[ccp4bb] What is the meaning of Fbar in solve ?
Hi everyone: Could anyone tell me the meaning of Fbar in the MADFBARFILE in solve? Does Fbar stand for delta f prime or just f prime for heavy atom? By the way, I want to learn more about how solve work, but I have no right to access papers about solve. could anyone send me pdf copies of following papers: Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr. 1999 Apr;55(Pt 4):849-61 MAD phasing: treatment of dispersive differences as isomorphous replacement information. Acta Crystallogr D Biol Crystallogr. 1994 Jan 1;50(Pt 1):17-23 MAD phasing: Bayesian estimates of F(A). Acta Crystallogr D Biol Crystallogr. 1994 Jan 1;50(Pt 1):11-6 Thanks ahead _ 使用 MSN 有问题怎么办？客服机器人来帮忙！ http://help.msn.cn/
Re: [ccp4bb] What is the meaning of Fbar in solve ?
In a vain attempt to head off another flurry of emails . can I state that CCP4 does not condone illegal file sharing, and breaking of copyright. To avoid any misunderstandings, please do not use ccp4bb to ask for PDFs of articles. You can usually ask the author in private. Regards Martyn On Thu, 2008-07-17 at 21:23 +0800, miwei wrote: Hi everyone: Could anyone tell me the meaning of Fbar in the MADFBARFILE in solve? Does Fbar stand for delta f prime or just f prime for heavy atom? By the way, I want to learn more about how solve work, but I have no right to access papers about solve. could anyone send me pdf copies of following papers: Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr. 1999 Apr;55(Pt 4):849-61 MAD phasing: treatment of dispersive differences as isomorphous replacement information. Acta Crystallogr D Biol Crystallogr. 1994 Jan 1;50(Pt 1):17-23 MAD phasing: Bayesian estimates of F(A). Acta Crystallogr D Biol Crystallogr. 1994 Jan 1;50(Pt 1):11-6 Thanks ahead _ 使用 MSN 有问题怎么办？客服机器人来帮忙！ http://help.msn.cn/ -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
[ccp4bb] Advice for phasing
Hi, I have a very good native data set. However, the selenomethionyl crystal has a different space group and always suffers from radiation damage. A three-wavelength data set was still collected, and after phasing in SHARP, some features can be seen but the map is not good enough for tracing. Then I did some heavy atom soaking with the native crystals and collected data at home, however, the crystal was again converted into the same space group as the selenomethionyl crystal. At lease 4 Hg sites can be found both by isomorphous difference Fourier calculated using the partial Se-MAD phase and by isomorphous difference Patterson, suggesting they should be real. Now with these information, what's the best way to do the phasing in SHARP, or in some other programs? I hope I have made myself clear; and I would like to supply more details. Any suggestion will be highly appreciated. Best regards, Junyu == Junyu Xiao Department of Biological Chemistry, University of Michigan Lab address: 3163 Life Sciences Institute University of Michigan 210 Washtenaw Avenue Ann Arbor, MI, 48109-2216 Phone: 734-615-2078 ==
Re: [ccp4bb] Advice for phasing
