Re: [ccp4bb] how to add atoms in refmac library
Hi, Zinc is very much present in the Refmac library. ZN zinc non-polymer 1 1C Are you using the correct atom id in your PDB file? It has to be ZN. Ganesh Le 14/02/13 21:28, Faisal Tarique a écrit : Dear all My protein has Zinc atom but the refmac does not identifies it during refinement..Can anybody please tell me how to add Zinc atom into the refmac library for the successful refinement of the coordinates. -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] remove job posting
Dear Jilliu, If you contact us here at the ccp4 help desk (c...@ccp4.ac.ukmailto:c...@ccp4.ac.uk) we can remove the advert from the CCP4 vacancies website. However, we can't remove it from the various archives of the mailing list that exist around the web. Let me know which advert you want removed. Best wishes, Ronan From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of jlliu liu Sent: 15 February 2013 04:09 To: ccp4bb Subject: [ccp4bb] remove job posting Can anyone tell me how to remove the job posting on CCP4BB? Thanks! -- Scanned by iCritical.
Re: [ccp4bb] Thanks for the new graphical CCP4 installer
Thank you Francois for positive feedback. Eugene On 15 Feb 2013, at 05:40, Francois Berenger wrote: It is easy to use and even nice looking. Regards, F. -- Scanned by iCritical.
[ccp4bb] Twilight update
Dear All, we have updated the ligand structure database distributed with the TWILIGHT package http://www.ruppweb.org/twilight/default.htm to include all PDB entries with an EDS entry up to the Jan 16 2013 release. The table contains now about 500 more flagged entries. As always, the disclaimer: TWILIGHT employs automatic ranking based on an arbitrarily selected resolution dependent real space correlation cutoff for ligand density and does NOT provide any further analysis - please inspect the density in each case - various causes can lead to a flagged entry (as explained in the accompanying publications). Editorial, paper, explanation caveats: http://journals.iucr.org/d/issues/2013/02/00/issconts.html http://journals.iucr.org/f/issues/2013/02/00/issconts.html Happy twilighting, BR Bernhard Rupp k.-k. Hofkristallamt Vista, CA 92084 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- The road to scientific serfdom is paved with Nature papers ---
[ccp4bb] EMBO Practical Course on Biological Small Angle Scattering (X-rays and neutrons) 6-10 May 2013
Dear colleagues we would like to announce an EMBO Practical Course on Biological Small Angle Scattering (X-rays and neutrons) to be held at EPN Grenoble from May 6th to 10th 2013 (*deadline for inscription is March 1st*): http://events.embo.org/13-SAXS/index.html Best Regards On behalf on the organizers Frank Gabel, Marc Jamin, Anne Martel, Sean McSweeney, Petra Pernot and Adam Round -- Dr David FLOT Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63 Structural Biology GroupFax : (+33) 4 76 88 26 24 ESRF B.P. 220, 6 rue Jules Horowitz e-mail : david.f...@esrf.fr F-38043 GRENOBLE CEDEX http://www.esrf.eu
[ccp4bb] HETATM automated chain assignment
Hello to the CCP4 bulletin board community, I would like to know if I could find a tool to automatically assign HETATM atom (or even, water molecules) to the nearest protein chain ? In my case, I have 4 protein chains in the asymmetric unit : A, B, C and D. I would like to assign each ions and each ligands (which are numerous) with the chain letter of the nearest residue that coordinate them. Usually, I rename everything by hand but as the in-house program of the PDBe AutoDep deposition tool automatically do that... I beg your pardon if this question has just been posted here. I didn't find any tool either in the CCP4 Suite or in the Extensions and Calculate menus of the Coot program (v0.7). Best regards. Romain Talon
Re: [ccp4bb] HETATM automated chain assignment
