[ccp4bb] ccp4-6.1.0-core-src.tar.gz TAR error
Dear Charles, to your information: I just downloaded the Version 6.1 source tar file to my x86_64 Linux box (SuSE 10.2, AMD64) and got the following tar error message. All other (LINUX-386 and both COOCH and PHASER) tar files were fine!! --- SNIP ... ccp4-6.1.0/lib/data/monomers/ps.resource ccp4-6.1.0/lib/data/monomers/full_names.list ccp4-6.1.0/lib/data/monomers/mon_lib_ind.cif ccp4-6.1.0/lib/data/monomers/mon_lib_ind2.cif tar: Skipping to next header tar: Archive contains obsolescent base-64 headers gzip: stdin: invalid compressed data--format violated tar: Child returned status 1 tar: Error exit delayed from previous errors --- SNIP May be a corrupt file? Regards Michael -- Dr. Michael Weyand mail: [EMAIL PROTECTED] Max-Planck-Institut fuer molekulare Physiologie, Otto-Hahn-Strasse 11 D-44227 Dortmund, Germany, fon: +49(0)231-133-2738, fax: +49(0)231-133-2797
Re: [ccp4bb] ccp4-6.1.0-core-src.tar.gz TAR error
Dear Michael, How did you do the download? I have just downloaded this file using the old fashioned command line ftp method, and it worked fine. I expect that there has been an error somewhere in the transmission. If you fetch the file from: ftp ftp.ccp4.ac.uk cd ccp4/6.1 get ccp4-6.1.0-core-src.tar.gz you should find that everything is fine. If not, please get in touch directly with the helpdesk at [EMAIL PROTECTED] and we will try to work out what is happening. Thanks best wishes, Graeme -Original Message- From: CCP4 bulletin board on behalf of Michael Weyand Sent: Thu 12/4/2008 8:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ccp4-6.1.0-core-src.tar.gz TAR error Dear Charles, to your information: I just downloaded the Version 6.1 source tar file to my x86_64 Linux box (SuSE 10.2, AMD64) and got the following tar error message. All other (LINUX-386 and both COOCH and PHASER) tar files were fine!! --- SNIP ... ccp4-6.1.0/lib/data/monomers/ps.resource ccp4-6.1.0/lib/data/monomers/full_names.list ccp4-6.1.0/lib/data/monomers/mon_lib_ind.cif ccp4-6.1.0/lib/data/monomers/mon_lib_ind2.cif tar: Skipping to next header tar: Archive contains obsolescent base-64 headers gzip: stdin: invalid compressed data--format violated tar: Child returned status 1 tar: Error exit delayed from previous errors --- SNIP May be a corrupt file? Regards Michael -- Dr. Michael Weyand mail: [EMAIL PROTECTED] Max-Planck-Institut fuer molekulare Physiologie, Otto-Hahn-Strasse 11 D-44227 Dortmund, Germany, fon: +49(0)231-133-2738, fax: +49(0)231-133-2797
Re: [ccp4bb] Temperature factor discrepancy
Hi Wim,
I think that the main question I would ask is how you calculate the
Wilson B factor with 3.0-3.5 A data ...
We have done a rather big study of about 12,000 structures and below
2.5 A, how you calculate the B can result to
major discrepancies. There is hardly a line to get the gradient of. If
you use some scaling to an ideal plot like BEST or ARP/wARP
(same algorithm there) the minimizer and 'spikes' can have a huge
influence.
btw, have you optimized in both cases the Bfactor restraints weight ?
I wonder if that would change things (it will change the FreeR ...)
See Ian Tickle's article
http://journals.iucr.org/d/issues/2007/12/00/gx5119/index.html
I would also expect to use tighter geometry in this resolution btw ...!
(don't be fooled if the current rmsd gives the lower Rfree: if you
change B weight this will very likely change!)
btw, why not use TLS ? For one thing you will get better FreeR and
hopefully better B factor refinement ...!
A.
