Re: [ccp4bb] delete subject
Hi all, This has indeed been a highly informative and educational thread from many view points, and it highlights the opportunities and challenges that scientists face today by having access to tools like the CCP4BB . I just wanted to touch on something that was briefly alluded to at the early stages of this saga, and it has to do with data confidentiality and to some degree understanding the various policies that your institution adheres to. I raise this issue for the benefit of students like Tom, who may not have been exposed to the various implications that this brings. In my view, understanding your institution's (or your lab's) data sharing policies is extremely important prior to taking such action. In some institutions and specially in industry, sharing data without prior approval would be grounds for dismissal or even worst (lawsuits come to mind). So as we all learn from Tom's experience in this thread, I think we should all use good judgment when seeking help and deciding when to share data to an open forum. My 2 cents. Francisco From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raji Edayathumangalam [r...@brandeis.edu] Sent: Thursday, March 28, 2013 7:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] delete subject Ed, I very much agree with you. We've all had to learn that questions posted to ccp4bb and the ensuing discussions take on a life of their own. Once one posts a question on ccp4bb, there's no such thing as steering the direction of the discussion on the ccp4bb and there's no such thing as the equivalent of screaming Stop! Stop! Stop! on the ccp4bb. Also, I don't believe people simply woke up one day and posted irritating or mean comments to ccp4bb. Ed was spot on for why some folks reacted the way they did to the post so let's acknowledge that as well. I didn't get the impression that any of the replies suggested that students stop posting questions. There are many many students on this BB who are in small institutions without even the minimal help at arm's length and who get tons of help from posting questions to the ccp4bb. That situation is not all that distant in my own memory and I suspect for many other experts on this BB. But posting 10MB attachments and getting the entire ccp4bb community to crowdsource towards problem solving is all good, but only to a certain degree. It may be great to get things done quickly with the collective intellect of the ccp4bb but there comes a point when the correct answers may get fed back at such a rapid speed that if one doesn't go back and try to figure stuff out for oneself, including the reasons/theory/logic behind the answers/solutions that the community has posted, it may be to the detriment of one's own learning, especially if one is in the early stages of learning the subject matter. Cheers, Raji On Thu, Mar 28, 2013 at 9:09 AM, Ed Pozharski epozh...@umaryland.edumailto:epozh...@umaryland.edu wrote: On Thu, 2013-03-28 at 12:15 +, Tom Van den Bergh wrote: I think this is a good time to end the discussion. As a general comment, discussions on boards like ccp4bb often digress and take direction different from you original intent. I may understand your desire to try to control the situation, but if people on this board feel that the questions of data sharing, student training, netiquette and proper choice of resolution cutoff are worthy of further discussion (that may not have much to do with specifics of your original request for assistance), it is their right too. What may have caused some extra grief is this unfortunate turn of phrase in your original post Could you try some refinement for me, because this is first structure that i need to solve as a student and i dont have too many experience with it. It goes a bit beyond the usual my R-values are too high what should I do question and may be instinctively construed as if you expect someone to actually do your work for you (I am sure that is not what you asked). So a bit of a vigorous reaction that you received likely results from misunderstanding your intent (albeit posting your data is very unusual and strengthens the impression) and perhaps misplaced feeling that you have abandoned attempts to resolve the problem independently too soon. I did *not* look at your data and therefore I may be completely wrong here, but it is my understanding that your actual issue was not realizing there could be more than one molecule in the asymmetric unit. More traditional route is to describe your situation in general terms and offer to provide data to those willing to take a closer look. Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] [off-topic] CNS solve profit license
Hi Genie, I'll ask someone from our Korea office to get in touch with you regarding your request. CNS for profit licenses do have to be licensed through Accelrys. Thanks, Francisco Francisco Hernandez-Guzman, PhD Sr. Product Manager Accelrys Software, Inc From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of JinSoo.Bae Sent: Thursday, March 14, 2013 4:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] [off-topic] CNS solve profit license Dear CCP4users biologists, I'm trying to get a CNS solve v1.3 profit license. I don't know how to contact person who deals with CNS profit license. Could you give the hint for getting the license or authorization for CNS program? Kind regards, Genie Genie 790-784 room 204, Dept of Life Science, POSTECH, san31, Hyoja-dong, Nam-gu, Pohang, Gyungbuk, Korea tel:82-54-279-8627 fax:82-54-279-8111
Re: [ccp4bb] How to compare B-factors between structures?
