[ccp4bb] combine Se-SAD phase with Model-phase
Hi, It would be of great help if you can give some suggestion on the following problem. I have two data sets of a complex molecule. One is native (3.6A) and the other is Se-der (4.5A). In one complex molecule I have one homo-dimer in complex with DNA( 2 times 90 aa + 2 times 15 na = ~MW 28000, call it as component 1) plus a second long helical protein(130 aa, call it as component 2). I have two such complex molecule in the AU (space gr. P65). I got a very good solution by PHASER(using native data) for the component 1, but component 2 has some ambiguity. I used the solution of component 1 and Se-der data to create Ano-diff Fourier map from model phase. I got clear peaks at 3.5 sigma exactly at the Met-S positions. I pulled out 11 Se sites, 9 of which are precisely exists at the right positions looked upon the model component 1). Other 2 are expecting on the two copy of component 2. What I did next? 1. I used CNS to create both SAD phase from Se and Model phase from component 1 and then combined them. Used the combine HL co-eff to run density modification and create 2Fo-Fc map. Very poor quality, but you can see some features. 2. Used only SAD phase from Se sites and run density modification followed by 2Fo-Fc map generation. Useless map. 3. Run SHARP/AutoSHARP with Se sites upto DM. Then run solvent flattening with model component 1. No good map. Do you know any other way to go from here? Running rigid.inp, anneal.inp, minimize.inp and bgroup.inp sequentially with the component 1 I reached R/R(free) 40%/45%. Any suggestion is well appreciated. Regards... Raja From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/
[ccp4bb] metal atoms written from coot in refmac
I have run across a problem and I am not sure where it originates from. When I use a pdb input file that contains a metal atom, say Cu, that has been written out by coot in refmac I get a read error of the sort that refmac does not recognize the Cu. If I then edit the pdb file and change CU to Cu under the atom name column. As shown below As written by coot: ATOM 3813 CUCu E 1 28.093 -26.964 -10.810 1.00 54.30 CU After editing: ATOM 3813 CuCu E 1 28.093 -26.964 -10.810 1.00 54.30 CU This pops up occasionally with other metal atoms also and while the work around is fairly easy it is an annoying problem. Has anybody else seen this before? and does anybody know why it happens? Len Leonard M. Thomas Ph.D. Director, Macromolecular Crystallography Laboratory Howard Hughes Medical Institute California Institute of Technology Division of Biology 1200 E. California Blvd. MC 114-96 Pasadena, CA 91125 626-395-2453 [EMAIL PROTECTED] http://www.br.caltech.edu/cmclab
Re: [ccp4bb] HKL2000 and gcc4 - redux
> mosflm Bill just beat me to writing the same. I would mention XDS as well. labelit will index your images http://adder.lbl.gov/labelit/ ... then you give the scripts to mosflm. there's plenty of Acta Cryst. there to read too. -bryan
Re: [ccp4bb] HKL2000 and gcc4 - redux
Agreed, but it's nice to have options, as I'm sure we've all experienced, one program (and sometimes it's HKL2000) just seems to work better than another with some data. But yes, being that this is the CCP4BB, mosflm does indeed rock. Thanks, Chris > From: Gerard Bricogne <[EMAIL PROTECTED]> > Date: Wed, 7 May 2008 23:23:34 +0100 > To: Chris Waddling <[EMAIL PROTECTED]> > Cc: > Subject: Re: [ccp4bb] HKL2000 and gcc4 - redux > > Dear Chris, > > Bill just beat me to writing the same. I would mention XDS as well. > > > With best wishes, > > Gerard. > > -- > On Wed, May 07, 2008 at 03:17:07PM -0700, William Scott wrote: >> mosflm is an incredibly great program, not to mention free as in beer... >> >> >> >> >> On May 7, 2008, at 3:07 PM, Chris Waddling wrote: >> >>> my frustration at HKL2000 not working > > -- > > === > * * > * Gerard Bricogne [EMAIL PROTECTED] * > * * > * Global Phasing Ltd. * > * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * > * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * > * * > ===
