Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?
Dear Peter, You are not alone with this. We have just found out about this bug. It appears to just be a problem with output formatting (the MTZ should be fine). We'll get a fix as soon as we can and will provide a link to 6.2.0's version of scala from the problems page as a workaround early next week. Sorry about this. David (CCP4) On Aug 3, 2012 7:13 PM, Peter Goettig peter.goet...@sbg.ac.at wrote: In the Windows version of the new CCP4 release SCALA produces a summary table (same in the full text) that contains only some rudimentary data, such as Overall InnerShell OuterShell Low resolution limit 19.97 0.00 0.00 High resolution limit 3.00 0.00 0.00 Rmerge 0.000 0.000 0.000 Rmerge in top intensity bin0.115- - Rmeas (within I+/I-) 0.000 0.000 0.000 aso while the final statement of SCALA is ** Normal termination ** Has anyone else experienced similar problems and found a way to solve them? Otherwise, I would ask the developpers to take care of the bugs. However, the corresponding tables generated by AIMLESS contain the full information. Regards, Peter Peter Goettig Structural Biology University of Salzburg Billrothstrasse 11 Salzburg, Austria
Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?
This must be a problem on Windows as it doesn't show up on OSX or Linux, and this code hasn't changed for a long time, I think David I guess you will feed this back to me: I don't have any way of testing on Windows Anyway, Aimless should be better :-) Phil On 4 Aug 2012, at 14:26, David Waterman wrote: Dear Peter, You are not alone with this. We have just found out about this bug. It appears to just be a problem with output formatting (the MTZ should be fine). We'll get a fix as soon as we can and will provide a link to 6.2.0's version of scala from the problems page as a workaround early next week. Sorry about this. David (CCP4) On Aug 3, 2012 7:13 PM, Peter Goettig peter.goet...@sbg.ac.at wrote: In the Windows version of the new CCP4 release SCALA produces a summary table (same in the full text) that contains only some rudimentary data, such as Overall InnerShell OuterShell Low resolution limit 19.97 0.00 0.00 High resolution limit 3.00 0.00 0.00 Rmerge 0.000 0.000 0.000 Rmerge in top intensity bin0.115- - Rmeas (within I+/I-) 0.000 0.000 0.000 aso while the final statement of SCALA is ** Normal termination ** Has anyone else experienced similar problems and found a way to solve them? Otherwise, I would ask the developpers to take care of the bugs. However, the corresponding tables generated by AIMLESS contain the full information. Regards, Peter Peter Goettig Structural Biology University of Salzburg Billrothstrasse 11 Salzburg, Austria
Re: [ccp4bb] Protein-Protein Interactions
In addition to what Francisco suggested, looking at the sequences with evolutionary highlited residues will provide additional info. If modeled structures are available , which is not the case with this query, investigating the corresponding electrostat potential using APBS might give evidence to cross check results obtained from other method. Hope it helps Manish Manish Chandra Pathak, Ph.D. Indian Institute of Science Education and Research ITI (Gas Rahat) Building Govindpura, Bhopal 462023 India tel: +91-750-4092340 -- On Thu, Aug 2, 2012 1:28 PM EDT Francisco Hernandez-Guzman wrote: Hi Lorenzo, I forgot to add that any experimental data that you can provide to guide the modeling is highly recommended and often necessary to validate your predictions. Modeling can be quite useful but you should be aware of its strengths and weaknesses. Cheers, Francisco From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Francisco Hernandez-Guzman Sent: Thursday, August 02, 2012 10:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein-Protein Interactions Hi Lorenzo, If the structure for your receptor is unknown, then you can use Homology Modeling methods to get a rough idea of the structure, MODELLER is a well know tool for this (http://salilab.org/modeller/). Of course depending on your % similarity to the template, the higher the % similarity, the more reliable your structure may be (of course assuming there are no major conformational changes, etc.) Now, to figure out the sites of interaction, you could use a shape based complementarity approach like the one used in the ZDOCK algorithm (http://zdock.umassmed.edu/software/). This gets to be a little bit trickier if your % similarity to your template is low, because the dissimilarity is often due to surface residue differences, which are obviously the ones you're interested on. On the other hand, if the source of interaction is driven mainly by hydrophobic forces, then an analysis using the spatial aggregation propensity method (http://pubs.acs.org/doi/abs/10.1021/jp911706q?journalCode=jpcbfk) may reveal interesting sites of aggregation. This method is a little bit more forgiving that the shape complementarity