PS If you want to try things overnight I tend to do something like this:
#!/bin/csh -f
#
echo xweight bweight rfactorrfree rmszbonds stats.log
foreach xweight ( 0.04 0.06 0.08 0.1 0.12 0.14 0.16 0.18 0.20 0.25 0.30)
foreach bweight ( 0.1 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0 2.5 3.0 )
#
#Put you REFMAC script here
# As you can eg obtain it from 'Run and View Command file
# make sure it has these two lines
weight MATRIX ${xweight}
temp ${bweight} 2.0 3.0 2.0 3.0
#
###
echo -n ${xweight} ${bweight} stats.log
#The line below will grep the right thing if you do 20 cycles of
refinement 10 TLS, 10 normal in my case
awk '(NF=11){if ($1==20) print $2, $3, $8}' refmac_${xweight}_$
{bweight}.log stats.log
end
end
#
On Dec 3, 2008, at 16:59, Wim Burmeister wrote:
I should have given the precision that the problem remains
unaffected by a change of the resolution range (even if I use for
example only 4.5 to 3 A resolution).
I am not using TLS and the data are quite isotropic. Rcryst values
are as expected for such a structure.
Anopther 3.5 A dataset does not show the problem (right column).
Wilson plot B-factor [Å2]
66
43
Refinement
Rcryst
0.186 (0.259)
0.190 (0.239)
Rfree
0.268 (0.408)
0.256 (0.278)
Rms deviations from ideal bondlengths (Å)
0.020
0.018
Rms deviations from ideal bond angles (°)
2.0
1.9
Average B-factor [Å2]
39
46
Values for the highest resolution bin are given in brackets.
Cheers
Wim
Wim Burmeister a écrit :
Dear all,
I have a 3 A structure refined with REFMAC which gives consistently
average atomic B-factors of 40 A2, whereas the B factor from a
Wilson plot is about 60 A2. Is there any explanation for such a
discrepancy?
There are no obvious problems:
No twinning, spacegroup P21 with two molecules in the asu, no
proper ncs symmetry. No pathologic Wilson plot, complete and
redundant dataset (although collected on several crystals with
serious problems due to radiation damage).
Interestingly, the Wilson plot of the Fcalc values is about 60 A2
as for Fobs in the output dataset.
Yours
Wim
--
***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9 FRANCE
E-mail: [EMAIL PROTECTED]
Tel:+33 (0) 476 20 72 82 Fax: +33 (0) 476 20 94 00
http://www.uvhci.fr
***
[ccp4bb] suggestions for UV spectrometer
Dear all, we would like to purchase a UV spectrometer for measuring protein concentrations (280nm), and I would like to here your comments and especially recommendations. We don't need anything fancy, a small, fast device would be sufficient. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] suggestions for UV spectrometer
Dear Tim -- On 4 Dec 2008, at 15:16, Tim Gruene wrote: we would like to purchase a UV spectrometer for measuring protein concentrations (280nm), and I would like to here your comments and especially recommendations. I love the Nanodrop system... I know you said you don't want anything fancy, but I like to spend as little protein as possible when measuring its concentration, and I like it fast and reproducible. Plus, in my hands, the Nanodrop system give very reproducible results. Small problem... expensive... You can find infos there: http://www.nanodrop.com/nd-1000-overview.html HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] suggestions for UV spectrometer
I would also recommend the nanodrop. It takes a whole spectra every measurement and there is no need to dilute your sample. You can demo it for a week and try it out. James M. Vergis, Ph.D. University of Virginia Molecular Physiology and Biological Physics MKWEINR 360A Snyder Building 480 Ray C. Hunt Drive PO Box 800886 Charlottesville, VA 22908-0886 phone: 434-243-2730 FAX: 434-243-8271 [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Tim Gruene Sent: Thursday, December 04, 2008 10:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] suggestions for UV spectrometer Dear all, we would like to purchase a UV spectrometer for measuring protein concentrations (280nm), and I would like to here your comments and especially recommendations. We don't need anything fancy, a small, fast device would be sufficient. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] tortion angle restraints in REFMAC
Acturally, I want to find a way to keep the OH tilted out of the neightbouring plane by about 10 degrees. At 2.1A resolution the REFMAC refinement tends to refine it into the plane even though I have included torsion angle restraint in the library for the ligand. I thought I could play with the weight or the esd of the target value but having trouble to achieve it. In CNS, adjusting the force constant of the target value is a way to tighten or loosen the restrain. I would like to know how to enforce a geometry effectively in REFMAC. Thanks for any comments. Huiying On Wed, 3 Dec 2008, Abhinav Kumar wrote: If you want to restrain the OH group to a plane, you need to include it in the plane definition, and not the torsion definition. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Huiying Li wrote: I want to impose restraints during REFMAC refinement on the tortion angles that control the tilting of an OH group from a plane in a ligand bound to the protein. A few things that confused me: 1. In library cif file, should I just increase or decrease the tor.value_angle_esd if I want to loosen or tighten the restraits? 2. What is the meaning of the last column in torsion angle parameters: _chem_comp_tor.period, in cif file? In the PDB output file REFMAC also lists the RMS and WEIGHT for the torsion angles, period 1 through 4. 3. In REFMAC gui under Geometric parameters, there is only one user controlled weight for torsion. By changing the weight here, does it change the torsion weight for all 4 periods? Thanks in advance for the help. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED]
