Re: [ccp4bb] error after install
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Joel, reinstalling operating systems is fairly common also to other ones than linux ;-) The behaviour of the command 'ccp4' is actually correct for it is aliased to tg@shelx8:/xtal/Suites/CCP4/ccp4-6.2.0$ type -all ccp4 ccp4 is aliased to `pushd $CCP4>/dev/null' I suppose you mean 'ccp4i' instead in order to start the CCP4 interface. About the python: What is the output of the command stat /opt/CCP4/Python-2.6.7/bin/python Maybe you do not have executable permission. Tim On 09/23/2011 12:29 AM, Joel Tyndall wrote: > Hi folks, > > My love/hate relationship continues with linux. I have had to > reinstall everything and when I install CCP4 6.2.0 It seems to work > fine but upon opening a shell I get the error below and by typing > ccp4 I simply get changed to the ccp4 directory. > > *** Fatal Error: Incomplete > libtbx environment\! *** > Please re-run the libtbx/configure.py command. > > On a little searching I found some evidence of this error before but > little solutions to the problem. When I run: > > python configure.py > > I get the error > > bash: /opt/CCP4/Python-2.6.7/bin/python: No such file or directory > > This file does exist. > > I am running Ubuntu 10.10 as a guest on a windows 7 machine. I am > running in a bash shell. This error occurs when nothing else is > installed. The libtx/configure.py is in three places > > /opt/CCP4/ccp4-6.2.0/lib/cctbx-utf/cctbx_sources/cctbx_project/libtx > /opt/CCP4/ccp4-6.2.0/lib/cctbx/cctbx_sources/cctbx_project/libtx > /opt/CCP4/ccp4-6.2.0/src/phaser/phaser-2.3.0/libtx > > I recently installed CCP4 6.1.12 with no issues. Any help to solve > this problem would be much appreciated > > Joel _ Joel Tyndall, PhD > > Senior Lecturer in Medicinal Chemistry National School of Pharmacy > University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: > jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te > Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 > Otepoti 9054 Aotearoa > > Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 > 4797034 > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOfEKOUxlJ7aRr7hoRAjDSAJsHVlJPFlBHxNmWty1NfvTz46pWzACg3QUk D4wNrN3iLTd/JFE4x1s0+rE= =BhZt -END PGP SIGNATURE-
Re: [ccp4bb] question regarding secondary-structure restraints
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Pete, Coot offers using secondary structure restraints, i.e. this does not refer to refinement but to model building where your calculations do not apply. It helps a great deal if you are looking at a patch of density at, say, 3.5A resolution which you recognise as alpha-helix or beta-strand and simply ask your model building program of choice to "place a helix here" which you can incorporate into your model or at least use as a guideline for correcting yours. Tim On 09/22/2011 10:18 PM, Pete Meyer wrote: > I've noticed that people seem to be using or recommending secondary > structure restraints for low resolution refinement lately, but I'm > somewhat confused about the logic underlying their use. > > Using ballpark figures from a system I'm familiar with: 3 atoms > (9 positional parameters), 4500 residues, 10 reflections and > 95000 geometric (bond and angle) restraints. > n_ref / n_param ~= 1.11 > (n_ref + n_geom) / n_param ~= 2.16 > > Assuming all residues are localized, and each residue provides 2 > secondary structure restraints (best-case scenario), this changes the > effective observation to parameter ratio to: > > (n_ref + n_geom + n_ss ) / n_param ~= 2.26 > > In short, the effective observation to parameter ratio improves by ~4%. > This seems like a relatively small improvement, especially if the > trade-off is that Ramachandran statistics can't be used for validation > anymore. It also seems like the improvement would decrease with larger > proteins (the number of additional parameters from adding a residues > increase faster than the number of secondary structure restraints that > residue could provide). > > Does anyone have any suggestions that could help clear things up? > > Thanks, > > Pete > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOfEamUxlJ7aRr7hoRAiIuAJ9g6X38mWhX7oMAGSX8+qQt0Es7cQCgq4+p WMegXgDLxuS2E5494O/EiE8= =ENms -END PGP SIGNATURE-
[ccp4bb] JRH input Re: [ccp4bb] Neutron data collection