Re: [ccp4bb] HKL2000 and gcc4 - redux
Dear Chris, Bill just beat me to writing the same. I would mention XDS as well. With best wishes, Gerard. -- On Wed, May 07, 2008 at 03:17:07PM -0700, William Scott wrote: > mosflm is an incredibly great program, not to mention free as in beer... > > > > > On May 7, 2008, at 3:07 PM, Chris Waddling wrote: > > > my frustration at HKL2000 not working -- === * * * Gerard Bricogne [EMAIL PROTECTED] * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] HKL2000 and gcc4 - redux
mosflm is an incredibly great program, not to mention free as in beer... On May 7, 2008, at 3:07 PM, Chris Waddling wrote: my frustration at HKL2000 not working
Re: [ccp4bb] HKL2000 and gcc4 - redux
After further reflection upon my HKL2000 post a few days ago, I felt I needed to clarify a few things and address some of the responses that I got to the post. Most of all, I think it necessary for me to offer my sysadmin an unqualified apology. First off, in no way was my he impeding our ability to get our work done. I vented my frustration at HKL2000 not working at him instead of at HKL. His assessment of the situation was to get guidance from HKL as to how best to proceed. After waiting weeks for a response from them, some of the stop-gap measures that other users also seemed to think should work, appeared to me to be our only recourse in the short term. In the end, it turns out Suse isn't officially supported by HKL, which may explain the amount of time it took to hear back from them about it. Between Suse 10.2 and 10.3, compatibility with previous releases was eliminated, and so some of the solutions presented by other users weren't going to work, either. I neglected to mention the OS we were using, and it turns out this is important. Not mucking with the guts of the OS is probably a good call, and so even temporarily putting a library where it doesn't belong may solve the symptom, but it doesn't solve the problem. Finally, to end my mea culpa on a positive note, thanks for the helpful responses to those who sent them. Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517
Re: [ccp4bb] How to create TLS file
The CCP4i method is to use the "Create / Edit TLS File" task in the "Refinement" module. I have used the TLSMD-server before, and I do like it. I did notice that my R-free would be lower if I used the server's definitions of TLS groups, but let Refmac do the TLS analysis from scratch instead of using the server's TLS values. Has anyone else seeen this? David On Wed, 7 May 2008 19:29:53 +0200 Georg Zocher <[EMAIL PROTECTED]> wrote: U Sam schrieb: Suggestion please. How TLS file is created to be used in Refmac refinement. Thanks. Sam _ Get Free (PRODUCT) RED™ Emoticons, Winks and Display Pics. http://joinred.spaces.live.com?ocid=TXT_HMTG_prodredemoticons_052008 I recommend to use the TLSMD-server (J Painter & E A Merritt (2006) Acta Cryst. D62, 439-450) http://skuld.bmsc.washington.edu/~tlsmd/ best regards, georg -- Dr. Georg Zocher BESSY-MX group BESSY GmbH Albert-Einstein-Straße-15 D-12489 Berlin Fon : +49-(0)30-6392 4973 Fax : +49-(0)30-6392 4975 email: [EMAIL PROTECTED] url : http://www.psf.bessy.de/ BESSY GmbH - Mitglied der Leibniz Gemeinschaft Vorsitzender des Aufsichtsrates: Prof. Dr. Dr. h.c. mult Joachim Treusch Geschäftsführer: Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Prof. Dr.Eberhard Jaeschke Sitz Berlin, AG Charlottenburg, HRB 14635 . --- David Cooper, Ph.D. University of Virginia Molecular Physiology and Biological Physics Jordan Hall, Box 800736 1300 Jefferson Park Ave Charlottesville, VA 22908-0736 Phone: (434) 982-3151 Fax: (434) 982-1616
Re: [ccp4bb] How to create TLS file
