Re: [ccp4bb] how to use electron scattering factors in REFMAC program?

Hi Benedetta Use an external keyword file that with the line 'source ec mb’ Best R Roberto A Steiner www.steinerlab.org https://twitter.com/steiner_lab roberto.stei...@kcl.ac.uk Randall Centre for Cell and Molecular Biophysics Facul

Re: [ccp4bb] Crystallizing a tough target

HOD crystallised at 150mg/ml https://www.pnas.org/doi/10.1073/pnas.0909033107 Once I set the wrong time on the centrifuge and it went up to >200 mg/ml. I am sure many others have similar stories. All the best Roberto Roberto A Steiner www.steinerlab.org https://twit

Re: [ccp4bb] alternatives to Consurf server

ConservFold from the Rodrigues lab at Warwick is something that you might consider. https://www.rodrigueslab.com/resources Roberto A Steiner www.steinerlab.org https://twitter.com/steiner_lab roberto.stei...@kcl.ac.uk Randall Centre

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

Difficult to be sure from a single angle pic but I would suggest Cys oxidation. There is an important 20 years old paper (see below) on Cys oxidation in a tyrosine phosphatase (like yours) Best Roberti] Nature *

Re: [ccp4bb] solvent mask for partial ligands

Dear Gottfried Assuming your modelling is correct you can always try occupancy refinement of your ligand (or simply test alternative values). Maybe that will help. You can also play with bulk solvent mask parameters. Keywords (both occupancy and mask parameters) can be found in https://www2.mrc-

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

urs. On 1 Dec 2023, at 14:35, Frank von Delft mailto:frank.vonde...@cmd.ox.ac.uk>> wrote: That's a press release, not a tool that can be tested. On 01/12/2023 12:19, Roberto Steiner wrote: Great paper indeed! However quite significant progress seems to have been achieved w

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

Great paper indeed! However quite significant progress seems to have been achieved with ligands as well (and not only)… https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/ Has anyone in the community put this to the test? Best wishes Roberto Roberto A Steine

Re: [ccp4bb] Alexey Vagin

Very very sad to hear this. I have some great memories of our time together in York several of which involve molecular replacement problems, Fortran77 code, and pubs. A brilliant mind and a good person. Will miss having someone calling me 'Rapierta' (Roberto pronounced with a Russian accent).

Re: [ccp4bb] Is this Spam? This looks like Spam.

IBE ccp4bb Roberto Steiner You are already subscribed to the CCP4BB list as "Roberto Steiner". > Roberto A Steiner Unknown command - "ROBERTO". Try HELP. … but I am now getting ccp4bb emails. Best wishes Roberto Roberto A Steiner www.steinerlab.org<http://www.steine

Re: [ccp4bb] resolution limit stuck in Refmac5

resolution limits? Are you using the original reflection file? Best Roberto Thanks for any thoughts, Jon Fleming Graduate Student Structural Biochemistry Laboratory (Huxford Lab) Department of Chemistry & Biochemistry San Diego State University --- Dr. Roberto Steiner Randall Divisi

Re: [ccp4bb] Deposition of riding H [was: Deposition of riding H]

does not restrain the plane to lie in its current orientation. One can find other, earlier programs, but they are small molecule specific. Regards, Pavel. --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Ca

Re: [ccp4bb] turn granular to crystal

hing like granular, they are rounded shaped and not so regular and also don't have sharp edges. See the attached pic. The current condition is PEG4000 and pH around 5. How can I improve this condition? Thanks a lot. --- Dr. Roberto Steiner Randall Division of Cell and Molecular Bi

Re: [ccp4bb] TLSMD Alignments

raduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campu

[ccp4bb]

function, just wandering if refmac could do it also. all suggestions are welcome. changyi --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0

Re: [ccp4bb] Deposition of a BUSTER refined structure

Dear Melanie On 2 Mar 2010, at 15:09, Melanie Vollmar wrote: Hi all I did my first deposition of a BUSTER refined structure and I was very surprised when I was asked for an "estimated error of free R value" and "estimated error of bin free R value" as well an "ESD based on Luzzati Plot"

Re: [ccp4bb] Alternative conformation in Mac Refmac5

Hi Heidi, I have noticed the same thing. Went back to Refmac v93 (mac version) and side-chains stopped flying. Needs a fix. Best Roberto On 11 Sep 2009, at 10:59, Heidi Tuominen wrote: Hi all, I have updated lately to ccp4-6.1.2. I have Macintosh. Now I have problem with alternative conf

Re: [ccp4bb] Low Bfactor values for waters after TLS

Hi Alasdair On 11 Sep 2009, at 09:46, Alasdair K. Mackenzie wrote: Greetings CCP4-ers, I have been running some TLS refinement which does wonders for my R/ Rfree values, but seems to give some spurious Bfactors/ADPs for the waters, e.g. B= 2. These low Bfactors appear relatively consistent