Dear Rex, These issues of energy overlaps are addressed in theory, for either diffraction probe, in Cruickshank, Helliwell and Moffat 1987 Acta Cryst, and also by the same authors in 1991 Acta Cryst for spatial overlaps, and in practice in eg Ren et al JSR 1999 and Nieh et al JSR 1999. Basically the predominance of singlet reflection Laue spots is a consequence of the probability of prime numbers and, where you do have energy overlapped spots, the effectiveness of energy overlaps' deconvolution arises where you have symmetry equivalents and/or multiple occurrences of the same hkl, which usually one does. The low resolution reflections in particular have a higher probability of occurring in multiples and thus are mainly the ones that require the deconvolution of intensities ie of the fundamental and its harmonic(s). The extracted intensities so obtained are actually of a very good precision. A high completeness through all the resolution range is overall readily achievable with Laue. Re point 2. These issues, and advantages, are explored in Blakeley et al 2004 PNAS which features freezing of such large crystals through to protein and ordered solvent, which there is more of, model refinement. Losses of diffraction quality for freezing attempts with bigger crystals in our experience is worse though ie more probable than with small crystals, and so if you don't have some sort of supply, would certainly be off putting, but obviously it's doable. Also it is my belief that as experience grows so will such procedures improve and the scope thereby widen, encompassing for example freeze trapping studies with neutrons as probe. Greetings, John Prof John R Helliwell DSc On 21 Sep 2011, at 10:52, REX PALMER wrote: > Re Neutron Data Collection: > 1. What are the limits to data set completeness imposed by a Laue experiment > versus those of monochromatic data collection? > 2. What problems are caused by flash freezing the larger protein crystals > used for neutron data collection which do not occur for X-ray data collection > ie because smaller crystals can be used. > Any help will be greatly appreciated. > > Rex Palmer > http://www.bbk.ac.uk/biology/our-staff/emeritus-staff > http://rexpalmer2010.homestead.com
[ccp4bb] Research Assistant Position in Molecular Biology at OPPF-UK
Research Assistant in Molecular Biology (Vacancy ID: 101125) Wellcome Trust Centre for Human Genetics, Division of Structural Biology Located at the Oxford Protein Production Facility - UK, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0FA Grade 6: Salary £25,854 - £30,870 with a discretionary range to £33,734 p.a. Applications are invited for a Research Assistant in Molecular Biology to join the Oxford Protein Production Facility- UK (OPPF-UK) team. You will be responsible for carrying out cloning and expression screening of recombinant proteins as part of the services offered by the OPPF-UK to other academic groups (http://www.oppf.ox.ac.uk/). You will be involved in the development and automation of high throughput approaches to molecular biology and have the opportunity to undertake original research leading to academic publications as part of our own research projects. You will have a BSc degree in biology, biochemistry or molecular biology and research experience in using recombinant DNA methods, including PCR, vector construction and transformation of E. coli. or experience of analysing protein expression by SDS-PAGE, Western blotting. The position is funded by the Medical Research Council and is fixed term until 30th June 2013 in the first instance. To apply for this role and for further details, including a job description and a person specification, please click on the link below: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=101125 Only applications received before 12.00 midday on 24th October 2011 will be considered. Please quote reference 101125 on all correspondence. You will be required to upload a CV and supporting statement as part of your online application.
[ccp4bb] How to get cif2mtz to handle new fields
The current version of the mmcif_pdbx dictionary at http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Index/index.html defines _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_FWT _refln.pdbx_PHWT as fields in which you can deposit coefficients from the computation of weighted Fo-Fc and 2Fo-Fc maps; this is marvellous, since previously it's been very unclear how you deposit maps. However, when I make an mmcif file with entries for these fields and pass it through the version of cif2mtz in ccp4-6.2.0, I get Line 77:data name "_refln.pdbx_DELFWT" not present in dictionary Line 78:data name "_refln.pdbx_FWT" not present in dictionary Line 79:data name "_refln.pdbx_DELPHWT" not present in dictionary Line 80:data name "_refln.pdbx_PHWT" not present in dictionary Is it possible to edit the dictionary? It appears to be supplied as lib/cif_mmdic.lib which is a binary file; presumably that's produced with some kind of compiler from some kind of source file, but I'm not sure how to start looking for the compiler and the source. Yours sincerely, Thomas Womack (Global Phasing)
Re: [ccp4bb] Zalman displays and Macs?
Here are the SwitchResX settings for the ZM-M220W that I alluded to in last
night's reply - these get it work via a Thunderbolt port using a DisplayPort to
VGA adapter cable on a new 27" iMac. I'm not sure if all these settings need
to be entered and even after entering the frequency specs the software could
not quite figure out the 1680x1050 resolution right. I thus configured it as a
Custom Resolution and got it to work.