U Sam schrieb: Suggestion please. How TLS file is created to be used in Refmac refinement. Thanks. Sam _ Get Free (PRODUCT) RED™ Emoticons, Winks and Display Pics. http://joinred.spaces.live.com?ocid=TXT_HMTG_prodredemoticons_052008 I recommend to use the TLSMD-server (J Painter & E A Merritt (2006) Acta Cryst. D62, 439-450) http://skuld.bmsc.washington.edu/~tlsmd/ best regards, georg -- Dr. Georg Zocher BESSY-MX group BESSY GmbH Albert-Einstein-Straße-15 D-12489 Berlin Fon : +49-(0)30-6392 4973 Fax : +49-(0)30-6392 4975 email: [EMAIL PROTECTED] url : http://www.psf.bessy.de/ BESSY GmbH - Mitglied der Leibniz Gemeinschaft Vorsitzender des Aufsichtsrates: Prof. Dr. Dr. h.c. mult Joachim Treusch Geschäftsführer: Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Prof. Dr.Eberhard Jaeschke Sitz Berlin, AG Charlottenburg, HRB 14635
[ccp4bb] How to create TLS file
Suggestion please. How TLS file is created to be used in Refmac refinement. Thanks. Sam _ Get Free (PRODUCT) RED™ Emoticons, Winks and Display Pics. http://joinred.spaces.live.com?ocid=TXT_HMTG_prodredemoticons_052008
Re: [ccp4bb] scala on mac osx - off topic, really
On May 7, 2008, at 5:57 AM, Chris Richardson wrote: I tried another tack. I edited the ccp4.info file (in /sw/fink/10.4/ unstable/main/finkinfo/sci) to download the scala_3.2.34 source code and unpack it over the top of the rest of the source. I'm fairly sure that you're *not* supposed to do it this way, but it worked and I haven't had any complaints that the newer version of scala is broken. There is no reason why that approach shouldn't work, but it might be cleaner to incorporate the differences as a patch. Just to be clear, CCP4 has no association with or official recognition even of what is in fink. It is just something I did, so please complain to me, not them. It is not their fault. I'll try to reconstruct what you did and update the fink package. gcc4.0 is a placeholder package in fink that designates the apple compiler has been installed gcc42 is a real package, and it contains, among other things, gfortran. gcc43 replaces gcc42. The two sets of shared libraries can coexist, but I updated all of my fortran-dependent packages (including ccp4) to use gcc43
[ccp4bb] Off Topic - Problems with Taylor Wharton CX-100 series dry shippers
Hi, Based on SER-CAT user input we are trying to assess the meantime between failure for the Taylor Wharton CX-100 series dry shipper. If you have experienced problems with the Taylor Wharton CX-100 dry shippers where crystals have been lost we ask you please complete the following survey. Please return the survey to me at the address below. I will then compile and post the results Thanks, John > Name: Institution: Number of Taylor Wharton CX-100 series dry shippers which have failed: Dry shipper model(s): Approximate date of failure(s) from date of purchase: Approximate number of roundtrip shipments to/from beamline at time of failure: Dry shipper contents samples in canes or samples in pucks: Shipping container (hard shell shipping case or other): Courier service used: Comments if any: > John Rose Ph.D. Assistant Director SER-CAT B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 = Phone: 706-542-1750 Fax: 706-542-3077
[ccp4bb] ad for POSTDOCTORAL POSITION IN STRUCTURAL BIOLOGY
To whom it may concern, Can you please post the ad shown her? Thanks POSTDOCTORAL POSITION IN STRUCTURAL BIOLOGY Department of Chemistry and Biochemistry University of Maryland, College Park We are seeking outstanding postdoctoral candidates holding a Ph. D. with a background in protein crystallography with related publication history. Additional experience in enzymology will be valuable. Additional qualifications are ability to collaborate closely with others and also to work independently, effective oral and written communications including maintenance of clear, accurate and complete lab work records. This position will be part of a collaborative effort between the laboratories of Profs. Barbara Gerratana and Nicole LaRonde LeBlanc. The overall study will consist of a multidisciplinary approach involving crystallography and enzymology. Start date is June 1, 2008 or as soon thereafter as possible. The initial period of employment is for one year starting as soon as possible with renewal for one to two years possible thereafter. Send curriculum vitae and names of three references to: *Dr. Barbara Gerratana, Dept. of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742 or to [EMAIL PROTECTED] */“EOE/AA” Barbara Gerratana Professor of Biochemistry Department of Chemistry and Biochemistry University of Maryland College Park, MD 20742 phone +1 301-405-1541 email [EMAIL PROTECTED]