Have a look at sortwater. http://www.ccp4.ac.uk/html/sortwater.html If you want to use it for non-water ions in addition to waters, you would need to run it a second time for each of the atom types using the water keyword to define the residue type and atom name. Also, it won't work for multi-atom ions, but could work for Na, Cl, K, Mg, Ca etc Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Talon Romain Sent: Friday, February 15, 2013 8:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] HETATM automated chain assignment Hello to the CCP4 bulletin board community, I would like to know if I could find a tool to automatically assign HETATM atom (or even, water molecules) to the nearest protein chain ? In my case, I have 4 protein chains in the asymmetric unit : A, B, C and D. I would like to assign each ions and each ligands (which are numerous) with the chain letter of the nearest residue that coordinate them. Usually, I rename everything by hand but as the in-house program of the PDBe AutoDep deposition tool automatically do that... I beg your pardon if this question has just been posted here. I didn't find any tool either in the CCP4 Suite or in the Extensions and Calculate menus of the Coot program (v0.7). Best regards. Romain Talon
Re: [ccp4bb] HETATM automated chain assignment
Dear Romain, I already ask this question to someone of the pdb staff during a deposition process, and he answer me that it is an in house program and they don't distribute theirs in house programs, so if this direction hit your mind, you can forget it directly. Meow... 2013/2/15 Talon Romain talon@gmail.com Hello to the CCP4 bulletin board community, I would like to know if I could find a tool to automatically assign HETATM atom (or even, water molecules) to the nearest protein chain ? In my case, I have 4 protein chains in the asymmetric unit : A, B, C and D. I would like to assign each ions and each ligands (which are numerous) with the chain letter of the nearest residue that coordinate them. Usually, I rename everything by hand but as the in-house program of the PDBe AutoDep deposition tool automatically do that... I beg your pardon if this question has just been posted here. I didn't find any tool either in the CCP4 Suite or in the Extensions and Calculate menus of the Coot program (v0.7). Best regards. Romain Talon
Re: [ccp4bb] Sighting of Protein Crystals in Vivo?!
Hi Jacob, check out Figure 1 in Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Redecke L, et al. Science. 2013 Jan 11;339(6116):227-30. and In vivo protein crystallization opens new routes in structural biology. Koopmann R. Nature Methods. 2012 Jan 29;9(3):259-62. best Savvas On 15 Feb 2013, at 20:44, Jacob Keller wrote: Dear Crystallographers, I was looking at some live, control HEK cells expressing just eGFP, and to my great surprise, saw littered across the dish what appeared to be small fluorescent needles (see attached--sorry about the size, but it's only ~1MB total.) Can these possibly be fortuitous protein crystals? They were too small to mount I think, and for what it's worth, parallel-transfected HeLa cells did not have these things. But, some needles could be seen in the DIC images as well, and the needles were only fluorescent with GFP filter sets, and not CFP, YFP, or texas red filters. I thought of whale myoglobin crystallizing on the decks of ships, but never thought I would see this Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** GFP_crystals_DIC.pngGFP_crystals_Fluorescence.png
Re: [ccp4bb] Sighting of Protein Crystals in Vivo?!
Of course, common in baculo: http://dx.doi.org/10.1038/emboj.2009.352 The EMBO Journal (2010) 29,505--514 *How baculovirus polyhedra fit square pegs into round holes to robustly package viruses* Xiaoyun Ji, Geoff Sutton, Gwyndaf Evans, Danny Axford, Robin Owen and David I Stuart On 15/02/2013 20:00, Savvas Savvides wrote: Hi Jacob, check out Figure 1 in Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Redecke L, et al. Science. 2013 Jan 11;339(6116):227-30. and In vivo protein crystallization opens new routes in structural biology. Koopmann R. Nature Methods. 2012 Jan 29;9(3):259-62. best Savvas On 15 Feb 2013, at 20:44, Jacob Keller wrote: Dear Crystallographers, I was looking at some live, control HEK cells expressing just eGFP, and to my great surprise, saw littered across the dish what appeared to be small fluorescent needles (see attached--sorry about the size, but it's only ~1MB total.) Can these possibly be fortuitous protein crystals? They were too small to mount I think, and for what it's worth, parallel-transfected HeLa cells did not have these things. But, some needles could be seen in the DIC images as well, and the needles were only fluorescent with GFP filter sets, and not CFP, YFP, or texas red filters. I thought of whale myoglobin crystallizing on the decks of ships, but never thought I would see this Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** GFP_crystals_DIC.pngGFP_crystals_Fluorescence.png
Re: [ccp4bb] Sighting of Protein Crystals in Vivo?!