Wouldn't it make sense to do MIRAS with both the Se and Hg derivatives, and add in some multi-crystal averaging from the native set? You seem like you are almost there, though. I assume you have already tried DM and NCS averaging (if there is any)? Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: Junyu Xiao To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, July 17, 2008 10:13 AM Subject: [ccp4bb] Advice for phasing Hi, I have a very good native data set. However, the selenomethionyl crystal has a different space group and always suffers from radiation damage. A three-wavelength data set was still collected, and after phasing in SHARP, some features can be seen but the map is not good enough for tracing. Then I did some heavy atom soaking with the native crystals and collected data at home, however, the crystal was again converted into the same space group as the selenomethionyl crystal. At lease 4 Hg sites can be found both by isomorphous difference Fourier calculated using the partial Se-MAD phase and by isomorphous difference Patterson, suggesting they should be real. Now with these information, what's the best way to do the phasing in SHARP, or in some other programs? I hope I have made myself clear; and I would like to supply more details. Any suggestion will be highly appreciated. Best regards, Junyu == Junyu Xiao Department of Biological Chemistry, University of Michigan Lab address: 3163 Life Sciences Institute University of Michigan 210 Washtenaw Avenue Ann Arbor, MI, 48109-2216 Phone: 734-615-2078 ==
Re: [ccp4bb] spam Re: [ccp4bb] Advice for phasing
For the SeMet dataset, which wavelength did you collect first? If it is the peak, you could try doing SAD with just the peak wavelength. Maybe combine the Se peak data with the Hg dataset (provided they are isomorphous) and do MIRAS as Jacob suggested. Bert van den Berg University of Massachusetts Medical School Program in Molecular Medicine Biotech II, 373 Plantation Street, Suite 115 Worcester MA 01605 Phone: 508 856 1201 (office); 508 856 1211 (lab) e-mail: [EMAIL PROTECTED] http://www.umassmed.edu/pmm/faculty/vandenberg.cfm From: CCP4 bulletin board on behalf of Jacob Keller Sent: Thu 7/17/2008 11:23 AM To: CCP4BB@JISCMAIL.AC.UK Subject: spam Re: [ccp4bb] Advice for phasing Wouldn't it make sense to do MIRAS with both the Se and Hg derivatives, and add in some multi-crystal averaging from the native set? You seem like you are almost there, though. I assume you have already tried DM and NCS averaging (if there is any)? Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: Junyu Xiao mailto:[EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, July 17, 2008 10:13 AM Subject: [ccp4bb] Advice for phasing Hi, I have a very good native data set. However, the selenomethionyl crystal has a different space group and always suffers from radiation damage. A three-wavelength data set was still collected, and after phasing in SHARP, some features can be seen but the map is not good enough for tracing. Then I did some heavy atom soaking with the native crystals and collected data at home, however, the crystal was again converted into the same space group as the selenomethionyl crystal. At lease 4 Hg sites can be found both by isomorphous difference Fourier calculated using the partial Se-MAD phase and by isomorphous difference Patterson, suggesting they should be real. Now with these information, what's the best way to do the phasing in SHARP, or in some other programs? I hope I have made myself clear; and I would like to supply more details. Any suggestion will be highly appreciated. Best regards, Junyu == Junyu Xiao Department of Biological Chemistry, University of Michigan Lab address: 3163 Life Sciences Institute University of Michigan 210 Washtenaw Avenue Ann Arbor, MI, 48109-2216 Phone: 734-615-2078 ==
[ccp4bb] pink/green paper?
