[ccp4bb] A new detector for my HKL2000 package
Dear all, I have collected a dataset on a Saturn 944HG CCD detector, and I want to process the data on HKL2000. The detector is not found in the list of the HKL2000 pop-up window in the beginning, what should I do to make the HKL2000 package recognize my dataset? I'm a computer dummy, so would you please tell me the way for dummies? Sincerely, Pattis ~(He's a junior crystallographer!)~
[ccp4bb] Problem with RCrane in coot-0.7
Hi, CCP4bbers: Did anybody here use the COOT plug-in RCrane? I download the COOT version 0.7 (coot-Linux-x86_64-centos-6-gtk2-python), and use the plug-in RCrane. However, after I optimized the rotamers, the RCrane window did not show any selectable rotamers (See the attached figure). BTW, I'm using the 64bit Scientific Linux 6.0. Any suggestions? Thanks a lot! Best, Jiawei Wangattachment: Screenshot-RCrane.png
Re: [ccp4bb] Problem with RCrane in coot-0.7
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jiawei Wang, a collegue of mine has been working on a different plugin for coot and observed the same behaviour on our computer while e.g. Bernhard Lohkamp could not reproduce this behaviour. It appears to be an odd combination between the python code for displaying the table and the Linux distribution (maybe not the right version of python or else), and I am not aware of a workaround. Said collegue of mine simply avoided using the particular python function for displaying a list of items, but this is of no help for you as a user, I am afraid. If you have access to a variety of Linux distributions, you may try a different computer, unless somebody else on this board now a real workaround / bug fix. Best, Tim P.S.: Personally I like this bug because it feeds my (pre-)judice of not liking python ;-) On 04/24/2013 11:24 AM, Jiawei Wang wrote: Hi, CCP4bbers: Did anybody here use the COOT plug-in RCrane? I download the COOT version 0.7 (coot-Linux-x86_64-centos-6-gtk2-python), and use the plug-in RCrane. However, after I optimized the rotamers, the RCrane window did not show any selectable rotamers (See the attached figure). BTW, I'm using the 64bit Scientific Linux 6.0. Any suggestions? Thanks a lot! Best, Jiawei Wang - -- - -- 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/ iD8DBQFRd6UQUxlJ7aRr7hoRArdcAKDHxco43mGe9ruL+LUuRwZQia8noACguLAV SUjRvQAntZuBVEZq0e1E1Zk= =dSe/ -END PGP SIGNATURE-
[ccp4bb] Anomalous atom or ligand?
Dear users, After detecting the anomalous peaks in a data, Is it necessary that there will be an anomalous atom in most of the peaks? In a particular case, a low ranking peak was assigned an anomalous atom because it was present in the native structure, while a peak with a rank higher than this one did not correspond to anomalous position in native structure. For eg. Peak 15 in ligand bound structure corresponds to the anomalous position in native structure, so anomalous atom was assigned. But Peak 3,4 in ligand bound structure does not correspond to anomalous position in native structure but it is present near the ligand which is beta and gamma Phosphates of ATP. The question is whether It is ATP or AMP and 2 anomalous atoms? Thanking you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Problem with RCrane in coot-0.7
On 24/04/13 10:24, Jiawei Wang wrote: Hi, CCP4bbers: Did anybody here use the COOT plug-in RCrane? I download the COOT version 0.7 (coot-Linux-x86_64-centos-6-gtk2-python), and use the plug-in RCrane. However, after I optimized the rotamers, the RCrane window did not show any selectable rotamers (See the attached figure). BTW, I'm using the 64bit Scientific Linux 6.0. Any suggestions? Thanks a lot! For the record, I get the same thing. :-( I'll get in touch with Kevin. Paul.
Re: [ccp4bb] Modelling Software for beta turn design
Hi Wenzong, I would certainly try it also another way. Choose you beta turn sequence. Insert it between the sequences of both beta stands and submit the whole sequence (beta-turn-beta) to homology modeling. Try every beta turn sequence to select top results. You could download MolIde (http://dunbrack.fccc.edu/molide/) and do the exercise in local mode. Best of luck, Nadir Mrabet Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet at univ-lorraine.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. On 23/04/2013 00:48, Wenzong Li wrote: Dear All, I want to use modelling software to design a tight beta turn replacing a loop between two beta strands. Can anyone suggest a program to do this sort of modelling? Thank you Wenzong
[ccp4bb] common proteins that oligomerize?
I am looking for easily-available proteins that exist in equilibrium between two or more known oligomeric states in solution. BSA is a possibility, but I am concerned that the rate constant for association may be rather slow. Fast exchange would be better. Does anyone know of other possibilities? Thanks Richard Gillilan MacCHESS Cornell University
Re: [ccp4bb] question about arginine sepharose 4B
Hi, You can make it :) There are a number of good ways to do so, but my favorite one is to order Cys-Arg dipeptide and then use iodoacetamide-agarose resin (very cheap) to load up the peptide. This method allows you to quantify the loading, if you care to know how much you immobilized and also it's extremely robust and specific. Artem On Tue, Apr 23, 2013 at 11:21 PM, Jacqueline Vitali jackie.vit...@gmail.com wrote: Dear all, Arginine sepharose 4B is an affinity column. If you have used it please let me know where you purchased it. GE Lifesciences used to sell it but discontinued it. I found it in China in the site http://www.pharmaceutical-sales.net and I corresponded with their sales representative Does anyone know this company? Are their products reliable? It is the only place I found this product. I would appreciate any information about this company or any place that may sell arg sepharose. Thank you. Jackie Vitali
[ccp4bb] Postdoctoral positions in structure and function of membrane proteins at the NIH
Dear all, Will you please bring this to the attention of suitable candidates ? Postdoctoral positions in structure and function of membrane proteins at the NIH The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows to start from September, 2013 or later. The broad interests of the lab are in membrane protein structure and function. We will combine macromolecular crystallography with functional assays with detergent-solubilized and liposome-reconstituted proteins to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab is part of the Cell Biology and Metabolism (CBMP) program and is part of a large and diverse macromolecular crystallography and NMR community in the NIH campus. There is ample opportunity to interact with other scientific groups across a broad range of scientific disciplines. CBMP is part of the National Institute of Child Health and Human Development (NICHD). Our lab also has an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). The DC Metro area is a wonderful place to live, the weather is pleasant and the NIH is a vibrant international community. Candidates must be motivated and have a strong background in biochemistry and structural biology. Experience with protein expression, purification and crystallization is required. Prior experience in membrane protein biochemistry will be an added advantage. Candidates should hold a Ph.D. degree by the time they join and have no more than one year of postdoctoral experience at the time of applying. To apply, please send an email of interest to anirban.baner...@nih.gov with a CV and a summary of previous research experience and future research interests. Best regards, Anirban
[ccp4bb] Too high function value for reflection ... refmac
Dear users, While refining the structure, I get a message in the log file - Too high function value for reflection 408 0 103.7139 Too high function value for reflection2766 0 110.8577 Too high function value for reflection3439 0 127.2363 Too high function value for reflection7706 0 110.2885 .. What does this mean? How does this effect refinement? Kindly explain. Thanking you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
