12.2%99.7* -120.642 72619 Robert S. Phillips Professor of Chemistry and of Biochemistry and Molecular Biol

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2019

/bessy-mx> in order to obtain updated information about our experimental setup and other requirements. Manfred Weiss and the HZB-MX team -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Germany _

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

__ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Germany ___

Re: [ccp4bb] challenges in structural biology

Hi Radu and all Could i humbly suggest some careful reflection before this ends up polarising the amazing structural biology community. Since the year dot everyone has been contributing to integrated approaches and I fear that the tone of this debate will create much negativity around the commu

[ccp4bb] Last chance to apply: Workshop "Diffraction Data Collection Using Synchrotron Radiation"

r. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Germany Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Au

[ccp4bb] Job opportunity in Berlin - HZB and Humboldt University advertise a postdoc position

crystallography beamlines (headed by Dr. Manfred S. Weiss) including supporting external users at the beamlines and will take part in graduate student education. Initially, a contract lasting until 31.12.2020 will be offered to the successful candidate with the possibility for an extension. The

[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2019

lmholtz-berlin.de>. Please visit our web page www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> to obtain updated information about our experimental setup and other requirements. -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Alber

[ccp4bb] Workshop "Diffraction Data Collection Using Synchrotron Radiation"

hop will fill up quickly. Participants are also expected to present a poster on their own work. As previously, the best poster will be awarded with an attractive prize. ## Manfred Weiss -- Dr. Manfred S. Weiss Macromolecular Crystallography H

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2019

de/bessy-mx> to obtain updated information about our experimental setup and other requirements. Manfred Weiss and the HZB-MX team -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Germany He

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2018

oltz-berlin.de<mailto:mswe...@helmholtz-berlin.de>. Please visit our web page www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> to obtain updated information about our experimental setup and other requirements. Manfred Weiss and the HZB-MX team -- Dr. Manfr

[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline extended to Sunday March 04, 2018

nd other requirements. Manfred Weiss and the HZB-MX team -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Germany Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Her

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2018

to obtain updated information about our experimental setup and other requirements. Manfred Weiss and the HZB-MX team -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Germany Helmholtz-Zen

[ccp4bb] Job opportunity in Berlin - HZB and MDC advertise a postdoc position

families (headed by Dr. Oliver Daumke). The successful candidate will also be involved in the operation of the BESSY II bio-macromolecular crystallography beamlines (headed by Dr. Manfred S. Weiss) and will take part in graduate student education. Initially, a three-year contract will be

Re: [ccp4bb] Difficult purification with imac columns

Hi Narayanan,We had similar problems with a membrane protein. It did bind Ni-NTA resin strongly. We washed out the resin (Ni-NTA) with high imidazole to sealer all other proteins and eluted out protein with very small concentration of SDS at room temp with shaking. Please read our paper in- Huan

[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2017

y-mx<http://www.helmholtz-berlin.de/bessy-mx> to obtain updated information about our experimental setup and other requirements. Manfred Weiss and the HZB-MX group -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2017

y-mx<http://www.helmholtz-berlin.de/bessy-mx> to obtain updated information about our experimental setup and other requirements. Manfred Weiss and the HZB-MX group -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein

Re: [ccp4bb] Problems with an exonuclease

Yes, washing IB with 10 % BPER  twice with sonication makes our IB (from various proteins) very clean before denaturation with 6M guanidine hydrochloride and further processing. Smita  On Wednesday, June 7, 2017 12:03 PM, Nicole Thomas wrote: I've found that washing my IB's with B-PER

[ccp4bb] one metalloid making multiple covalent bonds - generating library

== Dr. S. Thiyagarajan Faculty Scientist Institute of Bioinformatics and Applied Biotechnology Behind 3M and next to Arvind Mills Electronics City Phase I Bangalore 560100 Karnataka Ph: +91-80-28528900 ext 124 Fax: +91-80-28528904 === 

[ccp4bb] Ramachandran statistics and referee responsibility

are evident in the presentation of the data and not concealed? Thanks for your input! Evette Evette S. Radisky, Ph.D. Associate Professor and Consultant Department of Cancer Biology Mayo Clinic Cancer Center _ Griffin Cancer Research Building, Rm 310 4500

[ccp4bb] Job Posting: Director, Structural Biology and Biophysics - Takeda Pharmaceuticals

