Re: [ccp4bb] Resid for occupancy
Vu Thai wrote: Hi, I have a protein that binds nucleotides, and in my structure, it appears that the binding pocket is partial occupied by ADP and AMP; the beta phosphate of ADP is transfered to another molecule. I want to refine the structure with both ADP and AMP modeled in the sight and manually vary their occupancy to see what effects it will have. I was wondering if I need to keep the RESID number the same for the AMP and ADP molecule or do they need to be different? Thanks, vu They can have different residue numbers - providing they have occupancies which add up to = 1. But how completely do they overlap - you may do better to set the second phosphate occ to 0.5 and keep all the other atomas of ADP- to 1.0 You can always describe the phenonomem in the text.. Eleanor
Re: [ccp4bb] How many twinned crystals?
Crystals with messy spots smeared out in one direction with sometimes more than one maximum are probably better described as split crystals rather than twins, but if the splitting of the spots is clear enough the same procedures can be used to integrate them. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Thu, 6 Sep 2007, Eleanor Dodson wrote: Not an expert on integration at all, but is this true for mosaic crystals when spots overlap rather messily? Eleanor George M. Sheldrick wrote: Since processing non-merohedrally twinned crystals became routine in small-molecule crystallography, the number of such twins has increased dramatically. The data are often as good as from normal crystals and there is the advantage of getting a higher redundancy and greater completeness by collecting data from two or more crystals in different orientations at the same time! At the moment non-meroderally twinned protein crystals are often thrown away (e.g. because they don't index with programs designed for untwinned crystals) or one tries not to notice that the other components are there. I predict that when MOSFLM, XDS, HKL2000 etc. are able to index and integrate non-merodedral twins, they will suddenly become much more common for macromolecules too. At least there is no problem indexing and integrating merohedral twins, and some refinement programs can handle them, so most of the discussion in this list has been about merohedral twins so far. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Fri, 31 Aug 2007, Ian Tickle wrote: In the past twinned crystals must have been much more frequent than published twinned structures because the traditional reaction of crystallographers to twinning has been either to find a way of inhibiting it or chucking the crystals in the bin and finding a non-twinned form. But I guess that's changing now with better software and we're becoming more adventurous - maybe that's why we're hearing about more twinned crystals now. -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller Sent: 31 August 2007 18:32 To: CCP4BB@JISCMAIL.AC.UK Subject: How many twinned crystals? Since I joined this list, I have seen many many issues with twinned structures, but have never seen any personally. Granted, problems with twinning induce people to write to the list, making them seem more prominent, but does anyone have an idea what percent of crystals are twinned, or know of a ref about this? I always thought it was an anomaly, but All the best, Jacob Keller Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Best program to find whether a crystal is twinned ?
Within CCP4 SFCHECK and TRUNCATE provide an analysis the PHENIX Xtriage is excellent.. See http://www.ccp4.ac.uk/dist/html/twinning.html Eleanor Jobichen Chacko wrote: Dear All, Can you please inform me the programs available to find whether a crystal is twinned and also the data reduction programs for twinned crystals. Thanks in advance. Jobi From: CCP4 bulletin board on behalf of Ian Tickle Sent: Sat 9/1/2007 1:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How many twinned crystals? In the past twinned crystals must have been much more frequent than published twinned structures because the traditional reaction of crystallographers to twinning has been either to find a way of inhibiting it or chucking the crystals in the bin and finding a non-twinned form. But I guess that's changing now with better software and we're becoming more adventurous - maybe that's why we're hearing about more twinned crystals now. -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller Sent: 31 August 2007 18:32 To: CCP4BB@JISCMAIL.AC.UK Subject: How many twinned crystals? Since I joined this list, I have seen many many issues with twinned structures, but have never seen any personally. Granted, problems with twinning induce people to write to the list, making them seem more prominent, but does anyone have an idea what percent of crystals are twinned, or know of a ref about this? I always thought it was an anomaly, but All the best, Jacob Keller Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] ESRF Rolling access beamtime
Dear all, The ESRF is pleased to remind you about the procedure for applying for rolling access beamtime on its MX beamlines. The rolling access procedure is designed to improve access to ESRF MX beam-lines and encourage the use of ESRF facilities by smaller groups working in the MX field. This method of applying for beam-time can be used by scientists who are NOT included in a ESRF blocked group (BAG) and applications can be made at ANY time. Applications received under this new scheme will be reviewed electronically by the ESRF MX Beam Time Review Committee within 7-14 days of their reception at the ESRF and if beam-time is awarded this will be scheduled within 6-8 weeks after the time of application. The ESRF is currently accepting applications for rolling access beamtime required in November and December 2007. Further details of the scheme as well as details of application procedures are available at: http://www.esrf.fr/UsersAndScience/UserGuide/Applying/MXApplications/#standard Any questions regarding this new application mechanism should be initially directed to Debby Davison ([EMAIL PROTECTED]), or the the MX Beamline Operation Managers (Joanne McCarthy ([EMAIL PROTECTED]) and Didier Nurizzo ([EMAIL PROTECTED]).
