[ccp4bb] xtal programs free to non-academic users
Dear All, Sorry for a non-ccp4 question. I ask this question for a small starting company who wants to find out which programs are available free of charge for non-academic users. The ones I am familiar with all are free to academic users but not free to non-academic users. Would any one please name some possible choices for data processing, structure determination, refinement and validation? Thank you Rongjin Guan
Re: [ccp4bb] statistics of A/B
how about Delta method? see examples here: http://www.math.umt.edu/patterson/549/Delta.pdf = = = = = = = = On 2011-06-07 08:47:04 You wrote = = = = = = = = Thank you for the reply. Hypothesis: A and B are independent and normal distribution. Could you please explain more? Thanks. --- On Mon, 6/6/11, chris.mor...@stfc.ac.uk wrote: From: chris.mor...@stfc.ac.uk Subject: statistics of A/B To: capri...@yahoo.com Date: Monday, June 6, 2011, 4:00 AM HI, Do you have a hypothesis about the distributions of A and B? If so, there might be an analytic answer to your question, and certainly you can answer it by monte carlo simulation. Without a know distribution, it does not have an answer. From the mean and variance of A and B, you can work out the mean and variance of: A - B But not of: Log A Note that the answer you are looking for will be ill conditioned if the distribution of B includes points near 0. regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 https://www.pims-lims.org/ Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD If means and standard deviations of A and B are known, how to estimate the variance of A/B? Thanks. -- Scanned by iCritical.
[ccp4bb] reference on the van der Waals contact distance
Hello, I often see these vdW contact distance cut-off numbers (see below) in papers, but no reference was given. "Contact distances are the following maximum allowed values: C-C, 4.1 Å; C-N, 3.8 Å; C-O, 3.7 Å; O-O, 3.3 Å; O-N, 3.4 Å; N-N, 3.4 Å; C-S, 4.1 Å; O-S, 3.7 Å; N-S, 3.8 Å." I am curious how these numbers were developed. For example, S has a larger vdW radius than C, but the vdW contact cut-offs are the same as for C. Does any one know such an old reference or textbook for these numbers? Thanks Rongjin Guan
[ccp4bb] non-identical complexes in the asymmetric unit
Dear All, I have a structure with two complexes in the asymmetric unit, and the interactions on the interface are not the same in the two complexes. Briefly, there are two additional hydrogen bonds in one complex, but not in the other. This coule be due to crystallization artefact, but may have other explanations. Can anyone direct us to some references where this has been discussed before? Thank you very much Rongjin Guan
[ccp4bb] SAXS on a coiled coil protein
Sorry for a non-ccp4 question. We have determined a structure which is mainly a coiled coil motif. The two helices are from the same protein chain linked by a short turn. However, the SAXS data indicates that "this protein is probably natively unfolded or may have very flexible domains and linkers" as commented by our collaborators who did the SAXS experiments. Could this be due to the "shifting" of the turn connecting the two helices? Has this kind of "flexibility" in the turn position in a coiled coil motif been observed in other coiled coil structures? Thank you Rongjin Guan
[ccp4bb] molprobity in coot: BL WARNING:: reduce didnt run ok, so stop here!
Hello, I just installed Wincoot 0.6.1 and reduce/probe as well, and tested with several PDB files for probe/clash validation. For some PDBs it worked perfectly; but for my own model, it did not work and I have the following message: . Found 0 hydrogens (0 hets) Standardized 0 hydrogens (0 hets) Added 3946 hydrogens (0 hets) Removed 0 hydrogens (0 hets) Adjusted 113 group(s) If you publish work which uses reduce, please cite: Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747. For more information see http://kinemage.biochem.duke.edu BL WARNING:: reduce didnt run ok, so stop here! run_generic_script (probe, 0) My model was outputed from phenix refinement and I checked the format and can not see anything wrong. Can anyone give me some hints? Thanks Rongjin Guan
[ccp4bb] small molecule soaking screening
Hi All Sorry that this is a non-ccp4 question, but I hope I can get some good suggestions from the community. We have protein crystals under various conditons and want to soak them with different potential inhibitors. Most of inhibitors have very small molecular weights (200-300), so it become a problem how to detect if the small compounds have been soaked into the crystals or not. (co-crystallization experiments yielded no hits so far, though the free form is easy to be crysatllized under many conditions) We pay $500/day for local X-ray facility access, so we wonder if there are some more efficient ways that allow us to know if the small compounds soaked in or not, without collecting a whole data set for MR. We are also thinking if we can mix several compounds together for soaking, to reduce the combinations of soaking experiments with various compounds and crystals from various conditions. Is this practical, if some of them have pretty similar binding affinities to the protein? All comments/suggestions are welcome. Thank you Rongjin Guan
[ccp4bb] cryo-protection for crystals grown in ethanol
Dear All I got crystals from 20% Ethanol with 0.1M Tris pH 8.5. This is my first time to have crystals in Ethanol and want to get some suggestions of cryo-protection from those who have done this before. I am waiting for my time on home X-ray facility, and hope I can get some suggestions before that. Thanks, Rongjin Guan
[ccp4bb] detergent concentration used for membrane protein purification
Dear All sorry for a non-ccp4 related question. what is the typical concentration of detergents used in membrane protein purification? Is it usually within 1-10 times of CMC? My collaborator was using 10% DDM in purifying a membrane protein. I suggested to reduce it and now he is working with 2% DDM. He said lower than that the protein is not soluble. so another question is, can we purify the membrane protein first at high concentration of one detergent (say, 2% DDM), and then screen different detergents later to find a better one? Or it is better to screen the detergents first before purification? any suggestions will be appreciated. Have a nice holiday! Rongjin Guan
[ccp4bb] detecting RNA from possible protein-RNA complex crystals
Dear All I am trying to co-crystallize a protein and dsRNA complex, and looking for methods to detect RNA in the crystals. I am thinking about using Mass Spectrum, Nanodrop to measure OD280/260, etc, but I wonder if ther are some more sensitive and reliable ways. The crystals are grown in high concentration salts; the size is usually small but I do have several big ones which can be easily fished out. They can be dyed so definitely not salt crystals. Thanks Rongjin Guan
[ccp4bb] phosphorylation of protein is troublesome or not for crystallization
Dear all, Below is a question my friend asked me, but I have never worked on phosphorylated proteins. Has anyone worked on crystallizing phosphorylated proteins and can you comment on it? Thanks Rongjin Guan -- I would like to ask how feasible it is to crystalize protein containing post-translational modification, such as phosphorylation. To my limited knowledge, I think the heterogenicity of modified and unmodified proteins causes the major obstacle in the crystal structure. Is there any specific method to crystalized modified proteins (like phosphorylated proteins ) these days?
