Re: [ccp4bb] Mounting needle-shaped crystals
Dear Jack I can certainly recommend using the litholoops from molecular dimensions to mount the crystal you descibe. Most of the membrane crystal we start out with come as needles, the advantages is as mention before that the slight twist in the nylon loops isn't present. We do not have much success with the litholoops looking like little rackets. best Preben Tanner, John J. wrote: Dear CCP4, I'm looking for advice on mounting thin needles for low temperature data collection. Our needles are fairly long (100-200 microns) but only 20 microns or less thick. When I pick them up with Hampton loops (0.05-0.1 mm size), the crystals tend to break as they are moved out of the drop and through the liquid-air interface. I see that Mitegen sells MicroLoops E, which are advertised as working well for mounting needles. Can anyone recommend them? Can anyone recommend Mitegen MicroMeshes or another tool for mounting needles? Thanks, Jack Tanner -- Jens Preben Morth, Ph.D Aarhus University Department of Molecular Biology Gustav Wieds Vej 10 C DK - 8000 Aarhus C Tel. +45 8942 5025, Fax. +45 8612 3178 j...@mb.au.dk website: http://person.au.dk/da/j...@mb
Re: [ccp4bb] anisotropic data
Katja Schleider schrieb: Hi everybody, is there a way to improve crystals that diffract strongly anisotropic? We got data between 2.5 and 4.0 A and scala says we should cut these data at 3.9 A. It's such a... I want to solve this structure! greetings Katja Hi Katja, check out http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality - maybe some of those hints can be tried? HTH, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature smime.p7s. smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] crystallography teaching advice: f(S) ?
William G. Scott wrote: Howdie folks: I'm preparing my annual X-ray diffraction lectures, and am at the point where one replaces the atomic scattering factor with the integrated electron density. It has always bothered me how this is a bit obscure, since it really lies at the heart of the physical description. Is there a straightforward way to explain this? I guess it depends on what level the course is, but you seem to suggest that the students do not have an extensive physics training. We have generally skipped over that bit quite elegantly, which does not in any way detract from the understanding of the crystallography (albeit perhaps the physics part of it.) The point to emphasize is going from a description based on a point scatterer, to realizing that atoms are not infinitely small; indeed their sizes are approximately identical to the wavelength of the X-rays. From there, the integrals come easily by stating that you need to add up scattering contributions from all parts of the atom, which to a first approximation is well described as a spherical symmetric gaussian distribution of charge. Finally, the integrals are replaced by an experimentally determined scattering curve, where the angular components are integrated out, leaving only a radial component, which is consulted via table-lookup. Don't know if it's a better description, but it fast-forwards to the result which is most important in a crystallography context, and teleports the students across the hermeneutic circle ;-) Cheers, Morten -- Morten Kjeldgaard, asc. professor, MSc, PhD BiRC - Bioinformatics Research Center, Aarhus University C. F. Møllers Alle, Building 1110, DK-8000 Aarhus C, Denmark. Lab +45 8942 3130 * Fax +45 8942 3077 * Home +45 8618 8180 Mobile +45 5186 0147 * http://www.bioxray.au.dk/~mok
Re: [ccp4bb] Mounting needle-shaped crystals
Hi Charlie, The bending of needles is hard to avoid :) My advice is to investigate different areas of the needle using finely focused beam - in particular focus on the protruding end and on the area inside the loop. The protruding area is particularly good since it has the least solvent attached to it. One of those may work out :) There's an alternative to this and that's using a very large loop so the needle never touches the nylon. The disadvantage of this approach is obviously the large volume of solvent/oil present in the loop, resulting in large background scatter. As far as systematic absences lost due to special orientation - yes, although if you have a bent loop (similar to the cheater pins from the bygone days) that's not much of an issue. Additionally, precise selection of space group can be always made as the structure's solved :) Artem Useful summary, Artem. Two comments spring to mind. - I have had trouble with slight bending of needles when frozen like this, causing problems with mosaicity. (Presumably due to different forces acting on the parts of the crystal within and without the loop.) - You can have lots of trouble measuring systematic absences in crystals mounted like this as the unique axis in hexagonal or tetragonal is close to the rotation axis. Cheers, Charlie Artem Evdokimov wrote: Sorry, hit send by accident. Here it is: http://www.xtals.org/pdfs/needles.pdf Artem -Original Message- From: Artem Evdokimov [mailto:ar...