[ccp4bb] relations between groups and subgroups?
Dear all, I am not sure I understand point groups and relations between groups and subgroups anymore, and would appreciate some guidance. I was under the impression that all point groups were related to an original P1 cell, and that by applying specific lattice symmetries, one could get higher point groups. Thus, if one knows the symmetry operators, one could jump from one point group to another. Inspection of the reflections can then determine the real point group and space group. At least that's what I thought Mosflm was doing? Am I correct? P1 +(symm-opp)C2 + (symm-opp2)P3 same P1 +(symm-opp3) P2 + (symm-opp4)P222 If that's the case, could someone point to me where to find these symmetry opperators (International tables?), because it's not obvious to me. Or are these relations between groups and subgroups only true for certain crystals where the cell parameters are specific, and allows a symmetry operator to generate a higher symmetry point group? Thank you for your help. vincent
Re: [ccp4bb] diffraction protein or salt
Dear George, Le 13/11/12 11:17, George a écrit : Dear colleagues, There are some crystallographers with (much) more experience than me. I ‘ve attached few diffraction images which are not (in my opinion) typical salt but not typical protein either. Please let me know you suggestions. Is it worth investigating further those conditions or there are just salts crystals with large unit cell. Attached files: Crystal.jpg (Photo of crystal) dif_0.jpg (Diffraction 900 sec exposure/degree at 0 degrees) dif_90.jpg (Diffraction 900 sec exposure/degree at 90 degrees) dif_180.jpg (Diffraction 900 sec exposure/degree at 180 degrees) dif_270.jpg (Diffraction 900 sec exposure/degree at 270 degrees) protein: 3.3mg/ml in 20 mM TrisHCl pH 8, 150 mM NaCl, 5 mM DTT. Mother liquor: 28%Jefamine, 0,05mM Li2SO4, 10mM Tris pH 8.0 sitting drops, 1.2ul protein / 1.2ul mother liquor. Thanks in advance for your help, George Kontopidis
Re: [ccp4bb] diffraction protein or salt
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear George, the images don't look like a large cell to me: on the first image you can see spots from ice rings at about 4A and there are only very few spots inside that radius, all of which are at beyond 5A. I'd say there are traces of MgS04 or CaSO4, the Ca or Mg being left-overs from the expression media. Regards, Timd On 11/13/2012 11:17 AM, George wrote: Dear colleagues, There are some crystallographers with (much) more experience than me. I ‘ve attached few diffraction images which are not (in my opinion) typical salt but not typical protein either. Please let me know you suggestions. Is it worth investigating further those conditions or there are just salts crystals with large unit cell. Attached files: Crystal.jpg (Photo of crystal) dif_0.jpg (Diffraction 900 sec exposure/degree at 0 degrees) dif_90.jpg (Diffraction 900 sec exposure/degree at 90 degrees) dif_180.jpg (Diffraction 900 sec exposure/degree at 180 degrees) dif_270.jpg (Diffraction 900 sec exposure/degree at 270 degrees) protein: 3.3mg/ml in 20 mM TrisHCl pH 8, 150 mM NaCl, 5 mM DTT. Mother liquor: 28%Jefamine, 0,05mM Li2SO4, 10mM Tris pH 8.0 sitting drops, 1.2ul protein / 1.2ul mother liquor. Thanks in advance for your help, George Kontopidis From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Tuesday, November 13, 2012 8:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Reservoir buffer Acta Cryst. (2005). D61, 490-493[ doi:10.1107/S0907444905002726 http://dx.doi.org/10.1107/S0907444905002726 ] Expanding screening space through the use of alternative reservoirs in vapor-diffusion experiments J. Newman http://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Newman,%20J. Abstract: Setting up vapor-diffusion crystallization experiments against four different reservoir solutions showed that the reservoir solution may have a profound effect on the outcome of a crystallization experiment. This suggests that a facile way to increase crystallization space through screening is not to add more crystallization conditions to the process, but to set up the same conditions over different reservoirs. On 13/11/2012 06:03, Theresa Hsu wrote: Dear all In *initial screening* using vapor diffusion crystallization, does it matter whether the reservoir buffer is also the precipitant in the drop or just a high salt solution like 5 M NaCl? Thank you. Theresa - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQoiIZUxlJ7aRr7hoRAlOtAKD9vm5OgG/GH/SMXv4LwTybKnlU3gCghuVH dFhZk5C5gK3fjVG1z00+jzw= =VN4A -END PGP SIGNATURE-