[ccp4bb] xplot84driver problems
Hi, I've installed CCP4 on an Intel Mac running Mac OS X 10.4.10 using the binary installer from the automatic download page. Everything works fine and dandy except xplot84driver. This currently means I have to convert every plot file on the command line using pltdev then use Preview to view the PS as PDF, rather than just using the CCP4i pulldown menu. Initially xplot84driver complains that libifcore.dylib is missing. This appears to be an Intel compiler-specific library which I just happen to have in /opt/intel/fc/9.1.024/lib, as I once evaluated the beta release of the compiler. If I copy this to $CCPLIB or link from there to it, it complains that it doesn't have libifm.dylib, which in turn complains that it doesn't have libirc.dylib. Finally when all these libraries are linked to and loaded, xplot84driver complains about Bad plot84 file format and does not open the plot file. Does anyone have an idea what is going on? Thanks Derek -- Derek Logan tel: +46 46 222 1443 Molecular Biophysicsfax: +46 46 222 4692 Lund University Box 124, Lund, Sweden
[ccp4bb] glycosidic bonds for refmac library
Hello everyone, I have a couple of structures which contain oligomeric sugars in different conformations. Is there any general way of defining a glycosidic bond for the refmac library - instead of creating .cif files for every single ligand-structure ? Thank you very much in advance Eike
Re: [ccp4bb] xplot84driver problems
Did you make your plt file on the intel mac? I've noticed that ones I made on ppc give that error on my otherwise functional xplot84driver (in the fink package). I tried byte-swapping with dd but to no avail. I guess this is still the cutting edge of 1984 software? Bill On Thu, 6 Sep 2007 15:02:01 +0200 Derek Logan [EMAIL PROTECTED] wrote: Hi, I've installed CCP4 on an Intel Mac running Mac OS X 10.4.10 using the binary installer from the automatic download page. Everything works fine and dandy except xplot84driver. This currently means I have to convert every plot file on the command line using pltdev then use Preview to view the PS as PDF, rather than just using the CCP4i pulldown menu. Initially xplot84driver complains that libifcore.dylib is missing. This appears to be an Intel compiler-specific library which I just happen to have in /opt/intel/fc/9.1.024/lib, as I once evaluated the beta release of the compiler. If I copy this to $CCPLIB or link from there to it, it complains that it doesn't have libifm.dylib, which in turn complains that it doesn't have libirc.dylib. Finally when all these libraries are linked to and loaded, xplot84driver complains about Bad plot84 file format and does not open the plot file. Does anyone have an idea what is going on? Thanks Derek -- Derek Logan tel: +46 46 222 1443 Molecular Biophysicsfax: +46 46 222 4692 Lund University Box 124, Lund, Sweden
Re: [ccp4bb] xplot84driver problems
The file format is definitely machine byte order dependent. (see $CDOC/plot84.doc) A few years ago I was toying with the idea of making library code deal with swapping if need be... Never did it though William Scott wrote: Did you make your plt file on the intel mac? I've noticed that ones I made on ppc give that error on my otherwise functional xplot84driver (in the fink package). I tried byte-swapping with dd but to no avail. I guess this is still the cutting edge of 1984 software? Bill On Thu, 6 Sep 2007 15:02:01 +0200 Derek Logan [EMAIL PROTECTED] wrote: Hi, I've installed CCP4 on an Intel Mac running Mac OS X 10.4.10 using the binary installer from the automatic download page. Everything works fine and dandy except xplot84driver. This currently means I have to convert every plot file on the command line using pltdev then use Preview to view the PS as PDF, rather than just using the CCP4i pulldown menu. Initially xplot84driver complains that libifcore.dylib is missing. This appears to be an Intel compiler-specific library which I just happen to have in /opt/intel/fc/9.1.024/lib, as I once evaluated the beta release of the compiler. If I copy this to $CCPLIB or link from there to it, it complains that it doesn't have libifm.dylib, which in turn complains that it doesn't have libirc.dylib. Finally when all these libraries are linked to and loaded, xplot84driver complains about Bad plot84 file format and does not open the plot file. Does anyone have an idea what is going on? Thanks Derek -- Derek Logan tel: +46 46 222 1443 Molecular Biophysicsfax: +46 46 222 4692 Lund University Box 124, Lund, Sweden
