Re: [ccp4bb] Solvent content of membrane protein crystals
Das, Debanu wrote: Hi, There are at least 4 methods to try to estimate amount of detergent in a membrane protein crystal . In summary, someone wanting to estimate amount of detergent in their crystals and have sufficiently large and numerous crystals, could try out any of the above methods. The above techniques are quite well documented in literature. The first 3 can be done in-house and so can FTIR. I happen to have the reference for Ron Kaplan's TLC method at my fingertips: Eriks, L. R., Mayor, J. A. Kaplan, R. S. (2003). A strategy for identification and quantification of detergents frequently used in the purification of membrane proteins. Anal Biochem 323, 234-41. Sensitivity is limited by the amount of aqueous solution you can spot on a TLC plate. Probably could improve sensitivity by speed-vac-ing an aliquot to near dryness and redissolving in 50% methanol or something.
Re: [ccp4bb] mosflm orientation matrix and symmetry
Bryan, I think it would be more correct to say that the orientation matrix file applies to the Bravais type (e.g., hP--hexagonal primitive). Within the Bravais type you can substitute a different space group prior to integration. Nick From: Bryan W. Lepore [EMAIL PROTECTED] does the mosflm orientation matrix specify the crystal system and only the crystal system? i.e, given an orientation matrix from autoindexing, it would be correct to simply use keyword 'SYMMETRY SPACEGROUP' in mosflm to refine then integrate in any of the spacegroups within a given crystal system from autoindexing? -bryan
[ccp4bb] Quick soak method
Hi, I'd like to find out how successful the quick soak method for heavy atom derivatisation proposed by Radaev and Sun: Sun PD, Radaev S, Kattah M. Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases. Acta Cryst. 2002. D58:1092-1098. has been in comparison to the classical method of longer soaks at low concentrations of heavy atom compound. The method was quite successful in our hands a few years ago but (fortunately?) it's becoming increasingly rare that we use heavy atoms. I understand that evidence will necessarily be anecdotal, but let's not let that stop us. Derek -- Derek Logan tel: +46 46 222 1443 Associate professor fax: +46 46 222 4692 Molecular Biophysicsmob: +46 76 8585 707 Lund University Box 124, Lund, Sweden
Re: [ccp4bb] mosflm orientation matrix and symmetry
Hi Bryan, So, there are two answers to this question. If you are changing the spacegroup within the same lattice type (e.g. tP) then it is fine (this is probably what you mean by crystal system) - though you can do this by just running reindex symm whatever afterwards. If you want to change from one lattice to another (e.g. from oI to mC) then some recalulations will be necessary - the way I do this is as follows: Run othercell a program from the pointless collection with the original unit cell and symmetry, work through the output to find the reindex operator for the target unit cell and symmetry, convert this to a matrix and multiply the A and U matrices in the mosflm matrix file by this amount. Remarkably, this works fine, and I do it all the time. Hope this helps. Cheers, Graeme -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bryan W. Lepore Sent: 24 September 2007 19:22 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] mosflm orientation matrix and symmetry does the mosflm orientation matrix specify the crystal system and only the crystal system? i.e, given an orientation matrix from autoindexing, it would be correct to simply use keyword 'SYMMETRY SPACEGROUP' in mosflm to refine then integrate in any of the spacegroups within a given crystal system from autoindexing? -bryan
[ccp4bb] Crystallographic Post-doctoral Position in Champaign-Urbana, IL
An NIH funded post-doctoral position is available to work as part of a multi-disciplinary effort on structure determination of proteins involved in antibiotic biosynthesis (Science 311, 1464-1467). Candidate should have a background in standard protein purification, synchrotron data collection, SAD/MAD structure determination, refinement and validation. Our lab is equipped with an RAXIS IV+ +/H3R/Osmic/X-stream system. In addition, the University of Illinois is a member of LS-CAT (Beamlines 21-IDD, IDF, and IDG at Argonne) and we are routinely allocated up to a total of fourteen days of insertion device line access per 3-month run. Salary will be commensurate with experience. Urbana-Champaign is a friendly, energetic, midwestern college town with a very low cost of living, many student amenities, etc. We are located 2.5 hours from Chicago, 2 hours from Indianapolis and 3.5 hours from St. Louis. Please send a CV and 3 letter of reference to: Dr. Satish Nair Department of Biochemistry University of Illinois at Urbana-Champaign 600 S. Mathews Ave Urbana, IL 61801 [EMAIL PROTECTED]
[ccp4bb] SRS AP50 (April - December 2008) Open for Applications
