[ccp4bb] how to run shelx C/D/E using CCP4 GUI on windows
Hi everyone, Can anybody tell how to run shelx C/D/E within CCP4 GUI on windows system? Moreover, since shelx C/D/E within CCP4 using mtz file (structure factor) instead of sca file (intensity), would this matters in tough conditions? Thank you! Best regards Chen -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:che...@xtal.tsinghua.edu.cn 北京市海淀区清华大学生命科学馆201-212室 邮编：100084
[ccp4bb] seeking help about running SCALEPACK2mtz
Dear CCP4BBers: I'e got a problem about data processing when running SCALEPACK2mtz. Hope you can give me some advice on that. Here's my problem: I have an .sca file processed by HKL2000 about 4 years ago, I just ran the Scalepack2mtz program in order to transform it into .mtz file. However, the program keeps running. To ensure that the Scalepack2mtz program is ok, I use another .sca file for verification and it turns out that this file for verification is successfully transformed into .mtz file within seconds. I checked the .log file, the program keeps running when there are the following messeages: Mean acentric moments I from input data: I^2/I^2 = 2.360 (Expected = 2.000, Perfect Twin = 1.500) I^3/I^3 = 9.187 (Expected value = 6.000, Perfect Twin = 3.000) I^4/I^4 = 52.348 (Expected value = 24.000, Perfect Twin = 7.500) Mean acentric moments I from anisotropically corrected data: I^2/I^2 = 3.121 (Expected = 2.000, Perfect Twin = 1.500) I^3/I^3 = 12.788 (Expected value = 6.000, Perfect Twin = 3.000) I^4/I^4 = 57.952 (Expected value = 24.000, Perfect Twin = 7.500) does this means that the .sca file isn't processed properly? I also checked the scale.log file, and there are the following messages: Shell Summary of observation redundancies: Lower Upper % of reflections with given No. of observations limit limit 0 1 2 3 4 5-6 7-8 9-12 13-19 19 total 50.00 5.60 5.9 6.1 18.0 15.1 26.9 19.7 8.3 0.0 0.0 0.0 94.1 5.60 4.45 7.9 9.4 13.0 12.9 23.2 27.5 6.1 0.0 0.0 0.0 92.1 4.45 3.88 19.2 5.6 13.3 13.5 20.4 21.9 6.0 0.0 0.0 0.0 80.8 3.88 3.53 31.9 6.5 11.6 11.3 14.9 17.9 5.8 0.0 0.0 0.0 68.1 3.53 3.28 2.4 4.7 11.3 15.3 23.5 34.1 8.7 0.0 0.0 0.0 97.6 3.28 3.08 0.2 3.6 7.0 15.4 23.7 40.1 9.9 0.0 0.0 0.0 99.8 3.08 2.93 0.4 4.4 8.7 16.8 21.1 41.3 7.2 0.0 0.0 0.0 99.6 2.93 2.80 4.2 8.0 12.7 15.2 20.3 33.7 6.0 0.0 0.0 0.0 95.8 2.80 2.69 15.4 9.1 14.0 13.8 19.2 25.2 3.3 0.0 0.0 0.0 84.6 2.69 2.60 31.6 16.2 11.7 14.2 13.7 10.6 2.0 0.0 0.0 0.0 68.4 All hkl 11.8 7.3 12.2 14.4 20.8 27.1 6.4 0.0 0.0 0.0 88.2 This clearly indicates an ice ring problem in the data-collection process. However, the ice ring problem shouldn't have caused the error during the .sca to .mtz process. In fact, I have use it for structure-solvement, and currently the two R factor is around 30%. However, the large deviation of I^3/I^3 or I^4/I^4 do means something wrong. Would you tell me what exact mistakes did I make? Can I use this .sca file for subsequent structure solving and refinement? Great thanks for your help best regards chen --
Re: [ccp4bb] Anisotropic diffraction
Birtley and Curry used a novel optimization method, in their paper Crystallization of foot-and-mouth disease virus 3C protease: surface mutagenesis and a novel crystal-optimization strategy, which might be inspiring for you. 在 2012年4月28日 上午3:21，David Schuller dj...@cornell.edu 写道： Anisotropic truncation should have no effect on the space group symmetry. On 04/27/12 15:18, Theresa Hsu wrote: Dear crystallographers A very basic question, for anisotropic diffraction, does data truncation with ellipsoidal method change the symmetry? For example, if untruncated data is space group P6, will truncated data index as P622 or P2? Thank you. Theresa -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:che...@xtal.tsinghua.edu.cn 北京市海淀区清华大学生命科学馆201-212室 邮编：100084
Re: [ccp4bb] Server or software for B factor analysis
Why not just use PROCHECK program?