[ccp4bb]
Somebody out there (preferentially in the US) who is willing to sell his/her used MAR imaging plate. It should be in good working condition. Please contact me directly (not the ccp4bb). Best Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: [EMAIL PROTECTED] http://users.physik.tu-muenchen.de/marius/
Re: [ccp4bb] xplot84driver problems
Hi, Yes, I made the files on the Intel Mac. I've sent one to Charles Ballard for testing. They do also work wih pltdev. I agree about the antediluvial origins of xplot84driver, but for lack of anything better... Derek On Sep 6, 2007, at 17:15, [EMAIL PROTECTED] wrote: Did you make your plt file on the intel mac? I've noticed that ones I made on ppc give that error on my otherwise functional xplot84driver (in the fink package). I tried byte-swapping with dd but to no avail. I guess this is still the cutting edge of 1984 software? Bill On Thu, 6 Sep 2007 15:02:01 +0200 Derek Logan [EMAIL PROTECTED] wrote: Hi, I've installed CCP4 on an Intel Mac running Mac OS X 10.4.10 using the binary installer from the automatic download page. Everything works fine and dandy except xplot84driver. This currently means I have to convert every plot file on the command line using pltdev then use Preview to view the PS as PDF, rather than just using the CCP4i pulldown menu. Initially xplot84driver complains that libifcore.dylib is missing. This appears to be an Intel compiler-specific library which I just happen to have in /opt/intel/fc/9.1.024/lib, as I once evaluated the beta release of the compiler. If I copy this to $CCPLIB or link from there to it, it complains that it doesn't have libifm.dylib, which in turn complains that it doesn't have libirc.dylib. Finally when all these libraries are linked to and loaded, xplot84driver complains about Bad plot84 file format and does not open the plot file. Does anyone have an idea what is going on? Thanks Derek -- Derek Logan tel: +46 46 222 1443 Molecular Biophysicsfax: +46 46 222 4692 Lund University Box 124, Lund, Sweden
[ccp4bb] The X6A workbench - Fall session
The X6A workbench - Advanced Strucutral Biology Tools at the National Synchrotron Light Source scheduled for September 25 through 28 Is a hands-on course for those interested in getting acquainted with Synchrotron Radiation methods in structural biology. The course provides a comprehensive view of data collection and data analysis aspects of a synnchrotron experiment. The number of participants is limited to six as the program concentrates on the development of experimental skills. Further information can be found through the link http://protein.nsls.bnl.gov/mediawiki/index.php/X6A_Workbench
[ccp4bb] just how bad can phases be and still help
general question - perhaps the fundamental question - for anyone who had weak/poor/bad phases from some source, that were later actually used to solve a structure when combined w/ another source - HOW bad were the worst phases on their own, in terms of resolution, FOM, CC, e-density, (any other numbers)? what was MOST important in knowing the phases would help (presumably e-dens.). i.e, was it only when relatively better phases gave any interpretable density that it was known that the bad phases would help? -bryan
Re: [ccp4bb] just how bad can phases be and still help