Dear SRS Users, Applications are now invited for beam-time in allocation period 50 (April - December 2008) on PX station 10.1 at the SRS. The deadline for submission of proposals is Thursday 1st November. Further details on how to apply for beamtime can be found here :- http://www.srs.ac.uk/srs/userSR/AP50_announcement.htm Station 10.1 (http://www.biophysics.dl.ac.uk/srsbl10.html) at the SRS Daresbury is a world competitive high throughput PX/XAFS structural biology facility. It has a XAFS capable sagittal focussing monochromator (tuneable between 5 and 14 keV) a state-of-the-art MarMosaic CCD225 detector and a state of the art low-profile monolithic 4-element x-ray fluorescence Ge detector, with an energy resolution of 170-200 eV. This is the first time that such a high quality fluorescence detector is included as an integral part of a PX beamline. A crystal microspectrophotometer for measuring optical data is also available on-line. Station 10.1 is therefore ideally suited for combining optical, PX and XAFS data collection on the same protein crystal, identifying metal redox states of crystals in-situ, anomalous diffraction measurements, monitoring crystals for radiation damage and long wavelength (up to 2.3Å) SAD phasing experiments. In addition, automated cryogenic sample changing allows high-throughput crystal screening and data collection. Please feel free to contact me ([EMAIL PROTECTED]) or Richard Strange ([EMAIL PROTECTED]) if you have any questions. Yours sincerely, Mark Ellis --- Dr. Mark Ellis SRS Station Scientist 10.1 Researcher Molecular Biophysics Group Science and Technology Facilities Council Daresbury Laboratory Daresbury Science and Innovation Campus Warrington Cheshire WA4 4AD, UK tel : +44 (0)1925 603830 http://www.stfc.ac.uk fax : +44 (0)1925 603748 http://www.biophysics.dl.ac.uk
[ccp4bb] Pymol installation
Dear all. We have had success installing Pymol on any 32 bits PC, but we are having some troubles with 64 bits. The OS is linux ubuntu kernel: 2.6.15-29-amd64-generic x86_64 The pymol version is: pymol-0_99rc6-bin-linux-x86-glibc23.tgz The error message is: freeglut (./pymol.exe): ERROR: Internal error Visual with necessary capabilities not found in function fgOpenWindow X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 4 (X_DestroyWindow) Resource id in failed request: 0x0 Serial number of failed request: 16 Current serial number in output stream: 19 PyMOL: abrupt program termination. We have already installed the dependencies requested in the README file of the software (openGL, glutlibrary, python, tcl/tk and libpng). Can you provide any clues on how to proceed to get Pymol running? Thank you, João.
[ccp4bb] Alignment question
Hi all, I'm looking for a webserver that can take the alignment and produce a nice figure with the alignment annotated with sec. structure on top, and draw boxes around conserved residues. Long time ago I had used a server doing exactly what I described; unfortunately, I lost the information of that server from my computer and the memory could not help to find it in google. I'm sure there are many tools, but I'm interested in an easy-to-use one. Something to plugin the sequence/alignment and get a pretty alignment figure. I'd be appreciating if someone out there could point me to that server or similar ones. I looked at several tools available online in Expasy but none is doing what I did before. thanks in advance for your help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 --
Re: [ccp4bb] Alignment question
On Tuesday 25 September 2007 14:22, Ibrahim M. Moustafa wrote: I'm looking for a webserver that can take the alignment and produce a nice figure with the alignment annotated with sec. structure on top, I use TeXShade http://www.ctan.org/tex-archive/help/Catalogue/entries/texshade.html But it's a TeX package, not a web server. Might you be thinking of http://wavis.img.cas.cz/ ? -Ethan and draw boxes around conserved residues. Long time ago I had used a server doing exactly what I described; unfortunately, I lost the information of that server from my computer and the memory could not help to find it in google. I'm sure there are many tools, but I'm interested in an easy-to-use one. Something to plugin the sequence/alignment and get a pretty alignment figure. I'd be appreciating if someone out there could point me to that server or similar ones. I looked at several tools available online in Expasy but none is doing what I did before. thanks in advance for your help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 -- -- Ethan A MerrittCourier Deliveries: 1959 NE Pacific Dept of Biochemistry Health Sciences Building University of Washington - Seattle WA 98195-7742
Re: [ccp4bb] Alignment question
Thanks a lot for Francesco, Ethan, and Jessica. Yes, it is ESPrit. For unknown reasons, when I use keywords: sequence + alignment + tools in google that server never showed up. It is also worthy to look at the other servers suggested in the reply given below: Francesco Charlie Bond has a really nice program called ALINE. He used to have it on his website http://stein.bioch.dundee.ac.uk/~charlie/index.php? section=6 Alternatively, you can just e-mail him [EMAIL PROTECTED] Ethan Merritt I use TeXShade http://www.ctan.org/tex-archive/help/Catalogue/entries/texshade.html But it's a TeX package, not a web server. Might you be thinking of http://wavis.img.cas.cz/ ? Jessica Lynn, Espript can do exactly what you're asking, and if I figured it out, you'll be able to easily. I bet it's what you used before. It's really powerful. http://espript.ibcp.fr/ESPript/ESPript/ thanks a lot, Ibrahim At 05:22 PM 9/25/2007, you wrote: Hi all, I'm looking for a webserver that can take the alignment and produce a nice figure with the alignment annotated with sec. structure on top, and draw boxes around conserved residues. Long time ago I had used a server doing exactly what I described; unfortunately, I lost the information of that server from my computer and the memory could not help to find it in google. I'm sure there are many tools, but I'm interested in an easy-to-use one. Something to plugin the sequence/alignment and get a pretty alignment figure. I'd be appreciating if someone out there could point me to that server or similar ones. I looked at several tools available online in Expasy but none is doing what I did before. thanks in advance for your help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 -- -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 --
