[ccp4bb] Postdoctoral Position at PSI
We currently have an opening for a postdoctoral fellow in integrated structural biology, c.f. http://www.psi.ch/pa/offenestellen/Wissenschaft/2219 Michel O. Steinmetz (Biomolecular Research) Clemens Schulze-Briese (Swiss Light Source) Paul Scherrer Institut 5232 Villigen - PSI SWITZERLAND
[ccp4bb] Waters from Coote
Is there a preferred type of density map to use with Coote for identifying waters? Rex Palmer Birkbeck College
[ccp4bb] Solvent accessible regions of the channel (Pore)
Dear all; Can anybody help me how I can make the solvent accessible surface(inside) of the channel(pore)by pymol, or by any other programme. Thanks in Advance -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Phone: +43(1)427752224 Fax: +43(1)42779522
Re: [ccp4bb] Possible sulphate
Rex Palmer wrote: What seems to be a possible sulphate has been identified in our electron density. What steps could/should be taken to confirm or consolidate this assignment that would satisfy referees? Rex Palmer Birkbeck College Geometry of the interactions (and the shape of the electron density). Anomalous map. Even if you have only diffraction data collected at low wavelength you can always compute an anomalous map and see if the sulphur shows up. Fred.
Re: [ccp4bb] Solvent accessible regions of the channel (Pore)
Caver? http://loschmidt.chemi.muni.cz/caver/ cheers, charlie
Re: [ccp4bb] Third CCP4 workshop in USA, at APS, June 10-17
Dear Colleagues, This is a third and final call for applications for the third annual CCP4 school: From data collection to structure refinement and beyond which will be held at Advanced Photon Source, USA. Application deadline has been extended from Friday, April 9 to Tuesday, April 12. A full program and the list of speakers are now available. These and other details (application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2010/ Workshop will include data collection, processing, structure solution, model building, refinement, validation, deposition to PDB, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov
[ccp4bb] crystals of 1D
Hi All, I am dealing with a protein that crystallizes in 1D. The broom stick crystals does not yield with any improvement w.r.t their dimension. I have tried using different concentration of salt, ppt and pH around the parent condition, even tried seeding and temperature changing. However, any of these method does not help. Any suggestion is welcome. Thank you in advance. Sincerely Debajyoti
Re: [ccp4bb] Solvent accessible regions of the channel (Pore)
Dear Muhammed, HOLLOW (http://hollow.sourceforge.net) probably is OK. You can find a nice example at figure 2 of Ujwal et al., PNAS vol15(46), 17742-17747 (the interior surface of the mVDAC1 channel) HTH Jose Miguel --
Re: [ccp4bb] Possible sulphate
A reasonably strong peak on the S atom in an anomalous difference Fourier map. From: Rex Palmer rex.pal...@btinternet.com Reply-To: Rex Palmer rex.pal...@btinternet.com Date: Wed, 7 Apr 2010 09:00:59 -0500 To: CCP4BB@JISCMAIL.AC.UK Conversation: [ccp4bb] Possible sulphate Subject: [ccp4bb] Possible sulphate What seems to be a possible sulphate has been identified in our electron density. What steps could/should be taken to confirm or consolidate this assignment that would satisfy referees? Rex Palmer Birkbeck College
Re: [ccp4bb] crystals of 1D
Hi, i'm not sure if you try just seeding in your original condition. If yes, you could try matrix seeding. Another option would be addtitves or the silver bullets from McPherson. Sometimes sitting drop vs. hanging drop make a difference. Mutations at the surface are quite often an excellent alternative to get new crystal forms. Christian Am Mittwoch 07 April 2010 16:46:32 schrieb Debajyoti Dutta: Hi All, I am dealing with a protein that crystallizes in 1D. The broom stick crystals does not yield with any improvement w.r.t their dimension. I have tried using different concentration of salt, ppt and pH around the parent condition, even tried seeding and temperature changing. However, any of these method does not help. Any suggestion is welcome. Thank you in advance. Sincerely Debajyoti
Re: [ccp4bb] Solvent accessible regions of the channel (Pore)
