Re: [ccp4bb] crystal Packing

Dear Eswar, You could try to slow down crystallization somehow. There are several ways to accomplish this: 1) increase drop size 2) add small amounts of glycerol (1-5% v/v) 3) cover the reservoir solution with paraffin or silicon oil or a mixture of both in order to reduce the vapor-diffusion rate

[ccp4bb] digilab honeybee96 alignment tools

Dear all, We have a Digilab Honeybee96 pipetting robot with a few broken needles in the lab. I have got replacement needles from Digilab but their alignment tools are on backorder. Does anybody (preferably nearby) have these tools and would be willing to lend them to us? We would pay for shipping a

Re: [ccp4bb] Matthews coefficient

Dear Xinghua, Of course, you can have 2 molecules in the asu. However, if things don't it is worth to double-check your space group or check for twinning. Cheers christian xinghua qin wrote: > hi CCPeers > The Matthews coefficient of my protein is 3 calculated with > matthews-cell content ana

Re: [ccp4bb] Dual boot--windows 7 and Linux

Hi Tongqing, I have recently installed SuSe Linux 11.2 on a Dell Latitude E6510 and I can confirm that the system comes with Windows 7 pre-installed on 4 primary partitions: - Dell Utility - Windows Recovery - Windows - Reader (for Latitude ON) I was not sure if Linux cares to have the bootloader (

Re: [ccp4bb] Protein-DNA complex crystallisation

Hi Jhon, Here are a few hints for protein-DNA crystallization: 1.) Starting point for protein:DNA ratio is 1:1.2 for a tight binder. In your case it would be protein complex to DNA 1:1.2. I like to run size-exclusion chromatography (if applicable) to determine an optimal ratio with a slight excess

Re: [ccp4bb] programs to check the structure of DNA

Hi Alessandra, Here is a list of nucleic acid and protein-nucleic acid related tools (including the ones mentioned by Luca and Maia: 3DNA http://rutchem.rutgers.edu/~xiangjun/3DNA/ http://w3dna.rutgers.edu/ curves http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html nucplot http://www.biochem.ucl.a

Re: [ccp4bb] Molecular Replacement

Dear Muhammed, In case you have used phaser for MR you could try to either decrease sequence identity or increase the rmsd of the search model (both ways are equivalent). This allows also to account for flexibility/movements in your target protein like Tim explained. Cheers, christian Muhammed

Re: [ccp4bb] FW: [ccp4]: TDS upon flashcooling

Hi Rafael, If you really want to diffract your crystals frozen, I have two more suggestions for cryo-procedures which can be tried: a) annealing e.g. Harp, J.; Timm, D. & Bunick, G. Macromolecular crystal annealing: overcoming increased mosaicity associated with cryocrystallography. Acta Crystallo

Re: [ccp4bb] Solvent content of crystals vs. resolution?

Hi Jeremiah, It is interesting that I have just told a student about this feature today. You can pull up the information from the pdb directly (advanced search) or have a look into the following article: Kantardjieff, K. A. & Rupp, B. Matthews coefficient probabilities: Improved estimates for unit

Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

Thank you Dr. Sauter for making such an awesome movie. I am sure it will be very valuable for teaching as well as for showing the general public what we do. Definitely try to have the DVD ready for Christmas shopping... Best regards, christian claude sauter wrote: > Narayanan Ramasubbu a écrit :

Re: [ccp4bb] ccp not open in new users account

Hi, Probably, you have not set up the environment correctly for the new user account. Source the correct ccp4.setup file depending on your shell. You can also put this into the configuration file specific for your shell (e.g. for bash: ~/.bashrc or for C-shell ~/.cshrc) for csh source /home/chanda

Re: [ccp4bb] molecular replacement in phaser

Hi Lisa, There are many things you can try and the phaser manual gives a lot of useful information what to do in difficult cases. From my experience, it is quite difficult to find solutions for MR with nucleic acids. I recommend to search only for protein. As a side effect you can use this approach

Re: [ccp4bb] use of siliconized cover glass

Hi Sang Hoon, When you have a crystal stuck to non-siliconized glass you will appreciate coated cover slips. The crystal appears to be "superglued" onto the glass surface. This can also happen when you transfer a crystal to another glass plate (e.g. depression plate) and it sinks down to the bottom