Re: [ccp4bb] suggestions for UV spectrometer
We use a Beckman Coulter DU730. It has a small footprint if lab space is an issue. It will do single-wavelength, multi-wavelength, or take an entire spectrum in 0.5 nm steps if you desire. It comes with the standard 1 ml cuvette holder, but we also purchased the microcuvette accessory for volumes in the 100 uL range. We've been using the instrument for over a year now with no problems. Results for determining protein concentrations using the method of Pace et al * *Protein Sci.javascript:AL_get(this,%20'jour',%20'Protein%20Sci.');1995 Nov;4(11):2411-23 are very reproducible using this spec. On Thu, Dec 4, 2008 at 10:37 AM, James M. Vergis [EMAIL PROTECTED]wrote: I would also recommend the nanodrop. It takes a whole spectra every measurement and there is no need to dilute your sample. You can demo it for a week and try it out. James M. Vergis, Ph.D. University of Virginia Molecular Physiology and Biological Physics MKWEINR 360A Snyder Building 480 Ray C. Hunt Drive PO Box 800886 Charlottesville, VA 22908-0886 phone: 434-243-2730 FAX: 434-243-8271 [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Tim Gruene Sent: Thursday, December 04, 2008 10:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] suggestions for UV spectrometer Dear all, we would like to purchase a UV spectrometer for measuring protein concentrations (280nm), and I would like to here your comments and especially recommendations. We don't need anything fancy, a small, fast device would be sufficient. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]
Re: [ccp4bb] suggestions for UV spectrometer
Tim - I would recommend a spectrometer that records entire spectra, instead of one that takes readings at just 280 nm. Contributions from light scattering can be very strong and can give results that deviate from the true value by a factor of two or more. One cannot detect scattering without recording spectra. The most severe case we have had was someone who thought the protein concentration was 10 mg/mL (based on 280) when in reality (after subtraction of the scattering contribution) it was only 4 mg/mL. Lots of other, less severe cases as well. Hope that helps. Best - MM Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353 On Dec 4, 2008, at 9:16 AM, Tim Gruene wrote: Dear all, we would like to purchase a UV spectrometer for measuring protein concentrations (280nm), and I would like to here your comments and especially recommendations. We don't need anything fancy, a small, fast device would be sufficient. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] tortion angle restraints in REFMAC
Hi Huiying At 2.1A I would be very surprised if you see any density for the H atom in which case the refinement is not going to move it out of the plane whatever weight you give the torsion restraint. To answer your earlier questions the period of a torsion restraint is the number of energy minima in a complete rotation of the angle, so the OH bond will have a period of 2, and yes the same overall weight is applied to all torsions regardless of the period, though individual torsions will also be weighted by 1/sd^2. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Huiying Li Sent: 04 December 2008 16:35 To: Abhinav Kumar Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] tortion angle restraints in REFMAC Acturally, I want to find a way to keep the OH tilted out of the neightbouring plane by about 10 degrees. At 2.1A resolution the REFMAC refinement tends to refine it into the plane even though I have included torsion angle restraint in the library for the ligand. I thought I could play with the weight or the esd of the target value but having trouble to achieve it. In CNS, adjusting the force constant of the target value is a way to tighten or loosen the restrain. I would like to know how to enforce a geometry effectively in REFMAC. Thanks for any comments. Huiying On Wed, 3 Dec 2008, Abhinav Kumar wrote: If you want to restrain the OH group to a plane, you need to include it in the plane definition, and not the torsion definition. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Huiying Li wrote: I want to impose restraints during REFMAC refinement on the tortion angles that control the tilting of an OH group from a plane in a ligand bound to the protein. A few things that confused me: 1. In library cif file, should I just increase or decrease the tor.value_angle_esd if I want to loosen or tighten the restraits? 2. What is the meaning of the last column in torsion angle parameters: _chem_comp_tor.period, in cif file? In the PDB output file REFMAC also lists the RMS and WEIGHT for the torsion angles, period 1 through 4. 3. In REFMAC gui under Geometric parameters, there is only one user controlled weight for torsion. By changing the weight here, does it change the torsion weight for all 4 periods? Thanks in advance for the help. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED] 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] Postdoctoral Position in Macromolecular Crystallography
