Re: [ccp4bb] Shelx_install_in_ccp4iv6.0.2
Dear Xue yuan What file are you trying to install into CCP4i? The CCP4i interface for the SHELX programs is already included in CCP4 6.0.2 and so you should not have to install it yourself. However, in order for it to work you need the SHELX programs themselves to accessible on your system - this is completely separate from CCP4i, and CCP4i cannot do this for you. Instead you need refer to the SHELX website at http://shelx.uni-ac.gwdg.de/SHELX/ which should tell you how to obtain and install the programs. Hope this helps, best wishes Peter Xue-Yuan Pei wrote: > Dear All: > I am trying to install Shelx C/D/E/ into ccp4i(v6.0.2) using "system > administration" tool for task installation. It complains and said: This > may not be a valid ccp4i package. > How can I intall Shelx into CCP4i? Your help is highly appreciated > Regards > Xue yuan Pei, Ph.D > Department of Biochemistry > University of Cambridge > Cambridge CB2 1QA > U.K -- ___ Peter J Briggs, [EMAIL PROTECTED] Tel: +44 1925 603826 CCP4, [EMAIL PROTECTED] Fax: +44 1925 603825 http://www.ccp4.ac.uk/ Daresbury Laboratory, Daresbury, Warrington WA4 4AD
Re: [ccp4bb] chromatofocusing
Any old references for "universal buffers"... Johnson, and Lindsey, Analyst, 64 (1939). Ellis, D. A., Nature, 191 (1961). Prideaux, E. B. R. , and Ward, A. T. , J. Chem. Soc., 125, 426 (1924). Britton, H. T. S. , and Robinson, R. A. , J. Chem. Soc., 1457 (1931). But I never use these buffers myself and I don't know if these buffers are suitable for your column, you have to check chemical compatibility. Most chromatofocusing common troubleshooting is protein precipitation near isoelectric point, protein precipitation at unsupported pH and CO2 degassing adsorbed by buffer at high pH and released at low pH. Glycerol or betain can help you for protein precipitation and degassing / N2 storing for CO2 releasing. To optimize the resolution thin column and low flow rate are good choices. Michel.
Re: [ccp4bb] chromatofocusing
You might look at this paper: http://www.ncbi.nlm.nih.gov/sites/ entrez?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12433100 They used DEAE and have given (in the supporting materials) a ton of useful information. Cynthia On Sep 3, 2007, at 4:27 PM, James Fraser wrote: I'm forwarding this to the listserve for someone in my lab who is having trouble sending to the list. Replies to the list or directly to Nat Echols ([EMAIL PROTECTED]) are greatly appreciated... Not question about crystallography, but that's the ultimate goal: Has anyone used a custom-made buffer for use with the PBE media sold by GE? I found a bottle of Pharmacia PBE 94 and would like to use it, but if I did I would use it frequently and on a relatively large scale, so I'd rather not pay for the (expensive and proprietary) Polybuffer. Alternately, has anyone done something similar with DEAE/CM media? I've seen references to this (although I suspect the resolution won't be as good), but not very good descriptions. thanks, Nat Cynthia Kinsland, Ph.D. Cornell University Protein Facility Director 607-255-8844
[ccp4bb] Why is RANGES restricted to <60 in TRUNCATE ?