Hi Jacob, They are not too small to mount I think, at least 20 microns long (compared to the size of surrounding cells). But what do you mean by littered? There seems to be just one cell with crystals out of say 10 expressing eGFP. And why are there only 10 or so expressing GFP out of ~200 or more cells in the field? This does not look like transient expression using a normal plasmid... Very intriguing nevertheless! radu -- A. Radu Aricescu, PhD University Research Lecturer University of Oxford Wellcome Trust Centre for Human Genetics Division of Structural Biology Roosevelt Drive, Oxford OX3 7BN United Kingdom Phone: +44-1865-287564 Fax: +44-1865-287547 Original message Date: Fri, 15 Feb 2013 14:44:32 -0500 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Jacob Keller j-kell...@fsm.northwestern.edu) Subject: [ccp4bb] Sighting of Protein Crystals in Vivo?! To: CCP4BB@JISCMAIL.AC.UK Dear Crystallographers, I was looking at some live, control HEK cells expressing just eGFP, and to my great surprise, saw littered across the dish what appeared to be small fluorescent needles (see attached--sorry about the size, but it's only ~1MB total.) Can these possibly be fortuitous protein crystals? They were too small to mount I think, and for what it's worth, parallel-transfected HeLa cells did not have these things. But, some needles could be seen in the DIC images as well, and the needles were only fluorescent with GFP filter sets, and not CFP, YFP, or texas red filters. I thought of whale myoglobin crystallizing on the decks of ships, but never thought I would see this Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** GFP_crystals_DIC.png (938k bytes) GFP_crystals_Fluorescence.png (586k bytes)
Re: [ccp4bb] Sighting of Protein Crystals in Vivo?!
My favorite: Hum Mol Genet. 2000 Jul 22;9(12):1779-86. Link between a novel human gammaD-crystallin allele and a unique cataract phenotype explained by protein crystallography. Kmoch S, Brynda J, Asfaw B, Bezouska K, Novák P, Rezácová P, Ondrová L, Filipec M, Sedlácek J, Elleder M. http://hmg.oxfordjournals.org/content/9/12/1779.long From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Friday, February 15, 2013 3:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Sighting of Protein Crystals in Vivo?! Of course, common in baculo: http://dx.doi.org/10.1038/emboj.2009.352 The EMBO Journal (2010) 29,505-514 How baculovirus polyhedra fit square pegs into round holes to robustly package viruses Xiaoyun Ji, Geoff Sutton, Gwyndaf Evans, Danny Axford, Robin Owen and David I Stuart On 15/02/2013 20:00, Savvas Savvides wrote: Hi Jacob, check out Figure 1 in Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Redecke L, et al. Science. 2013 Jan 11;339(6116):227-30. and In vivo protein crystallization opens new routes in structural biology. Koopmann R. Nature Methods. 2012 Jan 29;9(3):259-62. best Savvas On 15 Feb 2013, at 20:44, Jacob Keller wrote: Dear Crystallographers, I was looking at some live, control HEK cells expressing just eGFP, and to my great surprise, saw littered across the dish what appeared to be small fluorescent needles (see attached--sorry about the size, but it's only ~1MB total.) Can these possibly be fortuitous protein crystals? They were too small to mount I think, and for what it's worth, parallel-transfected HeLa cells did not have these things. But, some needles could be seen in the DIC images as well, and the needles were only fluorescent with GFP filter sets, and not CFP, YFP, or texas red filters. I thought of whale myoglobin crystallizing on the decks of ships, but never thought I would see this Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu *** GFP_crystals_DIC.pngGFP_crystals_Fluorescence.png
[ccp4bb] Structure Refinement
Dear All I have a data at 2.75A. I process it in Space group P3121, using HKL3000. Run a molrep,find three molecule in a unit cell. I am trying to refine it with phenix, the R and R-free stuck at 34 and 41 respectively. Crystal: The crystal seems multiple thin plates and I tried to freeze the possible single crystal (plate). Any suggestion would be highly appreciated!! Bashir Muhammad Bashir Khan ** Structural Genome Consortium (SGC) University of Toronto Canada
Re: [ccp4bb] Structure Refinement