Re: [ccp4bb] scala on mac osx - off topic, really
On 7 May 2008, at 13:32, Andreas Förster wrote: a colleague is running ccp4 6.0.2 on a MacBook with Timid Tiger. Built-in Scala is 3.2.25. Because of a bug, he wants to upgrade Scala. Running Scala 3.3.2-beta5 or 3.2.34 (phil's binaries) fails because gcc shared libraries are missing. I ran into exactly the same problem. After wasting plenty of time trying to to get gcc4.0 and gcc43 to coexist happily, I tried another tack. I edited the ccp4.info file (in /sw/fink/10.4/unstable/main/ finkinfo/sci) to download the scala_3.2.34 source code and unpack it over the top of the rest of the source. I'm fairly sure that you're *not* supposed to do it this way, but it worked and I haven't had any complaints that the newer version of scala is broken. If you'd like me to send you the edited ccp4.info file or executable, I'd be happy to do so. I don't want to put them on ccp4, because they're so bodged that they'll probably cause more harm than good in the wild. Regards, Chris -- Dr Chris Richardson - sysadmin, Structural Biology Section, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] scala on mac osx - off topic, really
Hey all, a colleague is running ccp4 6.0.2 on a MacBook with Timid Tiger. Built-in Scala is 3.2.25. Because of a bug, he wants to upgrade Scala. Running Scala 3.3.2-beta5 or 3.2.34 (phil's binaries) fails because gcc shared libraries are missing. Here's the setup: [dyn1208-14:ttgt/TT/process] duolu% fink list gcc Information about 2696 packages read in 3 seconds. avr-gcc 4.2.0-1 GNU GCC for ATMEL AVR micro controllers broken-gcc 3.3-1 [virtual package representing a broken gcc compiler] gcc2 2.95.2-0 [virtual package representing the gcc 2.95.2 compiler] gcc2.95 2.95.2-0 [virtual package representing the gcc 2.95.2 compiler] gcc3.1 3.1-0 [virtual package representing the gcc 3.1 compiler] i gcc3.3 3.3-1819 [virtual package representing the gcc 3.3 compiler] i gcc4.0 4.0.1-5250[virtual package representing the gcc 4.0.1 compiler] gcc424.2.2-1000GNU Compiler Collection Version 4.2 gcc42-shlibs 4.2.2-1000Shared libraries for gcc4 Fink is fully up to date. As you can see, gcc4.0 and gcc3.3 are installed, but not gcc42 or gcc42-shlibs. Installation of gcc42-shlibs fails: [dyn1208-14:ttgt/TT/process] duolu% fink install gcc42-shlibs Password: Information about 2696 packages read in 0 seconds. Can't resolve dependency "cctools (>= 622-1)" for package "gcc42-4.2.2-1000" (no matching packages/versions found) Exiting with failure. cctools are installed in version 590 and are not upgraded further. What looked like an alternative to me, odcctools version 622, does not fulfill gcc42's requirements. [dyn1208-14:ttgt/TT/process] duolu% fink list cctools Information about 2696 packages read in 0 seconds. i cctools 590-1 [virtual package representing the developer tools] i cctools-extra1:590.18-1002 Extra software from cctools i cctools-single-module590-1 [virtual package, your dev tools support -single_module] i odcctools622.3-20060925Darwin cctools build system/code base to support gcc4 odcctools590 20060608-1Darwin cctools build system/code base to support g95 My questions are: Short of upgrading to Lazy Leopard, how do I get gcc42 and gcc42-shlibs installed on my colleague's laptop? Why are there no gcc4.0-shlibs? Why are different versions of gcc installed? Could I safely remove gcc3.3? On my own MacBook Pro (running Lazy Leopard) gcc4.0, gcc43 and gcc43-shlibs are installed, and I can see that gcc4-shlibs exist, but my colleague's fink doesn't see them. It's all mighty confusing to me. From the dark ages I dimly remember similar nightmares during a major gcc version change on linux. Are the reported problems somehow related to that? Thanks. Andreas