Hi Yarrow, I'm sure other visualizing tools can do this, but I just wanted to share that our free Discovery Studio Visualizerhttp://accelrys.com/products/discovery-studio/visualization-download.php can do this quite easily. Contact me off the list and we can set up a time when I can show you how to do this. I could also send you some instructions as well. Cheers, Francisco Sr. Product Manager Accelrys Software, Inc -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yarrow Madrona Sent: Monday, February 25, 2013 1:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to compare B-factors between structures? Thanks Nat, I was planning on plotting B-factors vs. residue anyway, so maybe this will save me time. I will take a look. -Yarrow Not a CCP4 solution, but the structure comparison program in the Phenix GUI will plot B-factors for different structures of the same protein. (I am happy to make additions or modifications to this, but so far I haven't received much feedback.) -Nat On Mon, Feb 25, 2013 at 12:08 PM, Yarrow Madrona amadr...@uci.edumailto:amadr...@uci.edu wrote: Hello, Does anyone know a good method to compare B-factors between structures? I would like to compare mutants to a wild-type structure. For example, structure2 has a higher B-factor for residue X but how can I show that this is significant if the average B-factor is also higher? Thank you for your help. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
Re: [ccp4bb] Improving Homology Models
Hi Jacob, In our experience using MODELLERhttp://salilab.org/modeller/ for the homology modeling part, followed by refinement with CHARMMhttp://www.charmm.org/ leads to structures with very reasonable high quality statistics as reported by MolProbity. Both programs are integrated in our commercial suite Discovery Studiohttp://accelrys.com/products/discovery-studio/, but you can also access them directly from their respective labs. Kind regards, Francisco Francisco Hernandez-Guzman, PhD, MBA Sr. Product Manager Accelrys Software, Inc. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, February 20, 2013 12:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Improving Homology Models Dear Crystallographers, it has been my experience that homology modelling programs get folds pretty well, but sometimes the details are pretty obviously bad, like too-close contacts. One might think that the modelling software would put in a sort of polishing step, but they don't seem to. Is there any way to trick the CCP4 or other software to fix these things, such as by simulated annealing or otherwise, I guess without any weight on the [non-existent] structure factors? Thanks, Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] Protein volume
Hi Theresa, You can use our free Discovery Studio Visualizer: http://accelrys.com/products/discovery-studio/visualization-download.php You can select the region of choice (in your case the transmembrane domain) and create a surface around it (Structure - Surface - Add). Then in the Molecular Data Table's Surface Tab (View - Data Table), you can find values for the Surface Area as well as Volume. Let me know if you have any trouble with this. Disclaimer: I work for Accelrys. Cheers, Francisco Sr. Product Manager Accelrys.com -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa Hsu Sent: Thursday, September 06, 2012 12:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Protein volume Dear all I have two membrane protein structures. Is there any tool to calculte the volume of transmembrane domain and solublle domain separately for comparison? Thank you.
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
Re: [ccp4bb] Calculating ED Maps from structure factor files with no sigma
I just wanted to take a moment to thank all of the respondents to the post. Indeed, my question was more practical in nature since I wanted to see the density around the ligand in question. From the first suggestions, I quickly did manage to generate the maps and accomplish my goal (special thanks to Robbie for actually sending me the converted mtz file from the PDB cif entry). The additional comments have also been highly educational and helpful to further my understanding of some more in-depth crystallography concepts. Thank you, Francisco PS The PDB_REDO (http://www.cmbi.ru.nl/pdb_redo/hf/1hfs/index.html) was indeed a great resource and I'm certain to use it again. Thanks! From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Francisco Hernandez-Guzman Sent: Tuesday, May 22, 2012 9:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Calculating ED Maps from structure factor files with no sigma Hello everyone, My apologies if this comes as basic, but I wanted to get the expert's take on whether or not the sigmaF values are required in the calculation of an electron density map. If I look at the standard ED equation, sigma's don't appear to be a requirement but all the scripts that I've looked at do require sigma values. I wanted to calculate the electron density for PDB id: 1HFS but the structure file only lists the Fo's, Fc's and Phases, but no sigmas. Would such structure factor file be considered incomplete? Thank you for your kind explanation. Francisco
Re: [ccp4bb] DNA/RNA modeling
Hi Jens, You can try the free DS Visualizer: http://accelrys.com/products/discovery-studio/visualization-download.php It comes with a free molecular builder for proteins, dna/rna and ligands. Please note that if you do need to make anything more interesting (energy calculations, minimizations, md, etc) will then need a license. I hope this helps. Francisco Full Disclaimer: I do work for Accelrys. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of jens j birktoft Sent: Wednesday, May 23, 2012 9:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] DNA/RNA modeling Hi everybody, Does anyone know of a (non-commercial) software that are suitable for modeling DNA/RNA structures. Coot is great, however I am looking something that allows more flexibility Thanks -- Jens J. Birktoft e-mail: jens.birkt...@nyu.edumailto:jens.kn...@gmail.com slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057
[ccp4bb] Calculating ED Maps from structure factor files with no sigma
