Re: [ccp4bb] DM NCS averaging question
Well - if the CCs are 0 then no averaging can take place.
You know you can let DM make the mask itself - are you using the GUI?
It shows you what to set..
Eleanr
zhan...@umbc.edu wrote:
Hi,
Thanks for reminding me checking the mask. I think their might be
something wrong with the mask, since when DM read in the mask, it says:
Number of columns, rows, sections ... 84 74 69
Map mode 0
Start and stop points on columns, rows, sections -53 30
80 153 -4 64
Grid sampling on x, y, z 136 260 150
Cell dimensions . 135.57100
260.11200 150.2 90.0 101.14000 90.0
Fast, medium, slow axes .ZXY
Minimum density . 0.0
Maximum density . 0.0
Mean density 0.0
Rms deviation from mean density . 0.0
Space-group .4
Number of titles 1
It seems the mask is just null. However, I converted it to a map file, and
coot clearly showed the mask, so I am not sure why the null mask was found
by DM. Moreover, the NCS CCs are just 0s for the mask.
Anyway, following is my NCSMASK script I used to generate the above mask,
where XYZIN is the reorganized pdb containing only a single fixed NCS unit
(chain A). and all the operations were generated by LSQKAB with Chain A
mapped to other chains. Not sure whether there is something wrong here or
not...
ncsmask xyzin ${PDB}_A.pdb mskout ${PDB}.msk eof
SYMM P1211
EXPAND 1.0
OVERLAP 3
AVERAGE 12
#Identical
ROTA MATRIX 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
TRAN 0.0 0.0 0.0
#AC
ROTA MATRIX -0.22748 0.97259 0.04813 -0.97372 -0.22662 -0.02273
-0.01120 -0.05203 0.99858
TRAN 101.4683781.74413 2.89341
#AD
ROTA MATRIX -0.90337 0.42792 0.02831 -0.42883 -0.90066 -0.07011
-0.00451 -0.07547 0.99714
TRAN 158.0331736.91842 3.25853
#AF
ROTA MATRIX -0.21272 -0.97702 0.01352 0.97675 -0.21300 -0.02424 0.02657
0.00805 0.99961
TRAN 100.69797 -81.01860-1.71365
#AG
ROTA MATRIX 0.61704 -0.78687 -0.01005 0.78590 0.61553 0.05899 -0.04023
-0.04429 0.99821
TRAN 32.50667 -65.76570 7.05504
#AH
ROTA MATRIX -0.85814 -0.51116 -0.04813 -0.51290 0.85771 0.03558
0.02310 0.05522 -0.99821
TRAN 156.1498142.2387348.93406
#AI
ROTA MATRIX -0.13703 -0.98975 -0.04032 -0.99048 0.13635 0.01902
-0.01332 0.04254 -0.99901
TRAN 95.9763082.3094852.82510
#AJ
ROTA MATRIX 0.69662 -0.71695 -0.02645 -0.71716 -0.69691 0.00230
-0.02008 0.01737 -0.99965
TRAN 25.8458859.7628653.68224
#AK
ROTA MATRIX 0.99467 0.10258 -0.01072 0.10259 -0.99472 0.00088 -0.01057
-0.00197 -0.4
TRAN0.47215-8.8608252.78315
#AL
ROTA MATRIX 0.55782 0.82946 0.02875 0.82987 -0.55793 -0.00466 0.01218
0.02646 -0.99958
TRAN 36.68436 -68.6383349.21587
#AM
ROTA MATRIX -0.30892 0.95102 -0.01113 0.95109 0.30890 -0.00370
-0.8 -0.01173 -0.3
TRAN 109.48987 -79.0555052.39334
#AN
ROTA MATRIX -0.93676 0.34855 -0.03147 0.34600 0.93589 0.06627 0.05255
0.05119 -0.99731
TRAN 162.32979 -29.2680045.41564
eof
The commonest error with averaging is getting the mask wrong.
Check that the CCs after application of the averaging start at a
reasonable value - 0.3 at least and increase with each cycle ( by the
way why do ncycle 1?)
But in the end the density will not be identical, the Fobs are not
perfectly symmetric so there will be differences. The best idea is to
average (with correct matrices - I always find that takes several pases
before I get them all right - then build molecule A and refit it over
the others before starting refinement.