*Job Description: * Director - Structural Biology and Biophysics Job ID 1602180 Location San Diego, California, United States; *OBJECTIVES:* The Director of Structural Biology and Biophysics leads all activities in the Structural Biology and Biophysics group at TCAL, including Molecular

[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2017

Please mark your calendar: The next MX-proposal application deadline: March 01, 2017 is approaching http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html Hereby we would like to invite the submission of new proposals for MX-beamtime at the HZB-MX beamlines for the next beam time p

Re: [ccp4bb] For stabilizing protein-protein complex

affinity also. It is definitely worth a try. http://www.jbc.org/content/283/7/4115.full Evette Evette S. Radisky, Ph.D. Associate Professor and Consultant Department of Cancer Biology Mayo Clinic Cancer Center _ Griffin Cancer Research Building, Rm 310 4500

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2017

HZB-MX group -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@

[ccp4bb] Slightly OT: crystallization teaching resources for kids

Can anyone point to some especially useful resources to help explain to kids (pre-chemistry, ~age 10-12) how and why molecules crystallize? Maybe a good online movie or animation? I am especially needing help with the concept of nucleation, and why nucleation is slower and then crystal growth f

[ccp4bb] Workshop "Challenges in Data Processing" Announcement

First come, first serve. Cheers, Karine + Manfred -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berli

Re: [ccp4bb] Instrument help: any comments on bench-top SPR

Bioptix is another option you may consider for your needs. if they still have the Bioptix Innovators program running you may also be able to have the instrument placed for a free timed trial with training to see if fits your needs. contact them to see. the sensor chips, one for amine-coupling is ab

Re: [ccp4bb] Another puzzle: 5gnn: SOLVED

Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein

Re: [ccp4bb] Protein precipitation

Hi Manjula, I will lyse the bacterials cells and monitor the degradation of the lysed protein in lysis buffer over 4-5 days before proceeding with purification.   What is the lifetime of this expressed protein once lysed?  How long can it stay after lysis without degradation or aggregation?   Doe

Re: [ccp4bb] Cleaved peptide density!

might help distinguish between residual activity of the mutant vs. contamination with wt enzyme. Good luck! Evette Evette S. Radisky, Ph.D. Associate Professor and Senior Associate Consultant Department of Cancer Biology Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San

[ccp4bb] ECM-29 - Abstract Deadline is Fast Approaching

he abstract deadline. Best wishes Manfred Weiss + Victor Lamzin MS Chairs -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web:

[ccp4bb] Postdoc position in Structural Characterization of a membrane-associated enzyme

Postdoc position in Structural Characterization of a membrane-associated enzyme Lookingfor an outstanding and highly motivatedindividual to start immediately in a postdoctoral position to study structureand mechanism of a membrane-associated enzyme involved in co-translationalmodification. The p

[ccp4bb] 2014 HZB User Meeting and fragment screening workshop

information can be found under: Users Meeting: http://www.helmholtz-berlin.de/user/usermeetings/user-meeting-2014/index_en.html Fragment screening-workshop: http://www.helmholtz-berlin.de/events/fragment-screening/index_de.html With best wishes Manfred & Uwe -- Dr. Manfred. S. Weiss Helmh

[ccp4bb] Biosynthesis Postdoctoral Fellow - Vancouver, Canada

We are seeking highly motivated postdoctoral fellows to join the Biosynthetic Enzymes Laboratory at the University of British Columbia in Vancouver, Canada (https://www.chem.ubc.ca/katherine-ryan). We are a dynamic group of researchers working at the interface of chemistry and biology. Our goal

Re: [ccp4bb] SOS from last century!

Hi Charlie, From molscript 2.1.2 you can directly create png, jpeg or gif also, default being postscript file. At least it is working in linux. I am not sure in iMac. Just type molscript -h. It should give the options... HTH -Karthik On 5/6/2014 10:45 PM, Carter, Charlie wrote: I need help

[ccp4bb] Postdoc position available

& Dr. Manfred S. Weiss, http://www.helmholtz-berlin.de/bessy-mx) and will take part in graduate student education. Initially, a two-year contract will be offered to the successful candidate with the possibility for an extension. The salary will be based on German federal TvÖD. The position is

Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)

ute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-3

Re: [ccp4bb] version incompatibility between phaser 2.5.6 and current ccp4i?