Display Information Panel: (gleaned from manual)
V. freq 56 - 75 Hz
H. freq 31.50 - 80.00 kHz
Pixel Clock 28.32 - 135 MHz
Default Resolution1680 x 1050 @ 60 Hz
Current Resolutions Panel:
Set to 1680 x 1050, 60 Hz (likely only available after setting custom
resolution in next panel)
Custom Resolutions:
Created a new one by clicking "+" button
Check the "Use simplified settings" button and selected CVT-RB from popup
menu
Set Active area as 1680 and 1050
Set Scan rate Vertical to 56.632 Hz
Selected Positive sync for Horizontal only.
Then saved and rebooted. Finally, it looks like you have to set the resolution
in the Displays panel for each use of the system (I use the Displays Menu bar
icon). And SwitchResX will set you back 14 ⬠(~$18) after a ten day demo
period.
Cheers,
Olve
==
Final (auto-calculated) result was the following:
Pixel Clock118.75 MHz
{ParameterHorizVert}
Active 1680 1050
Front Porch483
Sync width 32 6
Back porch 8021
Blanking 160 30 (not editable)
Total 1840 1080 (not editable)
Scan Rate 64.538 kHz 59.757 Hz
Selected Positive sync for Horizontal only
Final config became "1680 x 1050, 56.76 Hz"
Re: [ccp4bb] Neutron data collection
On 09/22/11 12:43, Jacob Keller wrote: Wow, neutrons are pretty cool! No radiation damage- Maybe we should be using neutrinos, in hopes of getting some data _literally_ before there is any damage. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] neutron data measurement
This thread caught my attention several days ago and I now have enough time to add my two cents worth. These are my own biases and probably do not reflect the views of my friends and colleagues at various neutron facilities. With respect to the size of crystals for neutron diffraction, a good rule of thumb is that there should be at least 10exp24 uniformly ordered unit cells in a D2O exchanged crystal to have successful diffraction on par with rotating anode data measured on a crystal with a tenth the volume. Several data sets have been measured from smaller crystals, and perdeuteration lowers the volume needed to extract useful information. Most of the neutron data has a resolution cutoff of 1.8 to 2.0Å, which permits unambiguous placement of deuterons and solvent molecules, especially when completing dual refinement of X-ray and neutron data from the same crystal. There have been a limited number of low temperature neutron diffraction experiments for several reasons. First, of the available neutron beamlines for macromolecular data measurement there are only one or two with open flow cryostats available, limiting the locations for standard macromolecular cryocrystallography. Second, there are a tremendous number of important structures that can be done at room temperature. It is difficult to justify the time needed for low temperature work to experimental review panels when crystals are available to resolve a knotty enzyme mechanism problem. Third, the size of crystal needed for successful neutron diffraction is right at the limit of the size of crystal that can be successfully flash-cooled without inducing excess mosaicity. Most neutron beamlines use some form of quasi-Laue data collection strategy. Mosaicities in excess of 0.5º render most crystals unusable for neutron data measurement. Remember that a lot of uniform unit cells are needed to get a usable diffraction signal from neutrons. Often a large flash-cooled cooled crystal appears to have low mosaicity when exposed to 0.5mm x-ray beam. However, when placed in the 3mm neutron beam, limited streaky low-resolution diffraction appears. It is difficult to judge the quality of flash-cooled neutron diffraction sized crystal without placing it in the neutron beam. Returning to point 2 it is difficult justify the time needed on fishing expedition. So far the only large crystals I have been able to flash-cool that met the demands of size and crystal perfection had very low solvent content or were grown in high levels of cryoprotectant. That said, several critical problems cry out for low temp neutron studies so there is every reason to persevere. I would be pleased to answer any questions off-line for those of you with more interest in neutron cryocrystallography. Finally with respect to radiation damage, Benno Schoenborn has had a myoglobin crystal in sealed capillary that he has used as a “standard candle” for testing neutron beamlines. There has been no discernable degradation of the crystal in all the years he has used it. The neutrons used for neutron diffraction are ‘cold’ neutrons, usually with energies of 1 – 10 meV. Damage could come from activated nuclei, but these are usually very limited on a molar basis within the crystal. As can be seen with Benno’s myoglobin crystal, 30 years of iron activation has yet to produce a measurable defect. Leif Hanson University of Toledo
