[ccp4bb] On the production of a two domain protein
Dear all, We are trying to characterize a protein consisting of two domains. We have successfully produced, purified and crystallized both domains independently. However, we are unable to overexposes a soluble form of the full-length protein. Can anyone provide a strategy to merge back the independent domains into a single protein chain or to modify the construct to succeed in the overproduction of the full-length protein? Armando To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Structural alignment and classification
Thank you all. What about the analysis? Does any program cluster the structures according to their structural similarity? Armando > El 6 mar 2023, a las 15:58, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> escribió: > > Hi Eleanor > > According to > > https://www.ccp4.ac.uk/html/gesamt.html > > "Gesamt aligns two or more structures…” > > and > > https://www.ccp4.ac.uk/html/superpose.html > > "superpose aligns and superposes two or more protein structures…” > > But the real expert is probably Eugene. > > Harry > >> On 6 Mar 2023, at 14:55, Eleanor Dodson wrote: >> >> Does Superpose or GESAMT align multiple structures? >> And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2 >> etc? >> Eleanor >> >> On Mon, 6 Mar 2023 at 14:53, Harry Powell >> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> Or you could use Gesamt - also in CCP4. >> >> Harry >> >>> On 6 Mar 2023, at 13:15, Kay Diederichs >>> wrote: >>> >>> Dear Armando, >>> >>> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign >>> (https://zhanggroup.org/US-align/). >>> In my tests, THESEUS sometimes crashed in different ways. USalign is very >>> robust; SUPERPOSE is fast. >>> >>> HTH, >>> Kay >>> >>> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert >>> wrote: >>> >>>> Dear all, >>>> I want to align several structures we obtained from a fragment screening >>>> campaign and cluster them according to RMSD. >>>> Is MNYFIT still running? What else can I run? >>>> Thank you >>>> Armando >>>> >>>> >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ >>> >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] Structural alignment and classification
Dear all, I want to align several structures we obtained from a fragment screening campaign and cluster them according to RMSD. Is MNYFIT still running? What else can I run? Thank you Armando To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023
Dear all, The registration for the next edition of the Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023 is open. The workshop has been organized at Instituto de Química Física Rocasolano CSIC since 2010 and it is meant for 25 graduate students or researchers with previous expertise in crystallography and/or CryoEM who need a deeper insight into the most advanced crystallographic and CryoEM techniques to carry out their research projects. The program traditionally covers aspects such as sample preparation, structure solution, model building, crystallographic refinement, validation, and analysis of the structural results, as well as an overview of the newest structural biology technologies. On top of these subjects, this year's program will include those aspects related to the impact of Artificial Intelligence methods on structure solution and low-resolution refinement. In addition, we will cover dynamic crystallography at XFEL and synchrotron and ligand building for drug discovery. You may find further information on our website (https://www.xtal.iqfr.csic.es/MCCS2023/index.html <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.xtal.iqfr.csic.es%2fMCCS2023%2findex.html=E,1,_6Q8g0pWDL046-LZ44gvaksBnMuEWPEnWs6dSM5ITyKFmfGLAZ-wAw4EL1OnPKfrAoDf9Hb1ndh68dyB4NhRkcMi2E59E10oYdB7mBQqlSCr=1>) Hoping to see you In Madrid Juan and Armando Armando Albert and Juan A. Hermoso Departamento de Cristalografía y Biología Estructural Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas Serrano 119, 28006 Madrid Spain To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023
Dear all, The registration for the next edition of the Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023 is open. The workshop has been organized at Instituto de Química Física Rocasolano CSIC since 2010 and it is meant for 25 graduate students or researchers with previous expertise in crystallography and/or CryoEM who need a deeper insight into the most advanced crystallographic and CryoEM techniques to carry out their research projects. The program traditionally covers aspects such as sample preparation, structure solution, model building, crystallographic refinement, validation, and analysis of the structural results, as well as an overview of the newest structural biology technologies. On top of these subjects, this year's program will include those aspects related to the impact of Artificial Intelligence methods on structure solution and low-resolution refinement. In addition, we will cover dynamic crystallography at XFEL and synchrotron and ligand building for drug discovery. You may find further information on our website (https://www.xtal.iqfr.csic.es/MCCS2023/index.html <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.xtal.iqfr.csic.es%2fMCCS2023%2findex.html=E,1,_6Q8g0pWDL046-LZ44gvaksBnMuEWPEnWs6dSM5ITyKFmfGLAZ-wAw4EL1OnPKfrAoDf9Hb1ndh68dyB4NhRkcMi2E59E10oYdB7mBQqlSCr=1>) Hoping to see you In Madrid Juan and Armando Armando Albert and Juan A. Hermoso Departamento de Cristalografía y Biología Estructural Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas Serrano 119, 28006 Madrid Spain To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Installing new version of CCP4