We do face the same problem. When we try to run the script in phaser-2.5.6, which hard earlier worked, it is not working and gives same error as Ed noted. However the same script runs fine with 2.5.2. We run everything with default parameters of phaser, still we face same problem ending with "

Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)

ute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-3

[ccp4bb] image of worn out rotating anode

-- S. Thiyagarajan Institute of Bioinformatics and Applied Biotechnology Electronics City Phase I Bangalore 560100 KA - India --

Re: [ccp4bb] Validity of Ion Sites in PDB

igmail.net/ iD8DBQFTGZUEUxlJ7aRr7hoRAtC+AKDr6cJzgWgUAWPO6AYmDHMlFs6gbwCg8+E/ Yj2NVdKiYBq9O28v9eCQWDA= =YkXc -END PGP SIGNATURE- -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30

Re: [ccp4bb] Sister CCPs

I'm sorry, but did you just use the words "crystallographers" and "modest" in the same sentence? :-) On Thu, Feb 13, 2014 at 6:41 AM, Eleanor Dodson wrote: > I agree with Frank - it keeps crystallographers modest to know how > challenging wet lab stuff still is.. > Eleanor > > On 12 February 201

[ccp4bb] "Soft X-rays in MX" session at the IUCr conference 2014

Dear all, at the 23rd IUCr congress (http://www.iucr2014.org/), which will take place in August this year in lovely Montreal, John Rose and I are organizing the microsymposium MS-40 titled "S-SAD and other applications of soft X-rays in MX". If you happen to have an exciting story,

Re: [ccp4bb] CCP4BB Digest - 22 Nov 2013 to 23 Nov 2013 (#2013-332)

Dear Nazia, Glad you are trying your hand at a membrane protein. You need to have detergents (like ldao, octylpoe ) in your refolding and purifcn buffer. Best wishes Krishnaswamy Mku On 24 Nov 2013 05:32, "CCP4BB automatic digest system" < lists...@jiscmail.ac.uk> wrote: > There are 6 messages tot

[ccp4bb] 2013 HZB User Meeting and HC1 workshop

ore information can be found under: Users Meeting: http://www.helmholtz-berlin.de/user/usermeetings/user-meeting-2013/index_en.html HC1-workshop: http://www.helmholtz-berlin.de/events/satelite-workshop-2013/ With best wishes Manfred & Uwe -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin

[ccp4bb] Phaser gives error in 6.4.0 version

Dear All, Installed the CCP4 6.4.0 version recently on CentoS 5. When I try to run phaser I get the following error. Apparently I can reproduce the error for different reflection file. This happens after getting the rotation, translation and packing function. Any suggestions to this problem is

Re: [ccp4bb] CCP4BB Digest - 11 Oct 2013 to 12 Oct 2013 (#2013-289)

Dear Dilip Badjugar, Perhaps it may be good to take a look at the unmodelled blobs and see if there is any large densities left unexplained. Also how does the Rmerge vary with the resoln ? Is your data good upto 1.7A? Regards and wishes Krishnaswamy On 13 Oct 2013 04:33, "CCP4BB automatic digest

[ccp4bb] Postdoctoral position available: Structural biology of integral membrane proteins

membrane proteins in a variety of systems (mammalian, insect, yeast, bacterial) 2. Purify target membrane proteins to homogeneity 3. Crystallize and determine the macromolecular structure of these proteins, both alone and, where applicable, in complex with their ligand(s) START DATE: Immediately

Re: [ccp4bb] AW: [ccp4bb] str solving problem

Pramod Kumar. Graduate Student. Crystallography lab. Department Of Biotechnology. Indian Institute Of Technology Roorkee Uttranchal.247667 India +919359189657. -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macrom

[ccp4bb] Reminder: Announcement of the Workshop "Diffraction Data Collection Using Synchrotron Radiation"

p will fill up quickly. Participants are also expected to present a poster on their own work. As previously, the best poster will be awarded with an attractive prize. ## Manfred Weiss & Uwe Mueller -- Dr. Manfred. S. Weiss Helmholtz-

[ccp4bb] process data from two crystals in-house data

istics of the combined data set. I do not have HKL2000. Which (free) tool can handle two different diffraction data sets, process them together to give a single final data statistics.   Thanks and regards Thiyaga S. Thiyagarajan Centre of Excellence in Bioinformatics School of Biotech

Re: [ccp4bb] Problem in running ARP_WARP in CCP4i...solved....