Re: [ccp4bb] diffraction protein or salt
Sorry to disappoint you. It is a diffraction pattern from crystals of salt. Spending some time it is possible to check of which :-\ FF 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 Nov 13, 2012, at 12:17 , George gkontopi...@vet.uth.gr wrote: Dear colleagues, There are some crystallographers with (much) more experience than me. I ‘ve attached few diffraction images which are not (in my opinion) typical salt but not typical protein either. Please let me know you suggestions. Is it worth investigating further those conditions or there are just salts crystals with large unit cell. Attached files: Crystal.jpg (Photo of crystal) dif_0.jpg (Diffraction 900 sec exposure/degree at 0 degrees) dif_90.jpg (Diffraction 900 sec exposure/degree at 90 degrees) dif_180.jpg (Diffraction 900 sec exposure/degree at 180 degrees) dif_270.jpg (Diffraction 900 sec exposure/degree at 270 degrees) protein: 3.3mg/ml in 20 mM TrisHCl pH 8, 150 mM NaCl, 5 mM DTT. Mother liquor: 28%Jefamine, 0,05mM Li2SO4, 10mM Tris pH 8.0 sitting drops, 1.2ul protein / 1.2ul mother liquor. Thanks in advance for your help, George Kontopidis From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Tuesday, November 13, 2012 8:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Reservoir buffer Acta Cryst. (2005). D61, 490-493[ doi:10.1107/S0907444905002726 ] Expanding screening space through the use of alternative reservoirs in vapor-diffusion experiments J. Newman Abstract: Setting up vapor-diffusion crystallization experiments against four different reservoir solutions showed that the reservoir solution may have a profound effect on the outcome of a crystallization experiment. This suggests that a facile way to increase crystallization space through screening is not to add more crystallization conditions to the process, but to set up the same conditions over different reservoirs. On 13/11/2012 06:03, Theresa Hsu wrote: Dear all In *initial screening* using vapor diffusion crystallization, does it matter whether the reservoir buffer is also the precipitant in the drop or just a high salt solution like 5 M NaCl? Thank you. Theresa Crystal.jpgdif_0.jpgdif_90.jpgdif_180.jpgdif_270.jpg
Re: [ccp4bb] relations between groups and subgroups?
Hi The relations are in International Tables Vol A; in the 2006 edition you find them in section 9.2 by P.M. de Wolff, pp 750 - 755; the transformations for the 44 characteristic lattices (or lattice characters...) are in Table 9.2.5.1. In Mosflm, the autoindexing penalties are based on the differences between the result of the transformations applied to the real triclinic basis and what you would get if the result was perfect. On 13 Nov 2012, at 09:55, vincent Chaptal wrote: Dear all, I am not sure I understand point groups and relations between groups and subgroups anymore, and would appreciate some guidance. I was under the impression that all point groups were related to an original P1 cell, and that by applying specific lattice symmetries, one could get higher point groups. Thus, if one knows the symmetry operators, one could jump from one point group to another. Inspection of the reflections can then determine the real point group and space group. At least that's what I thought Mosflm was doing? Am I correct? P1 +(symm-opp)C2 + (symm-opp2)P3 same P1 +(symm-opp3) P2 + (symm-opp4)P222 If that's the case, could someone point to me where to find these symmetry opperators (International tables?), because it's not obvious to me. Or are these relations between groups and subgroups only true for certain crystals where the cell parameters are specific, and allows a symmetry operator to generate a higher symmetry point group? Thank you for your help. vincent Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] diffraction protein or salt