Now it is working. Thank you Armando > El 2 may 2020, a las 16:15, Armando Albert escribió: > > Is this normal? Waiting for ages….. > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Installing new version of CCP4
Is this normal? Waiting for ages….. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Structural Alignment
Thank you all, I have done it with chimera. It does structural alignment and use it as a template. Then, you can add sequences one after the other and align to this template. You can save this alignment in clustalw format and load it to ESPrit3 and do a nice picture. Armando > El 8 abr 2020, a las 19:22, Guillaume Gaullier > escribió: > > Hi Armando, > > This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/ > <https://www.cgl.ucsf.edu/chimerax/> > > More specifically, its matchmaker command will align two structures and print > the corresponding sequence alignment: > https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html > <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> > You can then save the sequence alignment to a file, and use it in your > favorite sequence alignment program along with the sequences for which you > don’t have a structure. > > This is one option among many, as pretty much every structure visualization > program can superimpose two similar structures (but I don’t know how many of > them make it as easy to save the sequence alignment). > > Hope this helps, > > Guillaume > > >> On 8 Apr 2020, at 19:04, Armando Albert > <mailto:xalb...@iqfr.csic.es>> wrote: >> >> Dear all, >> I want to align two structures and then, I want to align several sequences >> to that structural alignment. >> How can I do this? >> Armando >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Structural Alignment
Dear all, I want to align two structures and then, I want to align several sequences to that structural alignment. How can I do this? Armando To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Protein concentration for the initial crystallisation trials
Dear all, I was wondering how to guess the optimal protein concentration for the initial crystallisation trials. Is there any trick or assay other than the classic PCT from Hampton? Armando To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] how to generate a complete biomolecule out of the BIOMOLECULE record
Thanks. I did the following for each operator and worked fine. The CHAIN keyword renamed the original chain names. Armando # pdbset xyzin 5k7l.pdb xyzout 5k7l_GH.pdb << eof-1 transform 0.00 1.00 0.00 -1.00 0.00 0.00 0.00 0.00 1.00 0. 332.7 0 CHAIN A G CHAIN B H end eof-1 El 18/01/2017, a las 11:16, Tim Gruene escribió: > Dear Armando, > > did you try the TRANSFORM command in pdbset? It seems appropricate to > generate > the other molecules. You probable need to do it separately for each operator > (except the first one, of course, the identity). > > Best, > Tim > > On Wednesday 18 January 2017 11:13:21 AM Armando Albert wrote: >> Dear all, >> Does any one know how to generate a complete biomolecule out of the >> BIOMOLECULE record from a pdb file that contains one of the four molecules >> forming a tetramer This is an Crio-EM model. >> Armando >> >> >> >> REMARK 350 BIOMOLECULE: 1 >> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B >> REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 >> REMARK 350 BIOMT2 1 0.00 1.00 0.000.0 >> REMARK 350 BIOMT3 1 0.00 0.00 1.000.0 >> REMARK 350 BIOMT1 2 0.00 -1.00 0.00 332.7 >> REMARK 350 BIOMT2 2 1.00 0.00 0.000.0 >> REMARK 350 BIOMT3 2 0.00 0.00 1.000.0 >> REMARK 350 BIOMT1 3 -1.00 0.00 0.00 332.8 >> REMARK 350 BIOMT2 3 0.00 -1.00 0.00 332.7 >> REMARK 350 BIOMT3 3 0.00 0.00 1.000.0 >> REMARK 350 BIOMT1 4 0.00 1.00 0.000.0 >> REMARK 350 BIOMT2 4 -1.00 0.00 0.00 332.7 >> REMARK 350 BIOMT3 4 0.00 0.00 1.000.0 >> REMARK 465 > -- > -- > Paul Scherrer Institut > Dr. Tim Gruene > - persoenlich - > Principal Investigator > Biology and Chemistry > OFLC/102 > CH-5232 Villigen PSI > > Phone: +41 (0)56 310 5297 > > GPG Key ID = A46BEE1A >
[ccp4bb] how to generate a complete biomolecule out of the BIOMOLECULE record
Dear all, Does any one know how to generate a complete biomolecule out of the BIOMOLECULE record from a pdb file that contains one of the four molecules forming a tetramer This is an Crio-EM model. Armando REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 REMARK 350 BIOMT2 1 0.00 1.00 0.000.0 REMARK 350 BIOMT3 1 0.00 0.00 1.000.0 REMARK 350 BIOMT1 2 0.00 -1.00 0.00 332.7 REMARK 350 BIOMT2 2 1.00 0.00 0.000.0 REMARK 350 BIOMT3 2 0.00 0.00 1.000.0 REMARK 350 BIOMT1 3 -1.00 0.00 0.00 332.8 REMARK 350 BIOMT2 3 0.00 -1.00 0.00 332.7 REMARK 350 BIOMT3 3 0.00 0.00 1.000.0 REMARK 350 BIOMT1 4 0.00 1.00 0.000.0 REMARK 350 BIOMT2 4 -1.00 0.00 0.00 332.7 REMARK 350 BIOMT3 4 0.00 0.00 1.000.0 REMARK 465