Re: [ccp4bb] structure alignment based on the ligand

Hi, To complete the responses you already have got, I recommend to use LSQMAN ( http://xray.bmc.uu.se/usf/lsqman_man.html ) for your alignment task. It can only compare two structures at a time but LSQMAN can easily be run script-based (using one structure as the reference). Select either all atom

Re: [ccp4bb] Second coordination sphere of a metal ion

Hi Nick, Have you checked the web services provided by Marjorie Harding? http://tanna.bch.ed.ac.uk/index.html http://eduliss.bch.ed.ac.uk/MESPEUS/ Maybe, you can also find information about water mediated contacts over there. The first web site gives also some links to other interesting web pages

Re: [ccp4bb] Lowest resolution you can do MR with

Hi, I cannot really answer what the lowest resolution for MR is but I have been successful with 4 A data for a protein-DNA complex and so I encourage you to try your 3.6 A data set. Of course, it also depends on the quality of your data, in particular how well/how many low resolution reflections we

Re: [ccp4bb] Coot Problem! adding r-nucleotide in DNA

Hi Yusuf, I had a similar problem once when my pdb file did not have the right format. Check your input coordinate file if your DNA nomenclature is correct for coot. Maybe, the program does not recognize your molecule as DNA. Good luck, christian Yusuf Akhter wrote: > Hi everybody! > I am using

Re: [ccp4bb] sticky crystals

Hi Savvas, If the very good suggestions you have already got from the ccp4bb do not help, try crystallization with agarose as an additive. Crystals form inside the very soft gel and they are hold in place by this meshwork. So, they are mechanically protected and do not fall down onto the bottom of

Re: [ccp4bb] OT: VectorNTI alternatives

Hi Darren, I can recommend another free tool: pDRAW32 ( http://www.acaclone.com/ ). It runs natively under Windows but I am using it with the emulator wine on Linux. Cheers, christian Darren Hart wrote: > Hello, > After several years of offering the molecular biology software VectorNTI > free to

Re: [ccp4bb] MR- Problem-76 % seqeunce identity-no solution

Hi Somu, Here are a few questions which might help: Are you sure about about your space group? Is another lattice/symmetry possible? Is twinning possible? Have you tried all possible space groups in MR? Have you tried different resolution ranges (e.g. all data, cut low resolution at 15 A, cut hi

Re: [ccp4bb] protein degradation

Hi Debajyoti, There is another simple thing you can try: Raise your NaCl concentration to 500 or 1000 mM in your lysis buffer. This helps to clean up your sample further and it might inhibit proteases in your lysate. Good luck, christian Debajyoti Dutta wrote: Hi, This is going to be an

Re: [ccp4bb] CNS error message with MR

Hi Jeff, I have seen this error before (with only DNA) when I had made mistakes in the chain selection (segids) in dna_rna-restreints.def. Best regards, christian J Knight wrote: Hello, Im working on a DNA, RNA, and protein ternary complex. Im having some trouble with refining using CNS an

Re: [ccp4bb] TMAO for crystallization

Hi Ruben, I have never used TMAO myself but this paper might give you a better idea: Jeruzalmi, D. & Steitz, T. Use of organic cosmotropic solutes to crystallize flexible proteins: application to T7 RNA polymerase and its complex with the inhibitor T7 lysozyme. J Mol Biol, 1997, 274, 748-56 T

Re: [ccp4bb] crystallisation

Hi Sajid, Just a simple test for your problem: Incubate your crystal longer in your cryo/stabilization solution. This helps sometimes to lower mosaicity. Of course, you can also try co-crystallization with glycerol (2%, 5% or 10%). Good Luck, christian sajid akthar wrote: Dear All My protein

Re: [ccp4bb] streak seeding in the presence of Ammonium sulfate

Hi Amit My advise is similar to Artem's: A colleague of mine has very good results in "immediate" streak seeding. He sets up drops covers them to avoid evaporation during all the handling and then, he starts streak seeding without delay. christian Artem Evdokimov wrote: I would instead try

Re: [ccp4bb] Off topic: ask about cryoprotectant selection using lithium sulfate as precipitant for crystal growth

Hi Donghui, I just want to draw your attention to the following article. It sums up suggestions which were already made by others for using concentrated (lithium) salt solutions for cryoprotection: Rubinson, K.; Ladner, J.; Tordova, M. & Gilliland, G. Cryosalts: suppression of ice formation in mac