EleanorHailiang Zhang wrote:
Hi,
I am using the following DM script to perform a NCS averaging. I have a
fundemental question: after NCS averaging, are the density distrubitions
of different NCS unit being averaged supposed to be the same? I found
they
are different by checking FCDM/PHICDM, and maybe I am wrong somewhere...
dm NCSIN ${PDB}.msk HKLIN ${PDBALL}.mtz HKLOUT ${PDBALL}-dm.mtz \
dmtest
mode AVER
ncycle 1
combine PERT
scheme ALL
solc 0.6213
#Identical
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
TRAN 0.0 0.0 0.0
#AC
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.22748 0.97259 0.04813 -0.97372 -0.22662 -0.02273
-0.01120 -0.05203 0.99858
TRAN 101.4683781.74413 2.89341
#AD
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.90337 0.42792 0.02831 -0.42883 -0.90066 -0.07011
-0.00451 -0.07547 0.99714
TRAN 158.0331736.91842 3.25853
#AF
AVER REFI
NCSMASK NMER 1
[ccp4bb] SUMMARY: ROSETTA for MR model generation
Summary to answers to question about MR-based models generated by ROSETTA (thanks to all who replied so quickly): ***De novo methods*** 1. Arcimboldo (suggested by Isabel Uson Finkenzeller and Peter Grey) Nature Methods 6:651-3. Crystallographic ab initio protein structure solution below atomic resolution is based on PHASER, SHELXE and CONDOR. ***In fact this program did the job!!!*** http://chango.ibmb.csic.es/ARCIMBOLDO/ http://en.wikipedia.org/wiki/Giuseppe_Arcimboldo 2. ROSETTA and MD model comparison (by jonathan elegheert) - the smaller the protein the better. There really is an upper limit; every amino acid makes computation exponentially more intensive. - For some proteins it works better than for others. In literature, it has been suggested that the observed failures are not due to bad conformational sampling of the potential energy surface of proteins, but are rather due to the low-resolution scoring function, which sometimes fails to score the models resembling the native fold as the lowest energy structures. However, this observation is largely outweighted by the number of succesfull protein structure predictions, which make Rosetta one of the best structure prediction algorithms available to date. - In most publications, 1 models are generated and scored. I believe something like 10 is rather necessary. I don't know if you have access to multinode machines, but a cluster is definitely necessary. Installing the software to work with MPI is also no trivial task. - The tricky part is the scoring of the clusters of models you will generate; if you don't have the x-ray structure to score and benchmark against (since you want to use it for MR in the first place), you have to score against the most represenative structures of the largest low-energy clusters. And exactly this can be a problem (see 2nd point). - Say you'd get a model with 1.8 A rmsd with the 'real' structure (would be a very good result); this still would translate to a sequence identity of +- 30%, so already marginal. 3. ROSETTA and MRBumb (by Martyn Winn) We also had a look at this problem: D.J Rigden, R.M Keegan and M.D Winn Acta Cryst. D64 1288-1291 (2008) - Molecular Replacement using ab initio polyalanine models generated with ROSETTA Our approach is to use Rosetta to generate a large set of models, and feed these to MrBUMP to process. 4. Recent literature about ROSETTA (by Francois Berenger ) High resolution protein structure prediction and the crystallographic phase problem http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2504711/ Prospects for de novo phasing with de novo protein models http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631639/ ***Different servers and model preparation tools*** 1. Alternative servers for model preparation (Colin Levy): FFAS in conjunction with either ElNEMO or CASPR 2. MR models generated by ROSETTA and other web server tools(Phyre and I-TASSER)in conjunction with MR program REM and OEDM-DEDM phase refinement tool, both included into IL MILIONE (Acta Cryst (2009) D65 477-484) (Rocco Caliandro). www.ba.ic.cnr.it 3. PYRE-SERVER (Eike Schulz) http://www.sbg.bio.ic.ac.uk/~phyre/. 4. Balbes (Edward Snell) http://www.ysbl.york.ac.uk/~fei/balbes/index.html -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349
[ccp4bb] How to run PHENIX on a WINDOWS box using a virtual machine
Hello, I am posting the following information on behalf my colleague Professor Michael Blaber since the instructions for running PHENIX on Windows machine could be beneficial to the larger CCP4 community. Thanks. /FYI -- I have complied instructions on how to run PHENIX on a WINDOWS box using a virtual machine. Just one more hardware/software alternative. Instructions at:/ /http://mikeblaber.org/methods/winphenix.htm/ /Michael Blaber / -- Dr. Thayumanasamy Somasundaram [Soma] Director, X-Ray Crystallography Facility (XRF) Off. Ph: (850)644-6448| Lab Ph: (850)645-1333 Fax:(850)644-7244 | E-mail: tsomasunda...@fsu.edu URI: www.sb.fsu.edu/~soma | URI: www.sb.fsu.edu/~xray Postal Address-- 91, Chieftan Way | KLB 414 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306-4380, USA.