[ccp4bb] Bulk solvent
Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando
[ccp4bb] Negative electron density in the Fo-Fc map at the binding site
Dear all, I am screening a small library of ligands against my protein crystals. Following a soaking with different ligands, I collect datasets to 1.9A resolution and refine them against an empty model without any problem. What is the meaning of a rather large negative electron density in the Fo-Fc map at the binding site?. Could it be related to an incorrect bulk solvent model? Thank you in advance Armando
[ccp4bb] Naccess
Dear all, Does anyone know how to properly cite Naccess for calculation of solvent accessible area (http://www.bioinf.manchester.ac.uk/naccess/)? Armando
[ccp4bb] problem with refmac and xloggraph
Dear all,
does anyone experience a problem viewing refmac results with Log Graph?
The window appears and disappears in less than one second and this is the
output on the terminal window:
Error in startup script: syntax error in expression 10 11 12 + 12: extra
tokens at end of expression
while executing
expr [string trim $ele] + $data(NCOLUMNS)
(procedure extract_tables_from_GRAPH line 44)
invoked from within
extract_tables_from_$filetype $input $arrayname
(procedure extract_tables_from_file line 31)
invoked from within
extract_tables_from_file $system(SCRIPT) $system(FORMAT) data
invoked from within
if { $system(SCRIPT) != } {
if { ![ElementExists system FORMAT] || $system(FORMAT) == } {
set system(FORMAT) [GetFileFormat $system(SCRI...
(file /Applications/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl line
2324)
invoked from within
source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]
(file /Applications/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl line 83)
Armando
Re: [ccp4bb] C2/I2 space groups
If you do not specify that you prefer C2, pointless change to I2. This is sometimes odd, for instance when running molrep or shelx (hkl2map) afterwards Armando I am out of the lab El 21/05/2014, a las 18:54, Roberto Battistutta roberto.battistu...@unipd.it escribió: Dear All, a question about C2 and I2 space groups. Processing a dataset, XDS output says C2, with dimensions 122.8, 56,9 81,5 and beta 125.1°. Aimless reindexes to I2 with 81.6, 56.9, 101.1 and 96.2°. Phenix (refine) returns a warning NOTE: non-standard setting used: I 1 2 1. In the PDB there are indeed several examples of I2 choices. The two space groups are equivalent as indicated in the International Tables (all with number 5), but why different programs use different conventions? Is there any rationale? By the way, the volumes of the two unit cells are very similar. Thanks, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it
Re: [ccp4bb] Low 280 absorbance imidazole?
Hi Phoebe, Could you please explain me how do you stain the piece of paper? Thank you Armando El 21/08/2013, a las 17:03, Phoebe A. Rice escribió: Hi Bernhard, If your cheap imidazole works fine aside from the absorption problem, there's always my favorite stone-age detection method: pencil a numbered grid onto a piece of filter paper, spot the fractions on it, and stain with coomassie. It'll tell you which fractions to load on a gel, and it goes easy on the budget as well. Phoebe ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp [hofkristall...@gmail.com] Sent: Wednesday, August 21, 2013 9:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Low 280 absorbance imidazole? Hi Fellows, could someone please point me towards the source of a known high purity imidazole with low absorbance at 280 nm? I am facing the problem of detecting a low absorption protein in high imidazole background after IMAC gradient elution. In the UV spectra of the 2 imidazoles I checked there is some contaminant that absorbs at 280… Thx, BR Bernhard Rupp Marie Curie Incoming International Fellow Innsbruck Medical University Schöpfstrasse 41 A 6020 Innsbruck – Austria +43 (676) 571-0536 bernhard.r...@i-med.ac.at Dept. of Forensic Crystallography k.-k. Hofkristallamt Vista, CA 92084 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ ---
Re: [ccp4bb] about coot
Dear Paul, 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that? You may want to open a different session in the same directory and not spoil the one you are using for refinement Armando I am out of the lab El 23/11/2012, a las 12:32, Paul Emsley pems...@mrc-lmb.cam.ac.uk escribió: On 23/11/12 08:54, Qixu Cai wrote: I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? (let ((imol (read-pdb coot-download/3rso.pdb)) (imol-map (make-and-draw-map coot-download/r3rso-refmac.mtz FWT PHWT 0 0))) (map (lambda (chain) (fit-chain imol chain)) (chain-ids imol))) 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? All and more, I think. They are in coot-top-dir/share/coot/python 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that?