one because of the intrinsic averaging that goes on to determine the site of aggregation. All of these methods and other simulations tools are available in the Discovery Studio suite from Accelrys. Disclaimer: I work for Accelrys as their Product Manager for the Life Science Modeling and Simulations suite of products. So, if you're interested in evaluating and gain access to these tools please contact me directly. Kind regards, Francisco Sr. Product Manager http://accelrys.com From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dr. Lorenzo Finci Sent: Thursday, August 02, 2012 6:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Protein-Protein Interactions Dear Colleagues, I have a question for all of you bioinformatics oriented structural biologists: How do I predict the sites of protein-protein interactions between two receptors that have been proven to interact biochemically but lack specific details regarding proximity. This is not a straightforward question for me, and I believe it is somewhat complicated. The complicated scenario involves a multitude of different subunits and isoforms. Also, there is not structural data to support all components involved, and thus I presume I should use the sequence based software. I am aware that there are different types of prediction software, either sequence or structure based predictions using different algorithms: http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/ Receptor 1: -Has 5 predicted subunits (Alpha)2-(Beta)2-(Gamma)1 1. Alpha (6 isoforms) 2. Beta (3 Isoforms) 3. Gamma (3 Isoforms) Receptor 2: -Is believed to be composed of (Alpha)3-(Beta)2 1. Alpha (4 isoforms) 2. Beta(1 isoform) Any advice or recommendation will be well appreciated! Sincerely, lorenzo Lorenzo Ihsan FInci, Ph.D. Postdoctoral Scientist, Wang Laboratory Harvard Medical School Dana-Farber Cancer Institute Boston, MA Peking University The College of Life Sciences Beijing, China
[ccp4bb] OFF TOPIC: recommendations for High Pressure Homogenizers
Sorry for the off topic question, but it is relevant to those that produce proteins for crystallographic purposes: We are looking to replace an old French Press with a high pressure homogenizer for cell disruption (E. coli and yeast). We are currently looking at the Avestin C3 and the Niro Panda 2000. I would appreciate any feedback (positive or negative) from users of these instruments (or any other competing homogenizer). Thanks in advance Marcelo
Re: [ccp4bb] OFF TOPIC: recommendations for High Pressure Homogenizers
[flame me if you can] ADVERTISEMENT I have been a happy customer since 2000 with a Avestin Emulsiflex C5 in Martinsried, a short dark period using french press (they are good for coffee, granted a different type of french press) and back to an Avestin C5. The advantage versus other systems is you can fix it yourself and you almost can't break it. If you only break E.coli you can hook it up to your regular lab pressurized air outlet then you will get approximately 15kPSI, with a dedicated compressor as we have you can go up to 25-30 kPSI e.g. for yeast. Jürgen P.S. some homogenizers tend to produce foam, I don't recall the brand I used in another department in Martinsried before we got the Emulsiflex but it was not good. On Aug 4, 2012, at 2:18 PM, Marcelo Carlos Sousa wrote: Sorry for the off topic question, but it is relevant to those that produce proteins for crystallographic purposes: We are looking to replace an old French Press with a high pressure homogenizer for cell disruption (E. coli and yeast). We are currently looking at the Avestin C3 and the Niro Panda 2000. I would appreciate any feedback (positive or negative) from users of these instruments (or any other competing homogenizer). Thanks in advance Marcelo .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] MR with Phaser
Thank you very much for your comments. I re-do the data process with P21, and use the output for Phaser. This time, Phaser finishes with good resolution, the TFZ is 28. And the model is tetramer. Cheers Uma On Thu, Aug 2, 2012 at 9:45 PM, Roger Rowlett rrowl...@colgate.edu wrote: A few thoughts: 1. Search for all possible space groups (e.g., P2 and P21 in this case). Be happy it isn't C222, which means 8 possible combinations of screw axes to search! As mentioned already, P21 is far more common than P2. I think P21 is one of the most common space groups in protein crystallography. 2. How are you determining how many copies of the search model go in the ASU? It is not necessarily one biological unit, or an integral number of biological units. Run a cell content analysis in Phaser (e.g. Matthews probability calculator) and start there, but consider the results a suggestion only. For larger ASUs, the predicted number is not very accurate. Six might actually be 4 or 8 chains. 