Dear developers, using the FALLOFF option in TRUNCATE to analyse the anisotropy of a high resolution data set (1.2 Ang.) it is impossible to enhance the number of bins to values higher than the default number of 60 (lower number is possible). How can I overcom this limit? To determine the positions of maxima in this plot it is neccessary to get more data points. Greetings, Juergen -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/
Re: [ccp4bb] solving structure of which 70% is known
Hi Raya, My reply comes late but maybe it is still relevant to you. I have a few suggestions for molecular replacement in phaser: * Input both protein models in your search (define both known structures as ensembles and search for both) * Give higher values (let's say 1.0, 1.2, 1.4) for the "rms difference" in "Similarity of PDB" * Allow a number of clashes as packing tolerance (check your log files how many clashes the "top solutions" have) * Run phaser with "all choices of alternative space group" (as mentioned before) Good luck, christian Raja Dey wrote: > Hello, > I am trying to solve a multi-protein DNA complex structure from a > 3.6 A native data set. The target structure is a dimer (95 aa in each > monomer) in complex with DNA( 15 base pairs) plus a second protein of 131 aa. > The data has been scaled to P6(1)22 sp. gr. and one target structure is > expected to be in the asymmetric unit that corresponds to 68% solvent > content. 70 % of the target structure is known in two parts(two different pdb > structures previously solved contributing 55% and 15% of the target > structure). I tried with molrep and phaser considering the first part(55%) as > the search model but it turned out to no good solution which all clashes with > symmetry related copies. If I assume the sp. gr. is not the case what else I > can try. Any suggestion is well appreciated. > Thanks... > Raja > ___ Dr. Christian Biertümpfel Laboratory of Molecular Biology NIDDK/National Institutes of Health phone: +1 301 402 4647 9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201 Bethesda, MD 20892-0580 USA ___
[ccp4bb] covalently bonded Ligand fit
Hi I am trying fit a ligand (organo phosphate) covalently bonded to residue Serine 250 in my structure. How can I connect this phosphate to Ser-O and during refinement (refmac and CNS), how should I mention in the ligand in the input and how should I number it? I use COOT as graphics. Thanks for suggestion. Sam. _ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us
Re: [ccp4bb] covalently bonded Ligand fit
If you are dealing with phosphoserine then there is a monomer called SEP that is phosphorilated serine. pdb coordinates are attached: regards Garib libcheck_SEP.pdb Description: Binary data On 4 Sep 2007, at 23:41, U Sam wrote: Hi I am trying fit a ligand (organo phosphate) covalently bonded to residue Serine 250 in my structure. How can I connect this phosphate to Ser-O and during refinement (refmac and CNS), how should I mention in the ligand in the input and how should I number it? I use COOT as graphics. Thanks for suggestion. Sam. _ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/ friends.aspx&mkt=en-us
[ccp4bb] Li ion scattering factor
Dear All, We have a structure under refinement with a putative Li bound to a potentially important allosteric site. I'd assumed that Li+ would lose an electron and have weaker scattering than Li Metal, but the entry for atomsf.lib has the same # of electrons for both entries while the entries for F and F-, Na and Na+ etc all differ by ±1 as expected. Since the coefficients for the scattering factor calculation are different for Li and Li+, I guess four crystallographic calculations that's all that matters? Li 3 30.037700 1.1282000.7508000.6175000.465300 3.9546001.052400 85.390503 168.261002 0.0010000.000.000.00 Li+1 3 30.016700 0.6968000.7888000.3414000.156300 4.6237001.9557000.631600 10.095300 0.0010000.000.000.00 I also have a general question about how ions are differentiated from the unionized atomic species in the PDB. Is the left shift by 1 character in column 3 and the last column, using Cl as an example below, how the PDB (and Refmac) distinguish Cl-1 from Cl? ATOM 4175 CLCL I 1 5.299 23.521 60.812 1.00 18.77 CL ATOM 3854 O THR B 220 -16.228 28.954 11.993 1.00 7.54 O Thanks for your input - Mark
Re: [ccp4bb] Li ion scattering factor
Number of electrons are rarely (if ever) used. In principle sum of the coefficients of gaussians should be equal to the number of electrons. Ions from nonions are distinguished by just addition charge on the element column. Example: ATOM 4175 CLCL I 1 5.299 23.521 60.812 1.00 18.77 CL ATOM 4175 CLCL I 1 5.299 23.521 60.812 1.00 18.77 CL-1 ATOM 3854 O THR B 220 -16.228 28.954 11.993 1.00 7.54 O Garib On 4 Sep 2007, at 23:54, Mark Mayer wrote: Dear All, We have a structure under refinement with a putative Li bound to a potentially important allosteric site. I'd assumed that Li+ would lose an electron and have weaker scattering than Li Metal, but the entry for atomsf.lib has the same # of electrons for both entries while the entries for F and F-, Na and Na+ etc all differ by ±1 as expected. Since the coefficients for the scattering factor calculation are different for Li and Li+, I guess four crystallographic calculations that's all that matters? Li 3 30.037700 1.1282000.7508000.6175000.465300 3.9546001.052400 85.390503 168.261002 0.0010000.000.000.00 Li+1 3 30.016700 0.6968000.7888000.3414000.156300 4.6237001.9557000.631600 10.095300 0.0010000.000.000.00 I also have a general question about how ions are differentiated from the unionized atomic species in the PDB. Is the left shift by 1 character in column 3 and the last column, using Cl as an example below, how the PDB (and Refmac) distinguish Cl-1 from Cl? ATOM 4175 CLCL I 1 5.299 23.521 60.812 1.00 18.77 CL ATOM 3854 O THR B 220 -16.228 28.954 11.993 1.00 7.54 O Thanks for your input - Mark