[ccp4bb] Postdoctoral position in X-ray crystallography
Applications are invited for a postdoctoral research position in the Das Lab, Department of Chemistry, Purdue University, West Lafayette, IN, USA. The position requires the applicant to work on structural and biochemical characterization of ubiquitin hydrolases (deubiquitinases) and their complexes with substrates, cofactors and inhibitors (see Boudreaux et al, PNAS, 107, 9117 (2010)). The applicant is also expected to work on an ongoing collaborative project on method development related to imaging of protein crystals (of ubiquitin hydrolases and others) using second order non-linear optical methods. We are looking for highly motivated candidates with extensive experience in biochemical studies, crystallization and structure determination of proteins by x-ray crystallography. Specifically, the candidate is required to have hands-on experience with protein purification, crystallization, X-ray data collection, structure determination and structural analysis. Applicants should send their CV and the names and contact information of at least three references via email to: Chitta Das Assistant Professor Department of Chemistry Purdue University 560 Oval Drive West Lafayette IN, 47907 Email address: c...@purdue.edu
[ccp4bb] CCP4 6.1.13 and ARP/wARP 7.1
Dear Colleagues, some of you might have noticed that ARP/wARP does not install cleanly with the latest version of CCP4, 6.1.13. We did some experiments ourselves and can confirm the observation of an incomplete installation that is only partly functional, the lack of the possibility of manual deinstallation and the following error message that appears at the time of running the ARP/wARP 'install.sh' script: can't read getcontentlist_array(TASK_MODULE,206): no such element in array NOTE: You can skip the next paragraph if you're not interested in how I reproduced the error and proceed to a bug fix. Sorry for the long paragraph. Two scenarios of CCP4+ARP/wARP installation were tested: Mac OSX 10.5 and Ubuntu Linux 9, x86_64. Both the latest versions of both softwares. The download of CCP4 was made from ccp4.ac.uk, a typical installation chosen, which included also the tclsh/bltwish components that the GUI depends on. The dmg-installer was used on the Mac to install into the folder /Applications, on Linux the downloaded file was just untarred in a folder of choice followed by running CCP4's 'install.sh'. The 'ccp4.setup_sh/csh' file was placed into the user's shell config file by sourcing it there: '.bashrc', '.cshrc', '.tcshrc' depending on the shell used. Starting from a terminal that has the new CCP4 environment setup, the ARP/wARP installation could be done. On the Mac however it is more complicated because the superuser owns the installation. Through 'sudo xterm' and in there 'source ~user/.cshrc' (to be replaced by your settings) the ccp4 environment is setup for the superuser. In both cases (on the Mac as superuser) 'cd' to the ARP/wARP folder, e.g. arp_warp_7.1, and run ARP/wARP's 'install.sh'. This script tries to install ARP/wARP into the CCP4 GUI automatically and this is where problems start. The error message from above, the 'Program List' contains no buttons from the installation, these are just in 'Model Building', manual deinstallation is not possible, the new tasks don't seem to be registered with the CCP4 GUI. The fix: The tcl-files that control the installation of a new software module read the file '$CCP4I_TOP/etc/UNIX/modules.def'. This file seems to have a line missing: In the block of 'TASK_MODULE' lines (around line 500) the entry 'TASK_MODULE,206 programlist' is missing. Please add it there at about the right place. Rerun the ARP/wARP installation and the error message should be gone, the installation should be complete, i.e. ARP/wARP buttons in 'program list', too, and the possibility of manual deinstallation. I hope this is helpful. Cheers, Gerrit.