A postdoctoral position in macromolecular crystallography is available at the three Cassiopeia beamlines at Max-Lab in Lund, Sweden, for a period of two years starting as soon as possible. The Danscatt consortium (www.danscatt.dk) is funding the position, and the successful candidate will work full time at Max-Lab. The postdoc will provide general support to all Cassiopeia users for 1/3 of the working time. The remaining 2/3 will be dedicated to collaborative projects, including publications, with Danish macromolecular crystallography laboratories, and to the development of new directions within macromolecular crystallography at Cassiopeia. Max-Lab has excellent crystallization robotics, crystal imaging facilities, and structure determination tools. With respect to new directions, the post-doc is expected to participate in: * Installation and implementation of a free mounting system for MX * Proof of principle studies for a solution SAXS beamline with the option for microfludics applications * Implementation of automated sample changers for crystal mounting at MX beamlines The successful candidate will refer to professor Michael Gajhede, Biostructural Research, Department of Medicinal Chemistry, University of Copenhagen ([EMAIL PROTECTED]), from whom further details on the position can be obtained. Further details concerning the Cassiopeia beamlines are available from beamline manager Thomas Ursby [EMAIL PROTECTED], see also cassiopeia.maxlab.lu.se. On 23 October 2008, the Swedish government expressed support for the construction of a unique third-generation synchrotron, the Max-IV, which is planned to house two superb MX beamlines and one beamline for solution SAXS. The post-doc is invited to participate in the development of the detailed plans for these beamlines. In addition, the Max-IV may become the neighbour of the new European neutron spallation source ESS, which will initiate a completely new era in neutron studies in structural biology. The post-doctoral position therefore offers a unique opportunity to establish research in the future European powerhouse of structural biology. For more information regarding the Max-IV and ESS, see: www.maxlab.lu.se and www.esss.se. The Danish user community in structural biology holds a unique position in frontier structural biology with many recent publications in leading journals, see examples below. Projects include ion-pumping membrane proteins, large macromolecular complexes involved in RNA metabolism, proteins from the immune defence, ligand-gated ion channels and transporters in the central nervous system, enzymes from the barley fatty acid metabolism, bacterial carbohydrate modifying enzymes and enzymes containing iron. Homepages of Danish MX laboratories: www.farma.ku.dk/BR, www.bioxray.au.dk, www.ccs.ki.ku.dk, www.crc.dk, and www.kemi.dtu.dk. Selected recent MX publications from Danish MX laboratories: * Pedersen BP et al. Crystal structure of the plasma membrane proton pump. Nature 2007, 450(7172):-4. * Morth JP et al. Crystal structure of the sodium-potassium pump. Nature 2007, 450(7172):1043-9. * Olesen C et al. The structural basis of calcium transport by the calcium pump. Nature 2007, 450(7172):1036-42. * Andersen CB et al. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science 2006, 313(5795):1968-72. * Fredslund F et al. Structure of and influence of a tick complement inhibitor on human complement component 5. Nature Immunol. 2008, 9(7):753-60. * Weyand F et al. Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter. Science 2008, Published Online October 16, 2008. * Naur P et al. Ionotropic glutamate-like receptor delta2 binds D-serine and glycine. PNAS 2007, 104(35), 14116-21. * Vestergaard B et al. A helical structural nucleus is the primary elongating unit of insulin amyloid fibrils. PLoS Biology 2007, 5(5) e134. Candidates may apply before receiving their PhD degree, but the successful candidate must have earned a PhD degree before the start of the appointment. Applications should be marked 08-322/MPD-22. Include in five copies: a current curriculum vitae, copies of relevant diplomas, a complete list of publications indicating those articles relevant to the position and copies of same, and a statement of teaching qualifications. Electronics applications will not be accepted. Applications should be sent to: Faculty of Pharmaceutical Sciences University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark Deadline for applications: 15 January 2009 at 12:00 noon. -- Professor Michael Gajhede Institute of Medicinal Chemistry University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Ø Denmark Phone: +45 35306407 Email: [EMAIL PROTECTED]