Hi, First I'm sorry for my blank message earlier. Doesn't this depend on the oscillation angle? If those images were collected using 0 to 1° oscillations, I would assume he has a badly diffracting protein crystal. Ganesh Le 13/11/12 11:34, Tim Gruene a écrit : -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear George, the images don't look like a large cell to me: on the first image you can see spots from ice rings at about 4A and there are only very few spots inside that radius, all of which are at beyond 5A. I'd say there are traces of MgS04 or CaSO4, the Ca or Mg being left-overs from the expression media. Regards, Timd On 11/13/2012 11:17 AM, George wrote: Dear colleagues, There are some crystallographers with (much) more experience than me. I ‘ve attached few diffraction images which are not (in my opinion) typical salt but not typical protein either. Please let me know you suggestions. Is it worth investigating further those conditions or there are just salts crystals with large unit cell. Attached files: Crystal.jpg (Photo of crystal) dif_0.jpg (Diffraction 900 sec exposure/degree at 0 degrees) dif_90.jpg (Diffraction 900 sec exposure/degree at 90 degrees) dif_180.jpg (Diffraction 900 sec exposure/degree at 180 degrees) dif_270.jpg (Diffraction 900 sec exposure/degree at 270 degrees) protein: 3.3mg/ml in 20 mM TrisHCl pH 8, 150 mM NaCl, 5 mM DTT. Mother liquor: 28%Jefamine, 0,05mM Li2SO4, 10mM Tris pH 8.0 sitting drops, 1.2ul protein / 1.2ul mother liquor. Thanks in advance for your help, George Kontopidis From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Tuesday, November 13, 2012 8:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Reservoir buffer Acta Cryst. (2005). D61, 490-493[ doi:10.1107/S0907444905002726 http://dx.doi.org/10.1107/S0907444905002726 ] Expanding screening space through the use of alternative reservoirs in vapor-diffusion experiments J. Newman http://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Newman,%20J. Abstract: Setting up vapor-diffusion crystallization experiments against four different reservoir solutions showed that the reservoir solution may have a profound effect on the outcome of a crystallization experiment. This suggests that a facile way to increase crystallization space through screening is not to add more crystallization conditions to the process, but to set up the same conditions over different reservoirs. On 13/11/2012 06:03, Theresa Hsu wrote: Dear all In *initial screening* using vapor diffusion crystallization, does it matter whether the reservoir buffer is also the precipitant in the drop or just a high salt solution like 5 M NaCl? Thank you. Theresa - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQoiIZUxlJ7aRr7hoRAlOtAKD9vm5OgG/GH/SMXv4LwTybKnlU3gCghuVH dFhZk5C5gK3fjVG1z00+jzw= =VN4A -END PGP SIGNATURE-
Re: [ccp4bb] diffraction protein or salt
Ganesh!!! NO WAY !!! FF 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 Nov 13, 2012, at 12:40 , Ganesh Natrajan ganesh.natra...@ibs.fr wrote: Hi, First I'm sorry for my blank message earlier. Doesn't this depend on the oscillation angle? If those images were collected using 0 to 1° oscillations, I would assume he has a badly diffracting protein crystal. Ganesh Le 13/11/12 11:34, Tim Gruene a écrit : -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear George, the images don't look like a large cell to me: on the first image you can see spots from ice rings at about 4A and there are only very few spots inside that radius, all of which are at beyond 5A. I'd say there are traces of MgS04 or CaSO4, the Ca or Mg being left-overs from the expression media. Regards, Timd On 11/13/2012 11:17 AM, George wrote: Dear colleagues, There are some crystallographers with (much) more experience than me. I ‘ve attached few diffraction images which are not (in my opinion) typical salt but not typical protein either. Please let me know you suggestions. Is it worth investigating further those conditions or there are just salts crystals with large unit cell. Attached files: Crystal.jpg (Photo of crystal) dif_0.jpg (Diffraction 900 sec exposure/degree at 0 degrees) dif_90.jpg (Diffraction 900 sec exposure/degree at 90 degrees) dif_180.jpg (Diffraction 900 sec exposure/degree at 180 degrees) dif_270.jpg (Diffraction 900 sec exposure/degree at 270 degrees) protein: 3.3mg/ml in 20 