在 2012年2月22日 下午6:24，Thomas Holder thomas.hol...@tuebingen.mpg.de 写道：
Hi Dialing,
if you know some python you can use PyMOL.
# get C-alpha b-factors as list
from pymol import cmd, stored
stored.bfactors = []
cmd.iterate('name CA', 'stored.bfactors.append((b,resv))')
# min/max b-factors with residue number
print min(stored.bfactors)
print max(stored.bfactors)
# data for plotting
x = [resv for (b,resv) in stored.bfactors]
y = [bfor (b,resv) in stored.bfactors]
# plot to a pdf file with matplotlib
from matplotlib.pyplot import figure
from matplotlib.backends.backend_pdf import PdfPages
fig = figure()
sub = fig.add_subplot(111)
sub.plot(x, y)
pp = PdfPages('bfactors.pdf')
fig.savefig(pp, format='pdf')
pp.close()
Hope that helps.
Cheers,
Thomas
On 02/22/2012 05:04 AM, Dialing Pretty wrote:
Dear All,
Will you please tell me a server of software which can draw a curve for
the B factor of the atoms in a protein PDB file from the first residue
to the residue?Or a server or software by which we can easily order the
B factors of the atoms in the PDB file according to the B factor in
decrease or in increase? Or to get the residues with the highest B
factor and the lowest B factor?
Cheers,
Dialing
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
Cheng Chen, Ph.D. Candidate
Laboratory of Structural Biology
Life Science Building,Tsinghua University
Beijing 100084
China
Tel:+86-10-62772291
Fax:+86-10-62773145
E-mail:che...@xtal.tsinghua.edu.cn
北京市海淀区清华大学生命科学馆201-212室
邮编：100084
Re: [ccp4bb] Off topic: Beryllium chloride
Beryllium chloride is very toxic. More care is needed when preparing it. 在 2011年10月4日 上午7:35，Peter Hsu hsuu...@u.washington.edu 写道： Sorry for the very off topic and dumb question, but does anyone know if BeCl2 needs to be prepared fresh for use (making BeF3) or can it be stored as a solution stock at room temperature/frozen? Thanks, Peter -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:che...@xtal.tsinghua.edu.cn 北京市海淀区清华大学生命科学馆201-212室 邮编：100084
[ccp4bb] Problems with adding ncs matrixs in PHENIX
I am working on a data set of an T=4 icosahedron protein crystal, employing molecular replacement methods. I've consulted a professor, he told me that my crystal is in fact isomorphous to the model so that there is no need for MR. So I figured such command lines: phenix.refine output.mtz model.pdb strategy=rigid_body+individual_adp Here, the 'output.mtz' represents my data file. 'Model.pdb' is the original model, which contains 4 molecules. Well. there is still the need for me to add in the non-crystallographic symmetry matrixes in this command lines, better in a file *.params. Longing for reply. Best regards, chen -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:che...@xtal.tsinghua.edu.cn e-mail%3ache...@xtal.tsinghua.edu.cn 北京市海淀区清华大学生命科学馆201-212室 邮编：100084