Re: [ccp4bb] suggestions for UV spectrometer
At the risk of dragging this discussion even further afield from crystallography: How can you get realistic numbers for concentrated solutions using the Nanodrop? I understand that the instrument reduces absorbance by using a very short path length. However, I thought that in order for the Beer-Lambert formalism to be applicable, the solution needs to be sufficiently dilute so that the chance of molecules shadowing one another is negligible. Isn't this condition violated for concentrated solutions (even with short path lengths)? Pat On 4 Dec 2008, at 1:27 PM, Michael Giffin wrote: We also like the Nanodrop... --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [EMAIL PROTECTED]
Re: [ccp4bb] suggestions for UV spectrometer
We too have a nano-drop. We really like it , but have not yet fully switched over. I agree with all the good things said about it , but here are the few times the nano drop falls short: 1) We still use the old spec ( 1 cm path length ) for things at a very low concentration , i.e for the monitoring free thiols in protein with ellman reagent , the absorbances are very low and give poor reproducibility on the nanodrop because of small path-length . Of course this can be overcome by using a lot of protein at a higher concentration and modifying the assay. 2) For very concentrated membrane protein samples which tend to have a large concentration of detergent . The reproducibility is not very good because of the high concentration of deteregent preventing a proper meniscus from forming. The solution to this is to dilute your sample so the dteergent concentration is manageable ( a few times the CMC instead of tens of times the CMC Other than for these issues we almost entirely use the nanodrop and would gladly recommend it Hari On Thu, Dec 4, 2008 at 1:27 PM, Michael Giffin [EMAIL PROTECTED] wrote: We also like the Nanodrop. Very fast, no cuvettes (breaking, washing, cleaning, uh nitric acid bath anyone?), and the .ndv data file is a delimited text file. Open in a text editor, copy and paste into a spreadsheet, and you have a convenient record of all of your stocks, including date, sample name, concentration, and full spectra. It is expensive, but so are good cuvettes. Mike Michael Giffin The Scripps Research Institute Department of Molecular and Experimental Medicine 10550 North Torrey Pines Road, MEM-131 La Jolla, CA 92037 email: [EMAIL PROTECTED] lab: 858-784-7758 On Thu, Dec 4, 2008 at 7:16 AM, Tim Gruene [EMAIL PROTECTED] wrote: Dear all, we would like to purchase a UV spectrometer for measuring protein concentrations (280nm), and I would like to here your comments and especially recommendations. We don't need anything fancy, a small, fast device would be sufficient. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] suggestions for UV spectrometer
Hi Tim, The Shimadzu UV2401PC comes at a reasonable price and has all features you might possible need in a Biochemistry lab. And if you like the option to use small sample volumes, I would suggest to by a TrayCell from Helma - you put it in a regular photometer, it guides the light through a microliter chamber and back into the photometer (it is essentially a cuvette with optics and a 1 or 5 microliter chamber). Costs a few hundred Euros . If you're sure you will never need regular cuvettes - go for Nanodrop. If you want more flexibility, Shimadzu plus TrayCell . Best Clemens --- Jun.-Prof. Dr. Clemens Steegborn Ruhr-University Bochum Physiological Chemistry, MA 2/141 Universitaetsstr. 150 44801 Bochum, Germany phone: ++49 234 32 27041 fax: ++49 234 32 14193 email: [EMAIL PROTECTED]
[ccp4bb] error message for using xfit in ccp4
Hello all, We would appreciate your help on an error message one of our graduate students has encountered using Xfit in CCP4. You can respond to him directly at: [EMAIL PROTECTED] Thank you Mona Rahman Forwarded Message --- Thanks Mona Here is error message for using the xfit in ccp4. xfit Starting XtalView 4.0 for OS: Linux version: 2.6.27.5-117.fc10.i686.PAE Copyright (C) 1992-9 Duncan McRee and The Scripps Research Institute Set LANG to C Color Table initialized with 136 values from /usr/local/XtalView/data/colors.dat XView warning: Cannot load font '-bh-lucida-medium-r-*-*-*-120-*-*-*-*-*-*' (Font package) XView warning: Cannot load font '-bh-lucida-medium-r-normal-sans-*-120-*-*-*-*-*-*' (Font package) XView error: Cannot open connection to window server: :0.0 (Server package) We are using Fedora 10 Thanks Jimin --- Mona N. Rahman, Ph.D. Department of Biochemistry Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] tortion angle restraints in REFMAC