Dear all, I have a request for a different kind of paper. Does anyone know of a supplier of the X-ray sensitive pink (or green) paper used to locate X-ray beams. James -- Dr. James Murray PX group SGC Oxford
Re: [ccp4bb] Advice for phasing
Hi - I would try SHARP; or to be exact be tempted to think less and use autoSHARP with the description of all datasets and only give it the Se sites for the seMet crystal. The same thing can also be done easily in Solve. In both cases I would start with unmerged data and let these programs do their nice scaling, which might be key for your case. Now, if one crystal system is converted to another by a simple soak, I presume they are related. Thus, it should be trivial (*) to figure out the relationship (transformation matrix) between the two. As soon as you do so use DMMulti from the CCP4, the phases from the Se/ Hg phasing experiment, and the good native data, together with the transformation matrix from above to do cross-crystal averaging. I suspect that one of your crystal systems will also have some NCS (I suspect that upon soak a crystallographic axis becomes non- crystallograpic) which you should of course also define and use. Presuming now, that your 'good' native is also in higher resolution I would use then the 'native' phases to run ARP/wARP (or Resolve, Buccanneer, ACMI; but I am biased) A. (*) As it has been noted before in the bb, climbing mountain Everest is trivial. It has been done before, its being done now, and will be done again. But it takes intense training and determination to succeed. Same as getting the transformation between the two related space groups. In both cases though, failure is also an option. On Jul 17, 2008, at 17:13, Junyu Xiao wrote: Hi, I have a very good native data set. However, the selenomethionyl crystal has a different space group and always suffers from radiation damage. A three-wavelength data set was still collected, and after phasing in SHARP, some features can be seen but the map is not good enough for tracing. Then I did some heavy atom soaking with the native crystals and collected data at home, however, the crystal was again converted into the same space group as the selenomethionyl crystal. At lease 4 Hg sites can be found both by isomorphous difference Fourier calculated using the partial Se-MAD phase and by isomorphous difference Patterson, suggesting they should be real. Now with these information, what's the best way to do the phasing in SHARP, or in some other programs? I hope I have made myself clear; and I would like to supply more details. Any suggestion will be highly appreciated. Best regards, Junyu == Junyu Xiao Department of Biological Chemistry, University of Michigan Lab address: 3163 Life Sciences Institute University of Michigan 210 Washtenaw Avenue Ann Arbor, MI, 48109-2216 Phone: 734-615-2078 ==
Re: [ccp4bb] pink/green paper?
CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK wrote on 07/17/2008 11:25:20 AM: Dear all, I have a request for a different kind of paper. Does anyone know of a supplier of the X-ray sensitive pink (or green) paper used to locate X-ray beams. James Hi James - I've used Gafchromic film (www.gafchromic.com) for that purpose. It has better spatial resolution than the pink/green stuff, but works essentially the same way: a spot on the film turns from clear to blue when exposed to X-rays. It won't get fogged by indoor light (although watch out for UV or sunlight) and there's no development needed. Gafchromic sells a whole bunch of films; I'm afraid I don't remember which one you should get. They're rated by radiation dose, but I don't remember how many Grays per second an X-ray generator will deposit in the film... - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
Re: [ccp4bb] 2D deviation plot
On Thursday 17 July 2008 09:48:08 Shawn Leeds wrote: Dear all, I am trying to generate 2D Ca deviation plots for my superimposed molecules as needed for publication. I am wondering what is the program of choice for such a purpose? I tried Lsqkab in CCP4, but wasn't sure what's the most efficient way of generating good quality 2D deviations plots from the output table. Would you suggest some solutions on this matter? Thanks! If you are happy with the table output by lsqkab, then making a publication quality version is as simple as running the following commands through gnuplot: set term postscript eps set output 'devplot.eps' set xlabel 'Residue' set ylabel 'Mainchain deviation' plot 'table.out' using 1:2 with lines title My Protein If you specifically want CA deviations rather than mainchain atoms, you can do more or less the same thing by first selecting only the lines for CA atoms in the lsqkab log file. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
[ccp4bb] mrBUMP - proxy to internet
Dear All I want to run MrBump. We have dynamic internet system in our institute. So I am not able to locate the proxy address. Any help please Sajid From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/
[ccp4bb] synchrotron remote data collection
Hello all, I am trying to put together a list of available beamlines that now do either remote data collection or mail-in collection. So far I've found: BNL mail-in facility SSRL all PX beamlines have remote capability ALS 4.2.2 beamline has remote capability Any input/corrections would be welcome, Christina
[ccp4bb] Imidazole's ability to chelate metal ions
Dear Crystallographers, Does anybody happen to know whether imidazole is able to chelate metal ions in solution? It seems reasonable that since it can compete for binding to IMAC resins, it should have some affinity for at least Ni++ and Co++, but what about metal ions like Ca++ and Mg++? I assume that the affinity is weak, but at the concentrations at which we are wont to use it in our elutions (~100-500 mM), does it not seem likely that other metal ions are being competed away from our proteins as well? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] ***