Re: [ccp4bb] Neutron data collection
Jacob Keller wrote: > Wow, neutrons are pretty cool! No radiation damage--and time > resolution? I guess this is since they have much higher energy, and > are measurable individually? What are the numbers for fluxes > (neutrons/sec)? Are the neutrons all at one energy, or is there a > bandwidth? The energy of neutrons is even lower when compared to X-rays. A neutron with a wavelength of 1.8A has an energy of about 25 meV. The flux at neutron sources compared to synchrotrons is unfortunately low: Diffractometer "LADI III" reactor ILL/France: 3 x 10^7 neutrons/sec/cm^2 (quasi-Laue, delta L / L = 20%) Diffractometer "BioDiff" reactor FRM II / Germany: 1 x 10^7 neutrons/sec/cm^2 (monochromatic, delta L / L = 2.5%) Diffractometer "BIX4" reactor JRR3M / Japan: 4 x 10^6 neutrons/sec/cm^2 (monochromatic, delta L / L = 2.0%) BUT you can detect hydrogen atoms even at a moderate resolution of about 2A ! With neutrons the scattering power of hydrogen/deuterium is "comparable" to the scattering power of carbon. You can even distinguish between isotopes. Since the nucleus is a point scatterer the "form factor" -for neutrons called scattering length- is not scattering angle depended. A typical measurement time is about 2-3 weeks for a crystal of 1 mm^3. I know...of course not every protein can be crystallized up to 1 mm^3 but if you have such a system and you are interested in the protonation states of amino acids in the active centre for example, than neutrons are worth a try for sure! If you fully deuterate your protein (which gets more and more routine work for example at the D-LAB at ILL/EMBL) you can even work with smaller crystals. Because of the relative low flux most reactor based neutron diffractometers for proteins uses large cylindrical neutron image plate detector, which cover a solid angle of about 2 Pi. At spallation sources (which are pulsed neutron sources) detectors with time resolution are used. This instruments (PCS in Los Alamos; iBIX in Japan and MANDI in Oak Ridge) are time of flight instruments. They uses the fact that neutrons with different energy/wavelength show different velocities ( a 1.8A neutron has a velocity of about 2200 m/s). They measure different wavelength neutrons at different time at the detector. Hope to see some of you as new "neutron users" in the future, cheers, Andreas -- Dr. Andreas Ostermann Technische Universität München Research reactor FRM II Instrument "BioDiff" Lichtenbergstr. 1 D-85747 Garching Tel.: +49-89-289-14702 Fax.: +49-89-289-14666 Email: andreas.osterm...@frm2.tum.de Web: http://www.frm2.tum.de/en/science/index.html
Re: [ccp4bb] Neutron data collection
That value, 2200m/s, is pretty slow--there are some bullets that go faster than that, I think... JPK On Fri, Sep 23, 2011 at 11:59 AM, Andreas Ostermann wrote: > Jacob Keller wrote: >> Wow, neutrons are pretty cool! No radiation damage--and time >> resolution? I guess this is since they have much higher energy, and >> are measurable individually? What are the numbers for fluxes >> (neutrons/sec)? Are the neutrons all at one energy, or is there a >> bandwidth? > > The energy of neutrons is even lower when compared to X-rays. > A neutron with a wavelength of 1.8A has an energy of about 25 meV. > The flux at neutron sources compared to synchrotrons is unfortunately low: > > Diffractometer "LADI III" reactor ILL/France: > 3 x 10^7 neutrons/sec/cm^2 (quasi-Laue, delta L / L = 20%) > > Diffractometer "BioDiff" reactor FRM II / Germany: > 1 x 10^7 neutrons/sec/cm^2 (monochromatic, delta L / L = 2.5%) > > Diffractometer "BIX4" reactor JRR3M / Japan: > 4 x 10^6 neutrons/sec/cm^2 (monochromatic, delta L / L = 2.0%) > > BUT you can detect hydrogen atoms even at a moderate resolution of > about 2A ! With neutrons the scattering power of hydrogen/deuterium > is "comparable" to the scattering power of carbon. You can even distinguish > between isotopes. Since the nucleus is a point scatterer the "form factor" > -for neutrons called scattering length- is not scattering angle depended. > A typical measurement time is about 2-3 weeks for a crystal of 1 mm^3. > I know...of course not every protein can be crystallized up to 1 mm^3 but > if you have such a system and you are interested in the protonation states > of amino acids in the active centre for example, than neutrons are worth a > try > for sure! If you fully deuterate your protein (which gets more and more > routine > work for example at the D-LAB at ILL/EMBL) you can even work with smaller > crystals. > > Because of the relative low flux most reactor based neutron diffractometers > for > proteins uses large cylindrical neutron image plate detector, which cover a > solid angle > of about 2 Pi. At spallation sources (which are pulsed neutron sources) > detectors > with time resolution are used. This instruments (PCS in Los Alamos; iBIX in > Japan > and MANDI in Oak Ridge) are time of flight instruments. They uses the fact > that > neutrons with different energy/wavelength show different velocities ( a 1.8A > neutron > has a velocity of about 2200 m/s). They measure different wavelength > neutrons at > different time at the detector. > > Hope to see some of you as new "neutron users" in the future, > cheers, > > Andreas > > -- > Dr. Andreas Ostermann > Technische Universität München > Research reactor FRM II > Instrument "BioDiff" > Lichtenbergstr. 