Hi Huiyang OK sorry for misunderstanding. I think that kind of out-of-plane restraint is usually enforced by means of a chiral restraint (even if the group in question is not chiral). You would need to calculate the expected chiral volume of the C atom for the target position of the O atom. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Huiying Li Sent: 04 December 2008 19:51 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] tortion angle restraints in REFMAC Thank you all for suggestions and explanations. I did not make it clear. The tilt angle I wanted to restrain is the one from a C-OH bond to a plane (The C is in the plane). The O atom of OH group is not in the planar restraint in the cif file. At 2.1A I can see the feature of tilting of this OH group from the initial density map when the ligand was absent. But the density seems not strong enough to convince REFMAC that there is a tilt there. I have used very low weight term of 0.05 in the GUI to down weight the X-ray term. Refinement still pushed OH into the plane. I wonder if there are other tricks that can impose the restraint for this torsion angle. Best, Huiying On Thu, 4 Dec 2008, Ian Tickle wrote: Hi Huiying At 2.1A I would be very surprised if you see any density for the H atom in which case the refinement is not going to move it out of the plane whatever weight you give the torsion restraint. To answer your earlier questions the period of a torsion restraint is the number of energy minima in a complete rotation of the angle, so the OH bond will have a period of 2, and yes the same overall weight is applied to all torsions regardless of the period, though individual torsions will also be weighted by 1/sd^2. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Huiying Li Sent: 04 December 2008 16:35 To: Abhinav Kumar Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] tortion angle restraints in REFMAC Acturally, I want to find a way to keep the OH tilted out of the neightbouring plane by about 10 degrees. At 2.1A resolution the REFMAC refinement tends to refine it into the plane even though I have included torsion angle restraint in the library for the ligand. I thought I could play with the weight or the esd of the target value but having trouble to achieve it. In CNS, adjusting the force constant of the target value is a way to tighten or loosen the restrain. I would like to know how to enforce a geometry effectively in REFMAC. Thanks for any comments. Huiying On Wed, 3 Dec 2008, Abhinav Kumar wrote: If you want to restrain the OH group to a plane, you need to include it in the plane definition, and not the torsion definition. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Huiying Li wrote: I want to impose restraints during REFMAC refinement on the tortion angles that control the tilting of an OH group from a plane in a ligand bound to the protein. A few things that confused me: 1. In library cif file, should I just increase or decrease the tor.value_angle_esd if I want to loosen or tighten the restraits? 2. What is the meaning of the last column in torsion angle parameters: _chem_comp_tor.period, in cif file? In the PDB output file REFMAC also lists the RMS and WEIGHT for the torsion angles, period 1 through 4. 3. In REFMAC gui under Geometric parameters, there is only one user controlled weight for torsion. By changing the weight here, does it change the torsion weight for all 4 periods? Thanks in advance for the help. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED] 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
Re: [ccp4bb] suggestions for UV spectrometer
I want to add I absotely hate the nanodrop. We've had a demo for it, and found the readouts to be very unreliable. Fluctuations of 20% and more. Just leaving the same drop in and measuring the sample multiple times gives different values (going in both directions, so not only due to evaportations). Sure, it's easy and fast, and maybe good to have a rough idea about your protein concentration, but I would never want to use it for exact measurements such as needed for e.g. a CD or an ITC instrument. I've heard other labs in our department have similar issues. We've also had a demo for the Nanovue from GE Healthcare: same issues - very large fluctuations from one sample to another. I suppose this is simply an inherent problem with small volumes... Cheers Filip Van Petegm On Thu, Dec 4, 2008 at 12:48 PM, Patrick Loll [EMAIL PROTECTED] wrote: At the risk of dragging this discussion even further afield from crystallography: How can you get realistic numbers for concentrated solutions using the Nanodrop? I understand that the instrument reduces absorbance by using a very short path length. However, I thought that in order for the Beer-Lambert formalism to be applicable, the solution needs to be sufficiently dilute so that the chance of molecules shadowing one another is negligible. Isn't this condition violated for concentrated solutions (even with short path lengths)? Pat On 4 Dec 2008, at 1:27 PM, Michael Giffin wrote: We also like the Nanodrop... --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [EMAIL PROTECTED] -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: [EMAIL PROTECTED] http://crg.ubc.ca/VanPetegem/