Hi Bashir, if you send me the data and model (directly to my email address, not the whole list), then I will have a look. Also, please note there is Phenix mailing list for Phenix specific questions. Pavel On Fri, Feb 15, 2013 at 12:35 PM, Muhammed bashir Khan muhammad.bashir.k...@univie.ac.at wrote: Dear All I have a data at 2.75A. I process it in Space group P3121, using HKL3000. Run a molrep,find three molecule in a unit cell. I am trying to refine it with phenix, the R and R-free stuck at 34 and 41 respectively. Crystal: The crystal seems multiple thin plates and I tried to freeze the possible single crystal (plate). Any suggestion would be highly appreciated!! Bashir Muhammad Bashir Khan ** Structural Genome Consortium (SGC) University of Toronto Canada
Re: [ccp4bb] Structure Refinement
A very likely possibility (but there may be others) is merohedral twinning, which can and often does occur in this space group, and these are typical R-values you would get stuck to in case of partial merohedral twinning. Checking the log file of truncate should be informative in this respect. Also: there cannot be three molecules in the unit cell as this space group has six asymmetric units. You probably mean three molecules in the asymmetric unit. Since crystallography is an exact science, one needs to be correct. Remy Loris Vrije Universiteit Brussel On 15/02/13 21:35, Muhammed bashir Khan wrote: Dear All I have a data at 2.75A. I process it in Space group P3121, using HKL3000. Run a molrep,find three molecule in a unit cell. I am trying to refine it with phenix, the R and R-free stuck at 34 and 41 respectively. Crystal: The crystal seems multiple thin plates and I tried to freeze the possible single crystal (plate). Any suggestion would be highly appreciated!! Bashir Muhammad Bashir Khan ** Structural Genome Consortium (SGC) University of Toronto Canada
Re: [ccp4bb] Sighting of Protein Crystals in Vivo?!
I am impressed that within a matter of hours, we now have a number of references for papers describing so-called in vivo crystallization. Wow, the benefits of a good network I guess. This kind of quick feedback would be fantastic for authors who are writing review articles... Dave Waugh On 2/15/13 3:27 PM, Michael Kothe michael.ko...@genzyme.com wrote: My favorite: Hum Mol Genet. 2000 Jul 22;9(12):1779-86. Link between a novel human gammaD-crystallin allele and a unique cataract phenotype explained by protein crystallography. Kmoch S, Brynda J, Asfaw B, Bezouska K, Novák P, Rezácová P, Ondrová L, Filipec M, Sedlácek J, Elleder M. http://hmg.oxfordjournals.org/content/9/12/1779.long From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Friday, February 15, 2013 3:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Sighting of Protein Crystals in Vivo?! Of course, common in baculo: http://dx.doi.org/10.1038/emboj.2009.352 The EMBO Journal (2010) 29,505–514 How baculovirus polyhedra fit square pegs into round holes to robustly package viruses Xiaoyun Ji, Geoff Sutton, Gwyndaf Evans, Danny Axford, Robin Owen and David I Stuart On 15/02/2013 20:00, Savvas Savvides wrote: Hi Jacob, check out Figure 1 in Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Redecke L, et al. Science. 2013 Jan 11;339(6116):227-30. and In vivo protein crystallization opens new routes in structural biology. Koopmann R. Nature Methods. 2012 Jan 29;9(3):259-62. best Savvas On 15 Feb 2013, at 20:44, Jacob Keller wrote: Dear Crystallographers, I was looking at some live, control HEK cells expressing just eGFP, and to my great surprise, saw littered across the dish what appeared to be small fluorescent needles (see attached--sorry about the size, but it's only ~1MB total.) Can these possibly be fortuitous protein crystals? They were too small to mount I think, and for what it's worth, parallel-transfected HeLa cells did not have these things. But, some needles could be seen in the DIC images as well, and the needles were only fluorescent with GFP filter sets, and not CFP, YFP, or texas red filters. I thought of whale myoglobin crystallizing on the decks of ships, but never thought I would see this Jacob -- David S. Waugh, Ph.D. Macromolecular Crystallography Laboratory Center for Cancer Research National Cancer Institute Bldg. 538, Room 209A Frederick, MD 21702-1201 +1 (301) 846-1842 wau...@mail.nih.gov http://mcl1.ncifcrf.gov/waugh.html --
Re: [ccp4bb] Sighting of Protein Crystals in Vivo?!