@xtals.org] Sent: Monday, October 05, 2009 9:05 PM To: 'Tanner, John J.'; 'CCP4BB@JISCMAIL.AC.UK' Subject: RE: [ccp4bb] Mounting needle-shaped crystals Hello felow MO crystallographer, For all it's worth, a while ago I've compiled a little document which describes mounting needles. I've converted it into PDF and posted it here: Nothing is built on stone; all is built on sand, but we must build as if the sand were stone Jorge Luis Borges -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tanner, John J. Sent: Monday, October 05, 2009 5:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Mounting needle-shaped crystals Dear CCP4, I'm looking for advice on mounting thin needles for low temperature data collection. Our needles are fairly long (100-200 microns) but only 20 microns or less thick. When I pick them up with Hampton loops (0.05-0.1 mm size), the crystals tend to break as they are moved out of the drop and through the liquid-air interface. I see that Mitegen sells MicroLoops E, which are advertised as working well for mounting needles. Can anyone recommend them? Can anyone recommend Mitegen MicroMeshes or another tool for mounting needles? Thanks, Jack Tanner -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406
Re: [ccp4bb] pointless, hi and low resolution
Dear Ariel I2 (== I 1 2 1) is the same space group as C 2, but with a different setting of the h l axes. You can use either, or you can force Pointless to choose the C2 setting Best wishes Phil On 6 Oct 2009, at 14:53, Ariel Talavera wrote: Hi there, I am integrating, with imosflm, a datset divided high and low resolution datasets. I first integrated the high resolution one in C2, but after running Pointless it suggested I121. The same happened during the low-resolution data integration, but the cell parameters are slightly different respect to the hi-resolution data. Should I fix the cell parameters during the integration of the low resolution data to the parameters obtained from the Pointless corrected hi- resolution integration? How often happen that pointless suggest a different space group respect to the cell refinement space group? Thanks a lot in advanced. Best, Ariel -- * Ariel Talavera Pérez, PhD Center of Molecular Immunology calle 216 esq. A 15, Atabey, Playa Havana 11600, CUBA tel: (53-7) 271 7933, ext. 221 fax: (53-7) 272 0644 email: talav...@cim.sld.cu *
[ccp4bb] Looking for a good review of successful SBDD.
I am looking for a good review on SBDD that includes a few successful attempts. Anyone know one? Thanks, Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver
Re: [ccp4bb] Looking for a good review of successful SBDD.
Scott Pegan wrote: I am looking for a good review on SBDD that includes a few successful attempts. Anyone know one? Williams et al 10.1016/j.cbpa.2005.06.007 Paul.
[ccp4bb] Professor Louis Delbaere
Dear Crystallographic Community, It is with great sadness that I inform you of the passing of Professor Louis Delbaere. Louis passed away suddenly on October 5th in Mississauga, Ontario, Canada while returning home to Saskatoon from an ACA Council meeting in Buffalo, NY. At the end, Louis was surrounded by his family - his wife Carol, his son Christian and his daughter Michelle. Louis was an incredibly active member of our community, serving as the Canadian Rep to the ACA from 1999-2001, a member of the ACA Communications Committee from 2003-2006, and as President of the ACA in 2005. He was the current president of the Canadian National Committee for Crystallography, a member of the IUCr Executive Committee, and led the successful Canadian bid to bring the 2014 IUCr congress to Montreal. Louis mentored numerous crystallographers, many of whom continue his legacy as active crystallographers themselves. His contributions, friendship and enthusiasm for science, and in particular crystallography, will be truly missed. Funeral arrangements are being made for Louis in Saskatoon. If colleagues wish to send condolences, you can contact me directly at aude...@yorku.ca, and I will ensure that your wishes are passed on Carol and the Delbaere Family. Sincerely, Gerald Audette -- Gerald F. Audette, Ph.D. Assistant Professor, Department of Chemistry Centre for Research on Biomolecular Interactions York University Rm 456 Chemistry Building 4700 Keele St. Toronto, ON, M3J 1P3 Canada Phone: (416) 736-2100 ext. 33318 Fax: (416) 736-5936 Email: aude...@yorku.ca Web: http://www.yorku.ca/audette