Hi Bashir, In Pymol: 1. Show---Surface (will generate surface around the protein) 2. Setting-Surface---Cavities Pockets Only. (will show only Cavities inside) 3. Use cavity_cull command to set the filter for cavities. (eg. set cavity_cull, 40) Manish -- Manish Chandra Pathak, Ph.D. Department of Biochemistry Emory University School of Medicine 1510 Clifton Road, NE, Room G235 Atlanta, GA 30322 USA Tel: +1-404-727-2563 Fax: +1-404-727-2738 - Original Message From: Muhammed bashir Khan muhammad.bashir.k...@univie.ac.at To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, April 7, 2010 9:58:20 AM Subject: [ccp4bb] Solvent accessible regions of the channel (Pore) Dear all; Can anybody help me how I can make the solvent accessible surface(inside) of the channel(pore)by pymol, or by any other programme. Thanks in Advance -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Phone: +43(1)427752224 Fax: +43(1)42779522
[ccp4bb] PDBe to retire the OCA search system in October 2010
Dear PDBe users, The Protein Data Bank in Europe (PDBe; pdbe.org) will retire the OCA search system in October 2010. Users and developers relying on this service are advised to direct their links to the OCA site at the Weizmann Institute instead - http://oca.weizmann.ac.il/oca-bin/ocamain Developers who use OCA for programmatic access, e.g. in scripts to retrieve a list of entries that contain a certain ligand, may contact us (msdh...@ebi.ac.uk) for information on how to get the same information from the PDBe database. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk http://www.ebi.ac.uk/pdbe/ Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] crystals of 1D
Hi, Have you also considered substituting the components of your initial crystallization hit. For example, you can substitute the original PEG with others PEGs. You can also systematically replace the cations (CaCl2, MgCl2, etc) and anions (CaCl2, CaOAc, etc) from the original conditions. This approach has worked very well in the past for a number of crystals that were initially very thing needles or very thin plates. Along this line, CdCl2 is also a nice additive that seems a little underused. See Trakhanov Shttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Trakhanov%20S%22%5BAuthor%5D, Kreimer DIhttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Kreimer%20DI%22%5BAuthor%5D, Parkin Shttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Parkin%20S%22%5BAuthor%5D, Ames GFhttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Ames%20GF%22%5BAuthor%5D, Rupp B http://www.ncbi.nlm.nih.gov/pubmed?term=%22Rupp%20B%22%5BAuthor%5D, Protein Sci. javascript:AL_get(this,%20'jour',%20'Protein%20Sci.'); 1998 Mar;7(3):600-4. Good Luck, Melanie On Wed, Apr 7, 2010 at 10:46 AM, Debajyoti Dutta debajyoti_dutt...@rediffmail.com wrote: Hi All, I am dealing with a protein that crystallizes in 1D. The broom stick crystals does not yield with any improvement w.r.t their dimension. I have tried using different concentration of salt, ppt and pH around the parent condition, even tried seeding and temperature changing. However, any of these method does not help. Any suggestion is welcome. Thank you in advance. Sincerely Debajyoti http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline@middle?
Re: [ccp4bb] crystals of 1D
Have you tested how well they diffract? You should do that first. Sometimes small, ugly looking crystals can give good data. ho
Re: [ccp4bb] Solvent accessible regions of the channel (Pore)
Hello Muhammad, The comments thus far are spot on, but the choice depends on your objective. If you are looking for the probable substrate trajectory, CAVER (though I'd suggest MOLE http://mole.chemi.muni.cz/web/), but these lack detail of the solvent accessible surface. If you want fast rendering for analysis, the PyMol Setting..Surface..Cavities Pockets Only (play around with the radius, culling, and cutoff), but the surface is hard to edit and each parameter effects the surface displayed (make sure to use maximum quality display to get a accurate surface). For illustration and editing with detail try our program HOLLOW (http://hollow.sourceforge.net), but it is not as simple and is more computationally intensive. The website gives step by step instructions under the examples. For HOLLOW, I'd still suggest maximum quality display in PyMOl (only use when you are nearly finished because it is really slow) and open the channel by using the cylindrical search and hide surface for the generated object with q=0 to open the channel. Good luck. Franz Gruswitz Department of Biochemistry and Biophysics UCSF Mission Bay 600 16th St. S414 San Francisco, CA 94158
[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