Dear All, The problem is solved by updating the tcsh version from 6.14.00 to 6.14.17. Thanks to Santosh, Ioan and Lamzin. With regards S. Karthikeyan On 3/7/2013 7:55 PM, Ioan Vancea wrote: Dear Karthikeyan, In order to trace the error may I ask you, please, to change the first line in

Re: [ccp4bb] Problem in running ARP_WARP in CCP4i

rotron 800 Blackburn Road Clayton VIC 3168 Australia Ph: +61-4-67770815 (mobile) +61-3-85404276 (office) From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of S. Karthikeyan [skart...@imtech.res.in] Sent: Friday, March 08, 2013 12:38 AM

[ccp4bb] Problem in running ARP_WARP in CCP4i

Word too long. QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/auto_tracing.sh --- Thanking you With regards S. Karthikeyan

Re: [ccp4bb] GeForce Graphics cards

Hi Jason, aren't the current gaming monitors all (or mostly) 120 Hz? At least companies like alianware sell GeForce together with 120 Hz monitors. A On Wed, Feb 13, 2013 at 4:02 PM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Hi Alex, > > Thanks for asking before buying. You've av

Re: [ccp4bb] GeForce Graphics cards

Harry, I found this on pymol wiki "NVidia 3D NVision kit only supports DirectX software for GeForce (gaming cards) on Windows; users are reporting that they are not able to run PyMOL with NVision with these cards. Get a newer model low end quadro (> G8x graphics core) without the 3 pin mini din (e

Re: [ccp4bb] need some suggestions for crystallization

/6835.long I would avoid commercial preps of porcine elastase; I messed around with that one around 10 years ago using many reported crystallization conditions and suppliers but never got crystals. Evette S. Radisky, Ph.D. Assistant Professor Mayo Clinic Cancer Center Griffin Cancer Research

Re: [ccp4bb] Mac mini advice

Hi, I'm running a mac mini server. The file sharing seems to work fine - I'm not running NIS. There is a lag in software starting up - up to 20-30 s but once the software is loaded, it runs fine. We did some benchmarking with phaser last week & there was no perceivable differe

[ccp4bb] CCP4 package and update managers: relocating installations

27;m fairly new to MacOS and maybe there is a better way of doing this ….. Sid ---- Dr K S Sidhu Department of Biochemistry 1/61 Henry Wellcome Building Lancaster Road Leicester LE1 9HN Tel: 0116 229 7237 On 16 Jan 2013, at 15:27, Chris Richardson ma

[ccp4bb] Announcement of the Workshop "Diffraction Data Collection Using Synchrotron Radiation"

xpected to present a poster on their own work. As previously, the best poster will be awarded with an attractive prize. ## Manfred Weiss & Uwe Mueller -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie

[ccp4bb] comit mtzout writing problem...

Dear All, I am trying to run comit in slow mode. The programs runs fine till refmac where all the 'prefix' mtz files are created. However when I give the command to assemble all the mtz files using the command (separately): comit --prefix omit1 --mtzout omit1.mtz (OR) comit -prefix omit1 -mtzout

Re: [ccp4bb] Summary for scale out data

Hi Uma, In HKL2000, if you go to Report menu (near to Help menu) you will see the option for generation of tables. Hope this helps. With regards S. Karthikeyan On 7/31/2012 6:57 PM, Uma Ratu wrote: Dear All: I process my data using HKL2000. After scale, the program generates several

Re: [ccp4bb] Somewhat OT: question of professional courtesy

this was a primary structural analysis of a macromolecule, I would expect that a discussion of the structural comparison would include references to earlier work(s) on related molecules, but I have seen this happen where a group reinvents the wheel (sometimes rather badly) because they don't tak

Re: [ccp4bb] Somewhat OT: question of professional courtesy

AM To: Radisky, Evette S., Ph.D. Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Somewhat OT: question of professional courtesy -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Evette, the PDB lists the citation when you enter the PDB-ID in the search mask of any of the web-interfaces, which is

[ccp4bb] Somewhat OT: question of professional courtesy

ctice? Thanks! Evette Evette S. Radisky, Ph.D. Assistant Professor Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372

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