Hello everyone, My apologies if this comes as basic, but I wanted to get the expert's take on whether or not the sigmaF values are required in the calculation of an electron density map. If I look at the standard ED equation, sigma's don't appear to be a requirement but all the scripts that I've looked at do require sigma values. I wanted to calculate the electron density for PDB id: 1HFS but the structure file only lists the Fo's, Fc's and Phases, but no sigmas. Would such structure factor file be considered incomplete? Thank you for your kind explanation. Francisco
Re: [ccp4bb] X-PLOR
Nadir, There is an explicit bulletin board for questions regarding CNS and XPLOR. I would suggest posting your question there. http://tech.dir.groups.yahoo.com/group/cnsbb/ Cheers, Francisco -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nadir T. Mrabet Sent: Friday, April 27, 2012 6:34 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-PLOR Hi, Could someone explain to me the scientific details of the protocols used in X-PLOR to (1) build explicit hydrogen atoms onto X-ray structures and (2) optimize their positions? Many thanks in advance. Greetings, Nadir -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry INSERM U-954 Nancy University, 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.Mrabetat medecine.uhp-nancy.fr
Re: [ccp4bb] On pKa of Aspartic acid
Hi Deepak, With regards observed pKa shifts, Prof. Ondrechen from Northeastern University has had a long interest in this field. http://www.northeastern.edu/org/wp/ Under the computational tools that she has developed a program called THEMATICS that allows you to predict the pka of titratable amino acids and she has been able to predict shifts. Though the server seems to be down at this point, here is the reference: Y. Wei, J. Ko, L.F. Murga, and M.J. Ondrechen, BMC Bioinformatics 8:119, (2007) From the commercial side, Dr. Spassov from Accelrys has also been working on tools that predict protein ionization. In his work, he has also been able to predict significant pka shifts for functionally relevant residues. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2578799/ Cheers, Francisco From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Deepak Oswal Sent: Tuesday, February 07, 2012 3:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] On pKa of Aspartic acid Dear colleagues, We have solved the crystal structure of a human enzyme. The pKa of a catalytically critical aspartic acid has increased to 6.44. It is hydrogen bonded (2.8 Angstroms) to a water molecule that is supposed to donate a proton during the catalysis. Can anybody help me a) interpret the significance of this increase in pKa of the aspartic acid from 3.8 to 6.44 in context with the catalysis? Is this advantageous or detrimental? b) How is pKa related to an amino acids' ability to force a water molecule to donate a proton? c) At pH 7.4, the aspartic acid would be de-protonated irrespective of whether the pKa is 3.8 or 6.44; isn't that true? d) Have similar increase in pKa values observed for aspartic acids before? I would be grateful if anybody could explain or comment on the above queries. Deepak Oswal
Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment
Hello Wenhe, Have you tried using our free Discovery Studio Visualizer? http://accelrys.com/products/discovery-studio/visualization-download.php You can generate and color alignments using various properties like alignment similarity, chemical type, steric, and many others. In addition, you can select your own custom coloring for each property. I have attached a small screenshot of the view for your sample picture trying to match your coloring scheme. Cheers, Francisco Francisco Hernandez-Guzman, PhD, MBA Sr. Product Manager http://accelrys.com From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of WENHE ZHONG Sent: Thursday, February 02, 2012 9:32 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe attachment: sequence_alignment.jpg
Re: [ccp4bb] Off-topic: ELNs
Hi Seiji, A nice web base solution is the iLabber from Contur. It has been a popular option for many academic labs around the globe. http://www.contur.com/home/ Cheers, Francisco Sr. Product Manager Accelrys, Inc. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Seiji Sugiman-Marangos Sent: Monday, January 16, 2012 1:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Off-topic: ELNs Hi, off-topic question regarding electronic laboratory notebooks. Our lab is planning on moving from paper to digital record keeping and I was wondering which of the available ELN platforms are being used by the ccp4 community. We are primarily a crystallography lab but we would also need some versatility in the platform as some of our lab members are more focused on biochemistry. Any suggestions or comments would be greatly appreciated! Thanks, Seiji
Re: [ccp4bb] off-topic: Discovery Studio software
Correct, the DS Visualizer is not available for Mac OS at this point, however various emulators such as Parallels or VMWare have been used successfully. Without going into too much detail, there is a new version (3.0) of the visualizer which extends even further the capabilities of our previous free version. Here are some quick points of what is now included in this new version: - Molecular Builders - 3D plot visualization - 2D Protein-ligand interaction plot - Storyboard to capture workflow scenes (no script required) - Forcefield typing for preparation of simulation calculations - Protein reports - and much more... Many of the features that were previously available in the paid version, are now offered for free with this new version. I encourage everyone to give it a try. Thanks, Francisco Francisco Hernandez-Guzman Product Manager Accelrys, San Diego, CA From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sean Seaver [s...@p212121.com] Sent: Saturday, February 19, 2011 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] off-topic: Discovery Studio software Hi Padmaja, -Will it work on a Mac OS? No -Is there another program (free or cheaper) that will do everything DS does? Currently, there is a free version that you can use of DS. http://accelrys.com/products/discovery-studio/visualization-download.php Hopefully that will give you a feeling if the program will fit your needs. -Any other comments from users/naysayers about DS We have up put up a couple of blog posts about DS that you may find helpful. Discovery Studio Visualizer 2.5 http://bit.ly/QgvNL 3 Selection Methods in Discovery Studio Visualizer http://bit.ly/4UIzcd Take Care, Sean P212121 http://store.p212121.com/
