[ccp4bb] New xds-gui XDSAPP V1.0 update release
we would hereby like to announce the update release of the XDS-GUI XDSAPP V1.0. This version presents a major update of the current XDSAPP software (Krug et al., 2012). XDSAPP is an expert system for the interactive and fully automatic data processing using XDS (Kabsch et al., 2010). The following new features have been integrated within this software: - New graphical user interface using Python2.6 or higher Qt4. - Introduction of semi-automatic data processing by re-shaping the workflow in a modular way - Separation of data processing and intensity analysis to avoid repeated recalculations during step-by-step processing. - Simple reloading of summary files for already processed data sets. These values can even be used as a starting point for further processing. - The new button Default parameters in the Settings tab allows the internal deletion of parameters in case a new processing with different parameters is needed. - Fully automatic command line based data processing mode XDSAPP has been tested on the following operating systems: - Scientific Linux 6.3 - Ubuntu 12.04 LTS - openSUSE 13.1 - OS X Mavericks 10.9.1 for Mac The software is free of charge for academic users and can be downloaded here: http://www.helmholtz-berlin.de/bessy-mx References: - Krug M., Weiss M. S., Mueller U., Heinemann U. (2012). J. Appl. Cryst. 45, 568-572 - Kabsch W. (2010). Acta Cryst. D66, 125-132 With best regards, The XDSAPP team (Uwe Mueller, Manfred Weiss Karine Sparta) xds...@helmholtz-berlin.demailto:xds...@helmholtz-berlin.de Dr. Uwe Mueller Soft Matter and Functional Materials Macromolecular Crystallography (BESSY-MX) | Group leader Elektronenspeicherring BESSY II Albert-Einstein-Str. 15, D-12489 Berlin, Germany Fon: +49 30 8062 14974 Fax: +49 30 8062 14975 url: www.helmholtz-berlin.de/bessy-mxhttp://www.helmholtz-berlin.de/bessy-mx email:u...@helmholtz-berlin.demailto:u...@helmholtz-berlin.de Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
[ccp4bb] Wilson plot of TRUNCATE
Dear All, Recently, I have used TRANCATE to process some data. There is a Wilson plot table in its log file. The first column of table is resolution, the second is ln(I/I_th). And the third column is named Best. I want to know what mean the best. Is it the theoretical estimate of Wilson plot? Best wishes, Tao Zhang
[ccp4bb] New ligand
Hello, we have a structure with a novel ligand. I used to use LIG for new ligands but now that is taken in the PDB by 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE. Any suggestions for a generic name that is not already used? thanks and best wishes, Louise
Re: [ccp4bb] New ligand
Hi Louise, You can go through the mon_lib_list.cif file of the CCP4 dictionary to get a name that is free (e.g. A97). It would be nice is a certain name would be reserved for this by the PDB. LIG was a good candidate, but it's gone just like other nice options (XXX, ZZZ, 000). Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Louise Fairall Sent: Wednesday, February 26, 2014 12:14 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] New ligand Hello, we have a structure with a novel ligand. I used to use LIG for new ligands but now that is taken in the PDB by 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2- .C.]PYRAZOLE. Any suggestions for a generic name that is not already used? thanks and best wishes, Louise
Re: [ccp4bb] keep ligand conformation
Garib kindly sorted out this problem and external harmonic works well for ligands now. He said that the next ccp4 update will include this version of refmac (5.8.0070 or later). Thanks again for your help. Best, Koji Dear all, I tried to keep a conformation of a ligand during refinement with Refmac5 (Ver. 5.7.0032), and I put a harmonic restraint as, external harmonic residues from 600 A to 600 A 600 is the residue number of the ligand. I checked structures with and without the harmonic restraint, but no change was found between the two structures at all. I also tried with and without sigma weight, but nothing changed again. external harmonic restraints worked for protein parts. I would appreciate any suggestions and comments. Thank you so much in advance, Koji
Re: [ccp4bb] Wilson plot of TRUNCATE
The Best column gives Wilson plot values obtained according to this reference: From the Arp/Warp page: We have implemented an expected Wilson plot derived by Popov Bourenkov (2003) On 26 February 2014 10:04, Tao Zhang zhang...@cryst.iphy.ac.cn wrote: Dear All, Recently, I have used TRANCATE to process some data. There is a Wilson plot table in its log file. The first column of table is resolution, the second is ln(I/I_th). And the third column is named Best. I want to know what mean the best. Is it the theoretical estimate of Wilson plot? Best wishes, Tao Zhang
[ccp4bb] Off Topic: Equipment Available.
Hi All. We have a Rigaku R-AXIS IV detector and controller which we would like to donate to create some space at our core facility. The equipment should be in good working order but hasn't been used in about 18 months. It is currently located at the Beth Israel Deaconess Medical Center in Boston, MA and has been crated for shipment. We ask that you take care of the crating and shipping costs. Please e-mail me if you are interested. Thanks Gabriel Birrane BIDMC X-ray Crystallography Core Facility Harvard Medical School 99 Brookline Ave, Boston, MA 02215 http://www.bidmc.org/Research/Core-Facilities/X-ray-Crystallography-Core.aspx This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
Re: [ccp4bb] New ligand
Hi Louise, for internal use the name of your ligand does not matter as long as you have a .cif file describing the restraints. I am not sure about the behavior of refmac, but in phenix the presence of a defined name in a .cif file takes precedence over any duplicate entry in your monomer library. As far as PDB submission is concerned: it is my experience that they will rename your ligand to some arbitrarily name anyhow upon annotating the entry, so I would not sweat that part too much. HTH Carsten -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Louise Fairall Sent: Wednesday, February 26, 2014 6:14 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] New ligand Hello, we have a structure with a novel ligand. I used to use LIG for new ligands but now that is taken in the PDB by 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE. Any suggestions for a generic name that is not already used? thanks and best wishes, Louise
Re: [ccp4bb] New ligand
Carsten, Phenix does do this a little differently and yes it ignores existing ligands (which I like). CCP4 comes with is own library of existing ligand cif files from the pdb which coot also uses. The best way is to try and find a unique code to call your new ligand. That way you can have some say in what it is coded rather than an arbitrary code. J -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Schubert, Carsten [JRDUS] Sent: Thursday, 27 February 2014 2:22 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] New ligand Hi Louise, for internal use the name of your ligand does not matter as long as you have a .cif file describing the restraints. I am not sure about the behavior of refmac, but in phenix the presence of a defined name in a .cif file takes precedence over any duplicate entry in your monomer library. As far as PDB submission is concerned: it is my experience that they will rename your ligand to some arbitrarily name anyhow upon annotating the entry, so I would not sweat that part too much. HTH Carsten -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Louise Fairall Sent: Wednesday, February 26, 2014 6:14 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] New ligand Hello, we have a structure with a novel ligand. I used to use LIG for new ligands but now that is taken in the PDB by 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE. Any suggestions for a generic name that is not already used? thanks and best wishes, Louise
[ccp4bb] Protein behaves as dimers in 2M NaCl and as high oligomers with 300mM NaCl
Hello everyone! I have run into a problem in a 55kD recombinant human protein crystallization (expressed in E.Coil). The purity is pretty good. However, it behaves as high oligomers in the buffer with 300mM NaCl and behaves as dimers with a little high oligomers in the buffer with 2000mM (2M) NaCl. I have already performed several screenings and tried several types of buffer, salt or different pHs, etc. Only very small crystals could be detected in the dimer drops. High oligomers seem could not be crystallized under various of conditions. Has anyone ever met the same problem? Could anyone give me some suggestions? Thanks very much! Cheers --- Tom Wong Structural Lab ---