1 > D-85747 Garching > Tel.: +49-89-289-14702 > Fax.: +49-89-289-14666 > Email: andreas.osterm...@frm2.tum.de > Web: http://www.frm2.tum.de/en/science/index.html > -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] neutron data measurement
> Third, the size of crystal needed for successful neutron diffraction is right at the limit of the size of crystal that can be successfully flash-cooled without inducing excess mosaicity. Can't the crystal be flash-cooled at high pressure? The inventors of the Crystal Harp in Zurich use a machine that does this automatically for cryo e.m., which many universities already have. On Fri, Sep 23, 2011 at 4:40 PM, Leif Hanson wrote: > This thread caught my attention several days ago and I now have enough time > to add my two cents worth. These are my own biases and probably do not > reflect the views of my friends and colleagues at various neutron > facilities. > > > With respect to the size of crystals for neutron diffraction, a good rule > of thumb is that there should be at least 10exp24 uniformly ordered unit > cells in a D2O exchanged crystal to have successful diffraction on par > with rotating anode data measured on a crystal with a tenth the volume. > Several data sets have been measured from smaller crystals, and > perdeuteration lowers the volume needed to extract useful information. Most > of the neutron data has a resolution cutoff of 1.8 to 2.0Å, which permits > unambiguous placement of deuterons and solvent molecules, especially when > completing dual refinement of X-ray and neutron data from the same crystal. > > > There have been a limited number of low temperature neutron diffraction > experiments for several reasons. First, of the available neutron beamlines > for macromolecular data measurement there are only one or two with open flow > cryostats available, limiting the locations for standard macromolecular > cryocrystallography. Second, there are a tremendous number of important > structures that can be done at room temperature. It is difficult to justify > the time needed for low temperature work to experimental review panels when > crystals are available to resolve a knotty enzyme mechanism problem. Third, > the size of crystal needed for successful neutron diffraction is right at > the limit of the size of crystal that can be successfully flash-cooled > without inducing excess mosaicity. Most neutron beamlines use some form of > quasi-Laue data collection strategy. Mosaicities in excess of 0.5º render > most crystals unusable for neutron data measurement. Remember that a lot of > uniform unit cells are needed to get a usable diffraction signal from > neutrons. Often a large flash-cooled cooled crystal appears to have low > mosaicity when exposed to 0.5mm x-ray beam. However, when placed in the 3mm > neutron beam, limited streaky low-resolution diffraction appears. It is > difficult to judge the quality of flash-cooled neutron diffraction sized > crystal without placing it in the neutron beam. Returning to point 2 it is > difficult justify the time needed on fishing expedition. So far the only > large crystals I have been able to flash-cool that met the demands of size > and crystal perfection had very low solvent content or were grown in high > levels of cryoprotectant. That said, several critical problems cry out for > low temp neutron studies so there is every reason to persevere. I would be > pleased to answer any questions off-line for those of you with more interest > in neutron cryocrystallography. > > > Finally with respect to radiation damage, Benno Schoenborn has had a > myoglobin crystal in sealed capillary that he has used as a “standard > candle” for testing neutron beamlines. There has been no discernable > degradation of the crystal in all the years he has used it. The neutrons > used for neutron diffraction are ‘cold’ neutrons, usually with energies of 1 > – 10 meV. Damage could come from activated nuclei, but these are usually > very limited on a molar basis within the crystal. As can be seen with > Benno’s myoglobin crystal, 30 years of iron activation has yet to produce a > measurable defect. > > > Leif Hanson > > University of Toledo > -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