Hi Bryan: I think the question is hard to answer because the idea of bad phases is not particularly well-understood (at least by me). Good phases give you a nice map. Weak phases give you a map that is weakly interpretable, but often can be improved by solvent flattening, NCS averaging, and so forth. Bad phases I would think have something inherently wrong with them, such as some systematic bias that would prevent you from getting to the right answer. I once gleefully showed my postdoctoral advisor phasing statistics for a macromolecule I had just solved. The overall phasing power was 0.6 for one derivative and 0.5 for another. Phasing power is roughly\ Sum |F(PH) - F(P)|/deltaE where deltaE is lack-of-closure error, so it is typically looked at as an average signal to noise value. I thought if the lack of closure error on average was roughly twice my heavy atom signal, the phases should be too weak to give a decent map. It turns out I can make a really nice map with only one of derivatives (either one). My postdoctoral advisor retorted When I introduced that statistic (I knew I was doomed at that point), I never meant to suggest that a phasing power less than 1.0 meant the phases were no good. I think the reason it works is because the lack of closure error is nearly random and the signal is not, and that, together with a low initial figure of merit and a high solvent content, it meant that the weak phases were good enough to make a nice map. I've also heard that pretty much anything better than pure random noise when combined with lots of NCS (viruses) can yield nearly perfect phases. The main thing is to avoid bad (meaning nefariously biased) phases. Bad partial models, bad molecular replacement solutions, bad heavy atom constellations, and anything else involving atoms in wrong positions is much more problematic than a correct heavy atom model with a weak phasing power. Low initial FOM in many senses are good, because density modification has more latitude to help. Bill Bryan W. Lepore wrote: general question - perhaps the fundamental question - for anyone who had weak/poor/bad phases from some source, that were later actually used to solve a structure when combined w/ another source - HOW bad were the worst phases on their own, in terms of resolution, FOM, CC, e-density, (any other numbers)? what was MOST important in knowing the phases would help (presumably e-dens.). i.e, was it only when relatively better phases gave any interpretable density that it was known that the bad phases would help? -bryan
Re: [ccp4bb] just how bad can phases be and still help
On Thu, 6 Sep 2007, William Scott wrote: I think the reason it works is because the lack of closure error is nearly random and the signal is not interesting notion Low initial FOM in many senses are good [..] because density modification has more latitude my understanding was that density modification is designed to make the FOM optimal, almost 1.0, always ; as such, the only discrimination that density modification provides is map interpretation, and at least not the _modified_ FOM. -bryan
Re: [ccp4bb] few organophophates coordiantes
Dear Sam The HIC-Up website link is http://xray.bmc.uu.se/hicup/ Hope it will help you Vijay Kumar, SRF Protein science and Engg. Division IMTECH, Sector -39A, Chandigarh INDIA U Sam [EMAIL PROTECTED] wrote Hi, Thanks for the reply to my earlier query. I am looking for the coordinates of few organophosphates which can bond covalently to protein as follows . 1) Para-oxon: O,O-Diethyl-O-para-nitrophenyl phosphate 2) Sarin: 2-(fluoro-methyl-phosphoryl)oxypropane 3) Soman: 3-(fluoro-methyl-phosphoryl)oxy-2,2-dimethyl-butane 4) Tabun: Ethyl N,N-dimethylphosphoramidocyanidate 5) DFP: 2-(fluoro-(1-methylethoxy)phosphoryl)oxypropane 6) VX: O-ethyl-S-[2(diisopropylamino)ethyl] methylphosphonothiolate I would like to know if anybody know the correct hiccup' site. I searched a similar site though google, but I did not find any good hit. JL Susman and Charles Millard groups did some studies with few of these organophosphates, but I donot see any complete structure of the organophosphates in their submitted PDBs. Appreciate suggestion/notes. Sam _ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+worldmkt=en-USform=QBRE - Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us.