mM TrisHCl pH 8, 150 mM NaCl, 5 mM DTT. Mother liquor: 28%Jefamine, 0,05mM Li2SO4, 10mM Tris pH 8.0 sitting drops, 1.2ul protein / 1.2ul mother liquor. Thanks in advance for your help, George Kontopidis From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Tuesday, November 13, 2012 8:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Reservoir buffer Acta Cryst. (2005). D61, 490-493[ doi:10.1107/S0907444905002726 http://dx.doi.org/10.1107/S0907444905002726 ] Expanding screening space through the use of alternative reservoirs in vapor-diffusion experiments J. Newman http://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Newman,%20J. Abstract: Setting up vapor-diffusion crystallization experiments against four different reservoir solutions showed that the reservoir solution may have a profound effect on the outcome of a crystallization experiment. This suggests that a facile way to increase crystallization space through screening is not to add more crystallization conditions to the process, but to set up the same conditions over different reservoirs. On 13/11/2012 06:03, Theresa Hsu wrote: Dear all In *initial screening* using vapor diffusion crystallization, does it matter whether the reservoir buffer is also the precipitant in the drop or just a high salt solution like 5 M NaCl? Thank you. Theresa - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQoiIZUxlJ7aRr7hoRAlOtAKD9vm5OgG/GH/SMXv4LwTybKnlU3gCghuVH dFhZk5C5gK3fjVG1z00+jzw= =VN4A -END PGP SIGNATURE-
Re: [ccp4bb] diffraction protein or salt
Hi Felix, It appeared to me when I first saw the images that there were some (very ) weak spots at low resolutions. I looked again and there aren't any. I stand corrected. Thank you Ganesh Le 13/11/12 14:01, Felix Frolow a écrit : Ganesh!!! NO WAY !!! FF 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 mailto:mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 13, 2012, at 12:40 , Ganesh Natrajan ganesh.natra...@ibs.fr mailto:ganesh.natra...@ibs.fr wrote: Hi, First I'm sorry for my blank message earlier. Doesn't this depend on the oscillation angle? If those images were collected using 0 to 1° oscillations, I would assume he has a badly diffracting protein crystal. Ganesh
Re: [ccp4bb] dihedral backbone generator
If you have an old copy of MOLEMAN (not MOLEMAN2!) lying around, this can be done very easily (ever since it was programmed on Valentine's Day 1993, in fact - I even remember who my Valentine was :-) - see: http://xray.bmc.uu.se/usf/moleman_man.html#S13 - READ your original model (PDB file) - EXPOrt as an internal coordinates file - then edit the file to modify the torsion angles - IMPOrt the edited file back into MOLEMAN - WRITe as a PDB file again Your molecule will now have the first atom at (0,0,0) and the x-axis along the first bond etc., so use LSQMAN to superimpose it back onto the starting model if you like. You can download source and executables for MOLEMAN, LSQMAN etc. here: http://xray.bmc.uu.se/markh/usf/ Example: read and export 3CBS - the first few lines of the internal coordinates file will look like this: BAD 1 N PRO A 1 0.000 0.000 0.000 1.00 31.62 0 0 0 BAD 2 CA PRO A 1 1.481 0.000 0.000 1.00 31.16 1 0 0 BAD 3 C PRO A 1 1.520 106.499 0.000 1.00 29.86 2 1 0 BAD 4 O PRO A 1 1.233 121.844-171.561 1.00 30.08 3 2 1 BAD 5 CB PRO A 1 2.511 34.402-114.723 1.00 31.63 3 2 1 BAD 6 CG PRO A 1 1.540 94.603 100.767 1.00 32.44 5 3 2 BAD 7 CD PRO A 1 1.535 100.667 -80.739 1.00 31.82 6 5 3 BAD 8 N ASN A 2 1.325 114.622 8.082 1.00 27.88 3 2 1 the torsion of atom 8 is the psi torsion of residue 1 (8 degrees) BAD 9 CA ASN A 2 1.452 122.416-179.619 1.00 25.61 8 3 2 this torsion is omega of residue 1 (-180) BAD 10 C ASN A 2 1.528 107.300-118.190 1.00 23.37 9 8 3 this torsion is phi of residue 2 (-118) BAD 11 O ASN A 2 1.227 119.971 -58.453 1.00 21.7110 9 8 BAD 12 CB ASN A 2 1.529 109.276 122.858 1.00 27.00 9 8 3 BAD 13 CG ASN A 2 1.510 112.642-171.476 1.00 28.5212 9 8 BAD 14 OD1 ASN A 2 1.228 120.881 -44.498 1.00 27.401312 9 BAD 15 ND2 ASN A 2 1.329 116.425 136.488 1.00 30.351312 9 BAD 16 N PHE A 3 1.330 117.436 121.273 1.00 22.0910 9 8 this torsion is psi of residue nr 2 (121) BAD 17 CA PHE A 3 1.466 120.994 179.948 1.00 21.611610 9 this is omega of residue nr 2 (180) etc. --Gerard On Mon, 12 Nov 2012, Ed Pozharski wrote: Does anyone know of a tool that would generate a protein molecule backbone from a set of phi/psi angles? I actually had written my own code to do this eons ago, but those were days of Matlab. My actual question is if in a particular protein the conformational change observed upon substrate binding can be accounted for by half a dozen residues changing their backbone conformation. I only expect to do it once, and thus trying to save time and not translate my old code (looks more like a cipher now). Cheers, Ed. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Terrific! I always thought it was X11-related as well. Thanks to Paul and Bernhard for the fix. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Nov 7, 2012, at 1:53 PM, Jon Agirre jon.agi...@gmail.commailto:jon.agi...@gmail.com wrote: Thanks for the heads-up. Bernhard and I have fixed several of these window-order problems, but this one slipped by us (neither of us use a Mac :-). Fixed in 0.7.1 That's great news, Paul. Thank you for fixing it and others for pointing it out. I've been always quite convinced that it was an XQuartz.app (aka X11 for OS X) related bug and therefore never reported it. Jon -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://www.ehu.es/jon.agirre http://sourceforge.net/projects/projectrecon/ +34656756888
Re: [ccp4bb] hkl2000 install
I believe cr_info should go in /usr/local/hklint along with site files. It does not have to be executable but must be readable by all. (chmod a+r cr_info) Regards, Dmitry Rodionov On 2012-11-13, at 12:33 AM, 王瑞 wrote: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] hkl2000 install
It will also look in the directory where you start HKL2000. Thierry -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dmitry Rodionov Sent: Tuesday, November 13, 2012 11:13 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] hkl2000 install I believe cr_info should go in /usr/local/hklint along with site files. It does not have to be executable but must be readable by all. (chmod a+r cr_info) Regards, Dmitry Rodionov On 2012-11-13, at 12:33 AM, 王瑞 wrote: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] hkl2000 install
cr_info can be in several places ~/ (user home directory) working directory /usr/local/lib ( This is the place where I keep it as it is a consensus location for cr_info) about /usr/local/hklint I am not sure, but if you say so, you probably know :-) FF 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 Nov 13, 2012, at 18:12 , Dmitry Rodionov d.rodio...@gmail.com wrote: I believe cr_info should go in /usr/local/hklint along with site files. It does not have to be executable but must be readable by all. (chmod a+r cr_info) Regards, Dmitry Rodionov On 2012-11-13, at 12:33 AM, 王瑞 wrote: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] hkl2000 install
Rui, I just noticed in your email you wrote cr_info.dat That is the cause of your problem If you actually added .dat extension. We have always kept ours in /usr/local/hklint Which is funny because it is not one of the folders suggested by HKL people. Thierry and Felix are right about other locations. Dmitry On 2012-11-13, at 11:26 AM, Felix Frolow wrote: cr_info can be in several places ~/ (user home directory) working directory /usr/local/lib ( This is the place where I keep it as it is a consensus location for cr_info) about /usr/local/hklint I am not sure, but if you say so, you probably know :-) FF 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 Nov 13, 2012, at 18:12 , Dmitry Rodionov d.rodio...@gmail.com wrote: I believe cr_info should go in /usr/local/hklint along with site files. It does not have to be executable but must be readable by all. (chmod a+r cr_info) Regards, Dmitry Rodionov On 2012-11-13, at 12:33 AM, 王瑞 wrote: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] Reservoir buffer
