Re: [ccp4bb] why I can't reproduce R based on the same program?

Thanks for all the advices. The REFMAC PDB didn't provide ksol and bsol in the author's refinement, otherwise I would fix them in my refinement. Best Regards, Hailiang > Hi Hailiang, > >> I want to reproduce the R factor provided by PDB file. The structure was >> refined by REFMAC, and so I thi

Re: [ccp4bb] why I can't reproduce R based on the same program?

Hi Hailiang, I want to reproduce the R factor provided by PDB file. The structure was refined by REFMAC, and so I think if I try a REFMAC refinement based on the pdb file and reflection data, the initial R factor given by REFMAC should be it. The pdb file provides residual B factors with TLS g

Re: [ccp4bb] Fab purification and crystallization

Dear Ivan, We faced the same problem for our Hya/Fab complex (clustered needles). By change the pH and doing microseeding, we were able to improve the crystals quality. For more information see our paper Padavattan, S., Schirmer, T., Schmidt, M., Akdis, C., Valenta, R., Mittermann, I., Soldatov

Re: [ccp4bb] why I can't reproduce R based on the same program?

I see in your script you used Weight Auto - play a bit with that value and you will find a better fit. Have you used the same TLS groups ? I don't see that you are using TLS refinement in your script. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistr

[ccp4bb] why I can't reproduce R based on the same program?

Hi there: I want to reproduce the R factor provided by PDB file. The structure was refined by REFMAC, and so I think if I try a REFMAC refinement based on the pdb file and reflection data, the initial R factor given by REFMAC should be it. The pdb file provides residual B factors with TLS given b

[ccp4bb] Beamtime at the ALS-BCSB beamlines

Dear All, September 15, 2010 is the deadline for the November/December 2010 Rapid Access Proposal cycle. All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal s

Re: [ccp4bb] How to define NCS in REFMAC

Dear Jürgen: Exactly! 1SS8, the tls-refined GroEL. I generated a PDB containing the total anistropic B values by TLS, based on which I want to reproduce the R factor by REFMAC as they used. Thanks for your advice, following is my script. Unfortunately, it failed to reproduce the PDB R factor... N

Re: [ccp4bb] Fab purification and crystallization

I assume you separate your complex over a size exclusion before setting up trays ? If not try that and see if you get better crystals. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615

Re: [ccp4bb] How to define NCS in REFMAC

Take a look at this part of a script, I added your NCS operators in two options. So you are working on GroEL ? Good luck, Jürgen #!/bin/csh -f set prevVer = 01 set prevRun = 00 set currVer = 02 set currRun = 04nolig set currData = my_latest_structure # set xyzin = omitted_ligands.pdb set xyz

[ccp4bb] Fab purification and crystallization

Hi CCP4bb, I have two questions regarding Fab purification and Fab-antigen complex crystallization and would really appreciate any input from the experienced board. 1) I have got some hits for Fab-antigen complex (150 kD) but they are all needle clusters. Whatever fine screen I formulate, it alwa

Re: [ccp4bb] List of commonly used cryoprotectants and buffer molecules

>Dear All, > >I am trying to find out which molecules are frequently used by X-ray >crystallographers serving as cryoprotectants or as buffer molecules. The >idea behind this is to sort native ligands from molecules that appeared in >the electron density just because they were used in the crysta

Re: [ccp4bb] List of commonly used cryoprotectants and buffer molecules

This cryocrystallography webinar lists some common cryoprotectants: http://www.rigaku.com/protein/webinar-001.html -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Chris Weichenberger Sent: Thursday, September 09, 2010 7:34 PM To: CCP4BB@JISCMAIL.A

Re: [ccp4bb] List of commonly used cryoprotectants and buffer molecules

ISRDB Cryoprotectant database for protein crystals is a good resource, not only for the cryoprotection methods but the freezing methods used from literature. http://idb.exst.jaxa.jp/db_data/protein/200304E02478000.html It is under maintenance at the moment though... HTH, Matt On Thu, Sep 9, 201

[ccp4bb] List of commonly used cryoprotectants and buffer molecules

Dear All, I am trying to find out which molecules are frequently used by X-ray crystallographers serving as cryoprotectants or as buffer molecules. The idea behind this is to sort native ligands from molecules that appeared in the electron density just because they were used in the crystalliza

[ccp4bb] How to define NCS in REFMAC

Hi there: The REFMAC manual give me a hard time to define the NCS during refinement. Can anybody give a first time user a sample script based on the following PDB header (NCS part only is ok, but please include how todefine tight restrant only for both positional and B ref, for both NCS groups)? T

Re: [ccp4bb] Human Haemoglobin Crystallization Protocol

How aboutAdachi, S., S. Y. Park, J. R. Tame, Y. Shiro, and N. Shibayama. 2003. Direct observation of photolysis-induced tertiary structural changes in hemoglobin. Proc Natl Acad Sci U S A 100:7039-44. Ito, L., T. Kobayashi, K. Shiraki, and H. Yamaguchi. 2008. Effect of amino acids and amino acid d

[ccp4bb] Human Haemoglobin Crystallization Protocol

Hi all, I'm looking for a good (or any) crystallization protocol for human haemoglobin. I've found some resources online but they want me to pay to download the PDFs. Does anyone know of any good protocols or at least where I might find this info? Thanks, ~Brennan~

Re: [ccp4bb] fail to install ccp4i task for arp warp

Dear Jochen, Huw and others, We have managed to reproduce the problem on a 64bit Mac with fink-installed CCP4. We can confirm that the problem appears to be related to 64bit TCL/bltwish as suggested by Huw. Invoking a 32-bit installation of fink alongside a 64 bit one can be tricky, so we propo

Re: [ccp4bb] non-identical complexes in the asymmetric unit

I use PISA to analyse this - sometimes the differences depend on the definition of "what is a hydrogen bond?" and unless you have very high resolution it is risky to say there are significant differences.. But certainly there are examples where the results are very significant indeed - you coul

Re: [ccp4bb] protein dimensions

pdbset gives it to you too. pdbset xyzin a.pdb end if you want the principal exes I still use Amore table function - that reorientates the model according to ppl axes then gives you the dimensions along each axis.. Tim Gruene wrote: On Wed, Sep 08, 2010 at 08:21:33PM +0200, Nikos Pinotsis w

Re: [ccp4bb] ARP/wARP 7.1; ccp 6.1.13 and Mac OSX 10.6 (64bit fink)

On 9 Sep 2010, at 01:57, Leiman Petr wrote: > Switch to the 64bit environment (source /sw64/bin/init.sh in a new terminal > window). Install ARP/wARP while in this terminal (not sure if this is needed > actually, probably not). > Then copy all the files from these directories: > /sw/share/xtal/ccp