Hi Jacob, Interesting topic. This reminds me the posters I saw on ACA 2010, on the femto-second infrared laser based instrument . That instrument utilizes the nonlinear optical properties of crystals of chiral molecules to detect very small crystalline materials from amorphous background: the crystals will double the frequency of the laser, turning the infrared light to visible light. I cannot recall the exact name of the technology now, unfortunately. Your case of observing in vivo GFP crystals is a little special in that the crystals are fluorescent. I guess if we scan cells over-expressing proteins with the above mentioned instrument, we might find that many proteins will do the same in cells. Naturally occurring in vivo crystals are not very rare. If we do not restrict the topic to proteins, then it is well known that many viruses readily crystallize in the host cell's nuclei and the resulting crystals or crystalline arrays can be observed under EM. And if we do not restrict the cells to mammalian cells, then there come the famous BT crystals. In addition, I just did some internet search and here are some interesting results: 1) Viral protein crystals can form in HEK cells infected by adenovirus (http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002894) 2) Bacterial infection can cause the infected epithelial cells to form pathological crystal-containing inclusion bodies in the cytosol (http://www.ncbi.nlm.nih.gov/pubmed/8940763). 3) Crystalline inclusion bodies are found in rabbit embryos (http://dev.biologists.org/content/44/1/31.full.pdf) and epididymis of the nine-banded armadillo(http://www.sciencedirect.com/science/article/pii/S0022532073800073). Actually if google crystalline inclusion body, there will be tons of literatures. 4) IgG crystallized in the ER when over expressed from a highly optimized CHO expression system (http://www.jbc.org/content/286/22/19917.abstract). This is particularly interesting as we know that whole IgGs are not so prone to crystallize, although the author do state that Crystallizing propensity was due to the intrinsic physicochemical properties of the model IgG. Given the prevalence of in vivo crystallization, especially considering their correlation with inclusion bodies, I think it is reasonable to suspect that there are some cases that the inclusion bodies formed during over expression of transgenic proteins in E. coli are crystalline. I expect that we will be enlightened on this issue by somebody on the BB soon. Zhijie From: Jacob Keller Sent: Friday, February 15, 2013 2:44 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Sighting of Protein Crystals in Vivo?! Dear Crystallographers, I was looking at some live, control HEK cells expressing just eGFP, and to my great surprise, saw littered across the dish what appeared to be small fluorescent needles (see attached--sorry about the size, but it's only ~1MB total.) Can these possibly be fortuitous protein crystals? They were too small to mount I think, and for what it's worth, parallel-transfected HeLa cells did not have these things. But, some needles could be seen in the DIC images as well, and the needles were only fluorescent with GFP filter sets, and not CFP, YFP, or texas red filters. I thought of whale myoglobin crystallizing on the decks of ships, but never thought I would see this Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu ***