Theresa, In addition to the comments provided, you do need to consider the vapor diffusion experiment process as a whole. The primary reasons why we put the precipitant mixture in the reservoir, aside from being lazy, is (1) it provides a straight forward and partially accurate starting point for making artificial mother liquors for handling and soaking soaking crystals and, more importantly (2) it ensures that ALL VOLATILE components come to the expected (assumed) equilibrium values. When I speak of volatile components, I mean not only organics (isopropanol, ethanol, etc.), but also components like ammonia from ammonium sulfate. Since the reservoir volume is often ~50x greater than that of the protein drop, mass action will significantly change the concentrations of the volatile components in the protein drop, which can markedly effect even pH. I know of one group where pH drifting (due to the reservoir solution having a different pH than the drop) had them losing the crystals until they figured that out. This also underscores the importance of having your students and tech keep good notebooks even for buffer making. While we have tried to use different concentrations of a standard PEG solution or LiCl solution as reservoirs, it turned out that we had to adapt it individually to any condition with a volatile component in the protein drop. In the end, inertia and laziness ended up with us returning to the old method. You may have more will power, but you also need to ensure reproducibility. Cheers, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On 13/11/2012 07:03, Theresa Hsu wrote: Dear all In *initial screening* using vapor diffusion crystallization, does it matter whether the reservoir buffer is also the precipitant in the drop or just a high salt solution like 5 M NaCl? Thank you. Theresa
Re: [ccp4bb] Glass Capillaries
Dear Michael, I work with capillaries in a regular bases to grow crystal and use them for RT data collection or cryogenic temperature data collection at home source or at synchrotron sources. I like better borosilicate glass capillaries from Triana (http://www.trianatech.com/), as Patrick has already mentioned, for the cylindrical type but if I need capillaries with a reservoir them I go for the standard power diffraction capillaries from http://www.capillarytubes.co.uk/acatalog/Borosilicate_Glass_Capillary_Tubes.htmlwhich are similar to those from Hampton ( http://www.capillarytubes.co.uk/acatalog/Borosilicate_Glass_Capillary_Tubes.html), etc. All of them will give you some background but any of them will affect dramatically your data quality. You can do a search in ActaD or F and get good inputs on that (=*367 articles match your search capillaries*). On my hands borosilicate capillaries are easier to handle than Quartz capillaries and probably cheaper. Gavi. Dr. José A. Gavira Gallardo Laboratorio de Estudios Cristalográficos IACT, (CSIC-UGR) Av. de las Palmeras, 4 18100 Armilla (Granada) Tel.: 958 23 Ext. 19 01 06 Fax: 958 55 26 20 e-mail: jgav...@iact.ugr-csic.es or g...@lec.csic.es web: http://lec.ugr.es/~gavi/ 2012/11/12 Michael Roberts mrobert...@talktalk.net Dear All, I would be interested to learn of other crystallographers' experience in their use of glass capillaries for protein crystal growth and X-ray diffraction clarity. There are many types of glass available - quartz, soda glass, borosilicate, etc. Are there specific types which people prefer for best results overall? Best wishes, Michael Roberts
[ccp4bb] off topic: oligomer detection
Anyone have any advice on how to detect whether my protein is forming oligomers? It is monomeric in the native state but I have reason to believe that it may be oligomerising in mild concentrations of urea (intermediate state). I have tried cross linking and BN PAGE and they are inconclusive. SE-HPLC does not work because at the concentrations required to produce a signal, this intermediate species aggregates. I do not have access to an ultracentrifuge. The dynamic light scattering equipment that is available to me is really a poor instrument which will not be sensitive enough to pick up changes in size (we are looking at about 5nm for the monomer and anything from 8nm for the oligomer). The only other option I can think of is SAXS. I will only be able to use that equipment in the middle of next year. I'm wondering if there is anything else, any other technique or idea that I have not thought about that I could try? I really just would like to show that the stoichiometry of the intermediate species is a multiple of the native state. If anyone has any suggestions, that would be great. Thanks Careina.