Re: [ccp4bb] Mounting needle-shaped crystals
I must agree that the less stressed part of a needle may be the end not contacting the loop or meniscus, but protrudes out the end/top. One can carefully manipulate the crystal so that it is not parallel with the pin either by having a bent loop or setting the crystal slightly diagonal to the loop. If it is held out long enough, then only that part is in the beam with no background from the loop or mother liquor. In fact, I have seen where the meniscus was the problem as it curved the crystal in questionthe part overhanging the loop diffracting quite nicely. Additionally, small molecule people will regularly use a small dab of grease (I prefer Apiezon N) on a loop or fiber to adhere the crystal and remove it from the batch...then freeze it. The advantage is simplicity, and one can remove a crystal from virtually all mother liquor. The disadvantages are it a bare crystal free from all liquor (must be frozen ASAP before it dehydrates) and depending on your skill and luck sometimes one gets more than one crystal. Finally, if there is a worry about dehydration, a tip is to move the crystal from the crystallization drop to oil increasing time for manipulation. (Again, my preference is PFPE). Kris PS For a thin layer of grease, try disolving the grease in a volatile solvent, dipping the loop or fiber in the solution, and let dry. From: Jürgen Bosch jubo...@jhsph.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, October 6, 2009 9:04:51 AM Subject: Re: [ccp4bb] Mounting needle-shaped crystals Hi Jack, you could try the following strategy: a) use a larger loop than your needle, then before freezing carefully dip the loop onto the glass slide to reduce the amount of liquid b) if your crystal is larger than your largest loop cut it c) see attached figure. The way I mount those type of crystals is not to break through the surface but instead to retract the loop and lift the crystal out of the drop. The tip of the crystal comes out as last. Typically the part of the crystal in the loop has a higher mosaicity due to this treatment as you slightly need to bend the crystal when fishing it out of the drop. d) The Mitegen loops are very useful Good luck, Jürgen On Oct 5, 2009, at 6:52 PM, Tanner, John J. wrote: Dear CCP4, I'm looking for advice on mounting thin needles for low temperature data collection. Our needles are fairly long (100-200 microns) but only 20 microns or less thick. When I pick them up with Hampton loops (0.05-0.1 mm size), the crystals tend to break as they are moved out of the drop and through the liquid-air interface. I see that Mitegen sells MicroLoops E, which are advertised as working well for mounting needles. Can anyone recommend them? Can anyone recommend Mitegen MicroMeshes or another tool for mounting needles? Thanks, Jack Tanner -- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tanne...@missouri.edu http://www.chem.missouri.edu/TannerGroup/tanner.html - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] SA composite omit maps in Phenix
Hi Jason, I just replied to very similar question to someone in person. Your options are: - all about SA omit maps and more: http://www.phenix-online.org/documentation/autobuild.htm ask Tom Terwilliger should you have any questions. - also, a good thing to check (the best actually; this option is available): Acta Cryst. (2008). D64, 515-524 Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias - You can use Average Kick Maps (see above slides) with the region in question omitted. This is available in phenix.refine. Some details about kick maps are in the slide #20: http://cci.lbl.gov/~afonine/rsr/afonine_05OCT2009_.pdf Please let me know if you have any questions or/and need any help. Cheers, Pavel. On 10/6/09 1:21 PM, Jason C Porta wrote: After searching the documentation and archives, I could not find an answer to a question regarding Phenix maps. I am trying to make an Fo-Fc composite omit map of a structure that has the solvent deleted. I want to create a map using Fo-Fc as the coefficient and with composite omit phases. How would I do this in Phenix? Also, what kind of map is being generated by default? What is the FP coefficient? Thanks in advance for any assistance Sincerly, Jason Porta Doctoral Candidate Dept. Biochemistry Molecular Biology University of Nebraska Medical Center Omaha, NE 68198 (402) 559-5533