Re: [ccp4bb] Quick soak method
Hi, I do not use their method as such - however, I love heavy atom soaks and do them any time I can, so I've got very similar experiences in the past. Heavy atoms can bind very quickly even from quite dilute solutions - the quickest I've ever soaked (and got useful data) was sodium chloroplatinate in under ten minutes at ~ 1mM concentration. The next quickest was K2Pt(NO2)4 which tends to take between 10 minutes and 30 minutes, almost regardless of the concentration. This is by far my favorite HAD reagent, incidentally. In general my soaks are all less than one hour with a few exceptions, such as iodine [not iodide!] soak to iodinate tyrosines which is typically better done during a day or so with very low amount of I2, via vapor phase. Artem Hi, I'd like to find out how successful the quick soak method for heavy atom derivatisation proposed by Radaev and Sun: Sun PD, Radaev S, Kattah M. Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases. Acta Cryst. 2002. D58:1092-1098. has been in comparison to the classical method of longer soaks at low concentrations of heavy atom compound. The method was quite successful in our hands a few years ago but (fortunately?) it's becoming increasingly rare that we use heavy atoms. I understand that evidence will necessarily be anecdotal, but let's not let that stop us. Derek -- Derek Logan tel: +46 46 222 1443 Associate professor fax: +46 46 222 4692 Molecular Biophysicsmob: +46 76 8585 707 Lund University Box 124, Lund, Sweden
Re: [ccp4bb] Quick soak method
Hi - sorry - rather than iodine I meant to say we had had success with Potassium Iodide (1M for 20 seconds)! Cheers James [EMAIL PROTECTED] wrote: Hi, I do not use their method as such - however, I love heavy atom soaks and do them any time I can, so I've got very similar experiences in the past. Heavy atoms can bind very quickly even from quite dilute solutions - the quickest I've ever soaked (and got useful data) was sodium chloroplatinate in under ten minutes at ~ 1mM concentration. The next quickest was K2Pt(NO2)4 which tends to take between 10 minutes and 30 minutes, almost regardless of the concentration. This is by far my favorite HAD reagent, incidentally. In general my soaks are all less than one hour with a few exceptions, such as iodine [not iodide!] soak to iodinate tyrosines which is typically better done during a day or so with very low amount of I2, via vapor phase. Artem Hi, I'd like to find out how successful the quick soak method for heavy atom derivatisation proposed by Radaev and Sun: Sun PD, Radaev S, Kattah M. Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases. Acta Cryst. 2002. D58:1092-1098. has been in comparison to the classical method of longer soaks at low concentrations of heavy atom compound. The method was quite successful in our hands a few years ago but (fortunately?) it's becoming increasingly rare that we use heavy atoms. I understand that evidence will necessarily be anecdotal, but let's not let that stop us. Derek -- Derek Logan tel: +46 46 222 1443 Associate professor fax: +46 46 222 4692 Molecular Biophysicsmob: +46 76 8585 707 Lund University Box 124, Lund, Sweden -- Professor James Whisstock NHMRC Principal Research Fellow / Monash University Senior Logan fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile)
Re: [ccp4bb] Quick soak method
I also solved a structure on our home CuKa source by SIRAS with 20-60sec in 0.5-1M KI. JPK ==Original message text=== On Tue, 25 Sep 2007 6:55:28 pm CDT James Whisstock wrote: Hi - sorry - rather than iodine I meant to say we had had success with Potassium Iodide (1M for 20 seconds)! Cheers James [EMAIL PROTECTED] wrote: Hi, I do not use their method as such - however, I love heavy atom soaks and do them any time I can, so I've got very similar experiences in the past. Heavy atoms can bind very quickly even from quite dilute solutions - the quickest I've ever soaked (and got useful data) was sodium chloroplatinate in under ten minutes at ~ 1mM concentration. The next quickest was K2Pt(NO2)4 which tends to take between 10 minutes and 30 minutes, almost regardless of the concentration. This is by far my favorite HAD reagent, incidentally. In general my soaks are all less than one hour with a few exceptions, such as iodine [not iodide!] soak to iodinate tyrosines which is typically better done during a day or so with very low amount of I2, via vapor phase. Artem Hi, I'd like to find out how successful the quick soak method for heavy atom derivatisation proposed by Radaev and Sun: Sun PD, Radaev S, Kattah M. Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases. Acta Cryst. 2002. D58:1092-1098. has been in comparison to the classical method of longer soaks at low concentrations of heavy atom compound. The method was quite successful in our hands a few years ago but (fortunately?) it's becoming increasingly rare that we use heavy atoms. I understand that evidence will necessarily be anecdotal, but let's not let that stop us. Derek -- Derek Logan tel: +46 46 222 1443 Associate professor fax: +46 46 222 4692 Molecular Biophysicsmob: +46 76 8585 707 Lund University Box 124, Lund, Sweden -- Professor James Whisstock NHMRC Principal Research Fellow / Monash University Senior Logan fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile) ===End of original message text=== *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)491-2438 [EMAIL PROTECTED] ***