3. Look at the crystal packing in Pymol, Coot, or in you favorite tool. You can do this by enabling a large symmetry molecule radius. If you see a regular lattice of proteins with nice solvent channels and protein-protein contacts, things are looking up. (But you can be fooled into a premature victory at times.) 4. Partial Phaser solutions may provide a big hint about how many molecules are in the ASU when packing is examined. Often the placement of the missing molecules is quite obvious, as it completes a solvent channel or fills in symmetrical protein-protein contacts. 5. Finally, look at the maps. Crappy maps probably mean the wrong space group, especially if chains don't pack well. Good maps with good packing usually mean you are on the right track. Cheers and good luck, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 8/1/2012 2:27 PM, Uma Ratu wrote: Dear All: I try to use Phaser to solve the structure by Molecular Replacement. The data set is collected @180 degree. I process the data using HKL, and have resonable good score: rejection (0.05), Linear R-factor (0.038), completeness (98.3), resolution (50-1.5). I then use Phaser to do MR. The parameter setting are: automated search components in asymmetric unit;number of residue 1332; number in asymmetric unit 1 perform search search using ensemble1 number of copies to search for 4 The protein is in tetramer form. I define this by using the residue number (1332) which is 4 x monomer. After run, Phaser only gave 9 partial solutions, and no solution with all components. The resulted PDB contains only dimer form of the protein, not the tetramer. And the first TFZ score is around 2.5, which is too low for MR. I have the report file of data processing and the summary of Phaser attached. Could you please advice which part is wrong, why can I get the tetramer form of the protein? Thank you Uma
[ccp4bb] CCP4-6.3.0 installation
Dear CCP4bbers, I am facing CCP4-6.3.0 installation problem. Unable to run make. Configuration is done. Getting error while running make (command not found). Please help. Thanks in advance, James
Re: [ccp4bb] CCP4-6.3.0 installation
On 08/04/2012 04:38 PM, james09 pruza wrote: Dear CCP4bbers, I am facing CCP4-6.3.0 installation problem. Unable to run make. Configuration is done. Getting error while running make (command not found). Please help. Thanks in advance, James Which operating system are you using? On RedHat/Centos/Fedora/ScientificLinux try: yum install make Can you tell from the error message whether it is make itself that is missing, or something else? Cheers, -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] CCP4-6.3.0 installation
Please note that we do now offer both 32 and 64 bit binary bundles of the CCP4 suite on Linux. With the new Package Manager, binary installation is supposed to be 'painless'. So you may like to try this, rather than feeling to ought to compile your own. Your feedback is welcome. Cheers David. On Aug 4, 2012 9:39 PM, james09 pruza james09x...@gmail.com wrote: Dear CCP4bbers, I am facing CCP4-6.3.0 installation problem. Unable to run make. Configuration is done. Getting error while running make (command not found). Please help. Thanks in advance, James
Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?
Yep, it's definitely our problem not yours, Phil ;-). I believe the only change to scala source since 6.2.0 was to up the maximum number of batches again. This new bug is probably related to the change of compiler for 6.3.0. We'll be trying to make sense out of this next week. Cheers D On Aug 4, 2012 2:34 PM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: This must be a problem on Windows as it doesn't show up on OSX or Linux, and this code hasn't changed for a long time, I think David I guess you will feed this back to me: I don't have any way of testing on Windows Anyway, Aimless should be better :-) Phil On 4 Aug 2012, at 14:26, David Waterman wrote: Dear Peter, You are not alone with this. We have just found out about this bug. It appears to just be a problem with output formatting (the MTZ should be fine). We'll get a fix as soon as we can and will provide a link to 6.2.0's version of scala from the problems page as a workaround early next week. Sorry about this. David (CCP4) On Aug 3, 2012 7:13 PM, Peter Goettig peter.goet...@sbg.ac.at wrote: In the Windows version of the new CCP4 release SCALA produces a summary table (same in the full text) that contains only some rudimentary data, such as Overall InnerShell OuterShell Low resolution limit 19.97 0.00 0.00 High resolution limit 3.00 0.00 0.00 Rmerge 0.000 0.000 0.000 Rmerge in top intensity bin0.115- - Rmeas (within I+/I-) 0.000 0.000 0.000 aso while the final statement of SCALA is ** Normal termination ** Has anyone else experienced similar problems and found a way to solve them? Otherwise, I would ask the developpers to take care of the bugs. However, the corresponding tables generated by AIMLESS contain the full information. Regards, Peter Peter Goettig Structural Biology University of Salzburg Billrothstrasse 11 Salzburg, Austria