Re: [ccp4bb] Lithium versus Sodium
Dear Matt, We were working with Hal2p a lithium inhibited Ins-mono-PPase like protein 10 years ago. We had good biochemistry showing that lithium replaced mg at the active site. We grow crystals in presence of Li and we worked with 1.6 A diffraction data. Unfortunatelly we did not see any electron density peak, however, the Li site displayed nice tetrahedral coordination having four oxygen atoms as ligands. Armando El 12/01/2012, a las 18:16, Matthew Franklin escribió: Hi Ed - There was a peak in the difference maps, as I recall. I believe it initially got built as a water, but that proved to be too many electrons, giving a negative peak. I removed the water, but it was clear that something needed to be there, at which point I started casting about for alternative atoms, and settled on lithium. I'm pretty sure I never tried to put sodium in there and see if it refined. Caveat: this work was all done eight years ago, and I don't have access to any of the files anymore. So I can't verify any of these statements! However, I did deposit Fobs for these structures, if you care to make your own maps... I just checked the structure in EDS, and the peak for the lithium is pretty low, around 0.6 sigma. I would say that it looked better in the maps I was using. Hope that helps, Matt On 1/12/12 11:22 AM, Ed Pozharski wrote: Matt, thank you, this is an excellent summary. One question remains - the lithium peak should be, afaiu, much lower than the water/sodium. Was there a peak in difference map or was placement based on identifying something that looked like a coordination site? Cheers, Ed. On Thu, 2012-01-12 at 10:23 -0500, Matthew Franklin wrote: On 1/12/12 9:42 AM, Ed Pozharski wrote: On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote: Do you have ultra-high resolution? Something I did not…. Are there many examples in the pdb of proteins with Li+ refined? http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/atemplate=het2pdb.htmlparam1=_LI 39 in total. Some are fairly low resolution (2.8A), and only five are higher than 1.2A. I'd think that placing lithium ion should be based on some extra-crystallographic evidence, plus maybe some structural considerations such as correctly placed coordinating ligands. Since I'm responsible for eight of those structures, I'll just say that I thought fairly hard before building a lithium into that peak, knowing that I couldn't really distinguish it from water or sodium. I was working with a 1.7 A map, and I put the lithium there based on three criteria: - the crystals grew in something like 2 M lithium sulfate, whereas the only source of sodium would have been from the buffer or the protein solution - there were two negatively charged residues coordinating the peak in question, suggesting it was a cation - the bond distances were consistent with lithium coordination, for what that's worth at this resolution That was the first structure (1TW7), and all of the others were treated the same since it was the same crystals soaked with different compounds in the same conditions. - Matt -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165
Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?
Does anyone have got a script to compute 3fo2fc map with CCP4? Armando El 29/07/2010, a las 23:38, Ian Tickle escribió: On Thu, Jul 29, 2010 at 8:25 PM, Pavel Afonine pafon...@lbl.gov wrote: Speaking of 3fo2fc or 5fo3fc, ... etc maps (see classic works on this published 30+ years ago), I guess the main rationale for using them in those cases arises from the facts that 2Fo-Fc = Fo + (Fo-Fc), 3Fo-2Fc = Fo +2(Fo-Fc) To be precise, it is actually 2mFo-DFc for acentric reflections and mFo for centric reflections I prefer to think of it rather as 2mFo - DFc = DFc + 2(mFo-DFc) for acentrics and mFo = DFc + (mFo-DFc) for centrics. Then it also becomes clear that to be consistent the corresponding difference map coefficients should be 2(mFo-DFc) for acentrics and (mFo-DFc) for centrics. Cheers -- Ian
[ccp4bb] Expression of a protein of 43KDa
I am trying to overexpress a His-tagged protein of 29KDa in E.coli (BL21-codon plus) and I end up with a highly expressed product that of 43KDa that binds to the Ni-column. I also have nice crystals. Does anyone have any experience on this. Armando
[ccp4bb] Bad r factor at low resolution
What does it mean having the R factors a high resolution lower than at low resolution?. Could be related to the fact my model is incomplete? Armando