[ccp4bb] About SAD phasing
Hi, All I would like to ask whether is it possible to allocate the Se site and obtain the phase by just using the SAD data set (no native dataset used)? Thanks, Qing
Re: [ccp4bb] About SAD phasing
Yes! Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Aug 30, 2010, at 21:32 , Jane Bailey wrote: Hi, All I would like to ask whether is it possible to allocate the Se site and obtain the phase by just using the SAD data set (no native dataset used)? Thanks, Qing
Re: [ccp4bb] About SAD phasing
Dear Qing, Many structures have been solved that way. Make sure you try solvent modification (flattening / flipping) on your map. This is because SAD will give two equally-probably estimates for the phase. The initial, unmodified map will use the average of the two, but solve modification should be able to break the amibiguity. It sounds like you're new to crystallography - do you have a local advisor to get help from? Phoebe = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 30 Aug 2010 20:32:26 +0200 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Jane Bailey jbailey.x...@googlemail.com) Subject: [ccp4bb] About SAD phasing To: CCP4BB@JISCMAIL.AC.UK Hi, All I would like to ask whether is it possible to allocate the Se site and obtain the phase by just using the SAD data set (no native dataset used)? Thanks, Qing
Re: [ccp4bb] About SAD phasing
Hi Qing, just want to add that it also may depend on the redundancy of the data. While good MAD experiments were performed with low redundancy (best to use a strategy for data collection) a successful SAD experiment often depends on high redundancy. Best Regards, Georg Am 30.08.2010 20:58, schrieb Phoebe Rice: Dear Qing, Many structures have been solved that way. Make sure you try solvent modification (flattening / flipping) on your map. This is because SAD will give two equally-probably estimates for the phase. The initial, unmodified map will use the average of the two, but solve modification should be able to break the amibiguity. It sounds like you're new to crystallography - do you have a local advisor to get help from? Phoebe = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 30 Aug 2010 20:32:26 +0200 From: CCP4 bulletin boardCCP4BB@JISCMAIL.AC.UK (on behalf of Jane Baileyjbailey.x...@googlemail.com) Subject: [ccp4bb] About SAD phasing To: CCP4BB@JISCMAIL.AC.UK Hi, All I would like to ask whether is it possible to allocate the Se site and obtain the phase by just using the SAD data set (no native dataset used)? Thanks, Qing
[ccp4bb] Format conversion of Shelx coordinate file
Dear All, What is currently the quickest/easiest way to convert a .hat file with fractional coordinates of heavy atoms generated by ShelxE to PDB format and/or a file format accepted by Sharp? I tried to use coordconv from ccp4, but it failed to make the conversion. Thank you. Regards, Florian --- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602
Re: [ccp4bb] error running reduce/probe in WinCoot
I also got same error with some of PDB files I got today after refinement. I checked some of the files of same project it works there. I don't know the difference why its happening. I was trying to fix molprobity flags and refine them. Looking for suggestions Thanks Yogi From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Julie Neubauer [julie.neuba...@gmail.com] Sent: Sunday, August 29, 2010 4:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] error running reduce/probe in WinCoot Hello, I'm trying to use the 'probe clashes' function in WinCoot. However, each time I try I get the following error message: Found 4580 hydrogens 0 hets Standardized 6012 hydrogens 0 hets Added 344 hydrogens 0 hets Removed 0 hydrogens 0 hets Adjusted 123 groups(s) If you publish work which uses reduce, please cite: Word, et al. (1999) J. Mol. Biol. 285, 1735-1747. For more information see http://kinemage.biochem.duke.edu BL WARNING:: reduce didn't run ok, so stop here! run_generic_script (probe, 0) I am aware that someone else had this problem and it was suggested that he solve it by changing which set of lines were commented out in the code. I have tried that, but found no difference when trying to run probe clashes afterward. Does anyone have any other suggestions? Thanks. Julie PCB, Duke University
Re: [ccp4bb] About SAD phasing
no it's called SAD exactly for that reason .. it's SAD that somebody developed a phasing method that does not solve the phase problem! sorry, stupid joke ... google (at least) is our friend btw ale P please don't print this e-mail unless you really need to *** Dr. Alessandro Vannini, PhD Cramer lab Gene Center, Deparment of Chemistry and Biochemistry Ludwig-Maximilian-Universität München Feodor-Lynen-Str. 25 81377 München Tel. : +49-89-2180-76955 On 30 Aug 2010, at 20:32, Jane Bailey wrote: Hi, All I would like to ask whether is it possible to allocate the Se site and obtain the phase by just using the SAD data set (no native dataset used)? Thanks, Qing