Re: [ccp4bb] cyseteine modification

You can also have a look at Active site structural features for chemically modified forms of rhodanese. Gliubich F, Gazerro M, Zanotti G, Delbono S, Bombieri G, Berni R. J Biol Chem. 1996 Aug 30;271(35):21054-61. Best Roberto On 19 Aug 2009, at 15:41, Debajyoti Dutta wrote: Dear Sir, Is

Re: [ccp4bb] quaternary structure comparison

check whether this arrangement that I see is something new I would like to perform a quaternary structure comparison. Is there any such tool available? A Google search wasn't very conclusive. Or is there a clever combination of available resources? Kind regards Eike --- Robe

Re: [ccp4bb] issues with TLS refinement

I might be wrong but it seems Garib has implemented some sort of line minimization for the tls part which causes the observed behavior. Garib? Roberto On 21 May 2009, at 00:39, Dima Klenchin wrote: The issue is: While running tls and restrained refinement, the program doesn't perform

[ccp4bb] postdoctoral position at King's College London (2)

Dear ccp4bb readers, £1,000 worth correction on my previous postdoc ad: London weighting is £2,323 and not £3,323. Apologies (all the rest is correct..), Roberto On 9 Mar 2009, at 09:49, Roberto Steiner wrote: Dear ccp4bb readers, --- King's College L

[ccp4bb] postdoctoral position at King's College London

rt of a research collaboration between the groups of Drs Sasi Conte and Roberto Steiner (Randall Division of Cell and Molecular Biophysics) and Professor Ajay Shah (Cardiovascular Division). Excellent infrastructure support is available to carry out the project. The salary is Grade 6,

Re: [ccp4bb] Twin refinement - selecting FreeR

Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/ --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London

Re: [ccp4bb] Off topic: Crystal degredation with age

falo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Email: esn...@hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here!Crystallization, how quaint! --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's Coll

Re: [ccp4bb] Choosing MR solutions in the case of perfect twinning with P41212?

Hi Francis, I would consider the possibility of a orthorhombic sg (a~b with twinning). If unlucky maybe even monoclinic. Cheers Roberto On 5 Feb 2009, at 18:10, Francis E Reyes wrote: It seems like this space group will be the death of me. I'm working on a structure in SG P41212 o

Re: [ccp4bb] generating omit maps

ng if there's a CCP4 >related program to generate omit maps. > >Thanks, >Kathleen --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail [EMAIL PROTECTED]

[ccp4bb] Coot and Hs

(that I know of) is to remove all Hs and generate them again (molprobity for example) prior to refinement. Cheers, Roberto --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848

Re: [ccp4bb] Setting drops with proteins that are hard to concentrate

intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London,

Re: [ccp4bb] Twinning: P43 apparently P42212

eived. Cheers, Charlie -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia [EMAIL PROTECTED] +61 8 6488 4406 --- Dr. Roberto Steiner Randall Division of Cell and Molecular

Re: [ccp4bb] refmac problem in running arp/warp

floor) University of Helsinki FIN-00014 Helsinki, Finland Tel. +358-9-191 58903 Fax +358-9-191 59940 -- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0

Re: [ccp4bb] A babyish question on coot

n old crystallographer to ask so babyish question. But your help can save me lots of time. Thanks Yanming -- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail [EMAIL PROTECTED]

Re: [ccp4bb] Stop Refmac from refining B factors?

-- Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353 --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's Ho

Re: [ccp4bb] monomer library in Refmac

ription: Binary data COM_mon_lib.cif Description: Binary data --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail [EMAIL PROTECTED]

Re: [ccp4bb] Question about glove boxes for protein crystallization

from Plas-labs (link below). http://www.plas-labs.com/ Thank you very much, Mathews Ps: If others are interested, I will post a summary. --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL

Re: [ccp4bb] NCS Phased Refinement

; Evette > > Evette S. Radisky, Ph.D. > Assistant Professor and Associate Consultant II > Mayo Clinic Cancer Center > Griffin Cancer Research Building, Rm 310 > 4500 San Pablo Road > Jacksonville, FL 32224 > (904) 953-6372 (office) > (904) 953-2857 (lab) > --- Dr

Re: [ccp4bb] how many stuck datasets are actually twinned?

(or would you not consider this a failed refinement). (My bias is that such data sets are almost never twinned and one should look elsewhere for the problem, but perhaps others know better.) Sue Sue Roberts Biochemistry & Biopphysics University of Arizona [EMAIL PROTECTED] --- Dr. R

Re: [ccp4bb] "B" in B-factor

: May be too trivial, I was just wondering what "B" stands for in the term "B-factor". Thanks Rajesh -- Rajesh Kumar Singh Institut fur Biochemie Universitat Greifswald Felix-Hausdorff-Str. 4 D-17489 Greifswald Germany E.Mail: [EMAIL PROTECTED] Phone: +49-3834- 86 43