[ccp4bb] Direct method solution at 1.15A
Hello everyone, I have a data set >99% completeness to 1.15A This is a 400 amino acid long protein and it has 7 Met (Sulfur peaks around 20sigma) And a tightly bound phosphate (P peak around 22sigma) Could I try and solve this directly or is it crazy idea? If so what program should I try? thanks Yuri
Re: [ccp4bb] Direct method solution at 1.15A
Yes you should. AND you are crazy. One of George's SHEL programs or perhaps SnB from the Hauptman group. Good luck! --Original Message-- From: Yuri Pompeu Sender: CCCP4 Bulletin Board To: CCCP4 Bulletin Board ReplyTo: Yuri Pompeu Subject: [ccp4bb] Direct method solution at 1.15A Sent: Sep 23, 2011 2:49 PM Hello everyone, I have a data set >99% completeness to 1.15A This is a 400 amino acid long protein and it has 7 Met (Sulfur peaks around 20sigma) And a tightly bound phosphate (P peak around 22sigma) Could I try and solve this directly or is it crazy idea? If so what program should I try? thanks Yuri Sent via BlackBerry by AT&T
Re: [ccp4bb] Direct method solution at 1.15A
I don't really get your question: assuming the sigmas you mentioned are in an anomalous map and therefore have been located, why don't you just plug it into your usual phasing algorithm? Jacob On Fri, Sep 23, 2011 at 1:49 PM, Yuri Pompeu wrote: > Hello everyone, > I have a data set >99% completeness to 1.15A > This is a 400 amino acid long protein and it has 7 Met (Sulfur peaks around > 20sigma) > And a tightly bound phosphate (P peak around 22sigma) > Could I try and solve this directly or is it crazy idea? > If so what program should I try? > > thanks > Yuri > > -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Direct method solution at 1.15A
I solved the structure using molecular replacement. Those sigmas are simply from my sigmaa 2mFo-DFc maps. I was wondering if I could try and solve sort of like small molecules are
Re: [ccp4bb] Direct method solution at 1.15A
Dear Yuri, There is a general rule that you need data to 1.2 Angstroms or better to solve a structure by ab initio direct methods. To be more precise, more than half the reflections between 1.1 and 1.2 A should have I>2sigma(I). So you are probably just within this limit. However it appears that the largest structures solved this way with no atom heavier than S were not more than half the size of your protein. The programs most often used for such crazy attempts are SnB, SIR and SHELXD. It would be a good idea to find a workstation with at least 32 CPUs and run the multi-CPU version of SHELXD and be patient, it might take a few weeks. If you just want to remove model bias (a serious problem with MR solutions using 3A data, but no problem with 1.15A data) you could try MRSAD phasing. There are many good programs for doing this, but a particularly simple way would be to use ANODE to find the anomalous sites from your MR solution and the new beta-test SHELXE for the density modification and tracing. The only other program you would need for this is SHELXC. I am still developing these programs but am happy to provide them on email request. No other programs, libraries etc. are needed because these programs have zero dependencies. Best wishes, George On Fri, Sep 23, 2011 at 07:49:33PM +0100, Yuri Pompeu wrote: > Hello everyone, > I have a data set >99% completeness to 1.15A > This is a 400 amino acid long protein and it has 7 Met (Sulfur peaks around > 20sigma) > And a tightly bound phosphate (P peak around 22sigma) > Could I try and solve this directly or is it crazy idea? > If so what program should I try? > > thanks > Yuri > > -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Direct method solution at 1.15A
Dear Yuri, If you have located all the heavy atoms (sulfur and phosphor) correctly, you could try sulfur-SAD phasing using the program OASIS. This program has a record of solving a 1206 residues protein with SAD signals from 22 sulfur atoms scattered under Cu-Ka radiation and a record of solving a 213 residues protein with SAD signals from 2 sulfur atoms scattered under Cr-Ka radiation. By the way please note that the OASIS in CCP4 6.2.x is not the uptodate version. You can get a better version from http://cryst.iphy.ac.cn. The latest version will be available on the website in the coming October. Best regards, Hai-fu On Sat, Sep 24, 2011 at 2:49 AM, Yuri Pompeu wrote: > Hello everyone, > I have a data set >99% completeness to 1.15A > This is a 400 amino acid long protein and it has 7 Met (Sulfur peaks around > 20sigma) > And a tightly bound phosphate (P peak around 22sigma) > Could I try and solve this directly or is it crazy idea? > If so what program should I try? > > thanks > Yuri > >
