Re: [ccp4bb] coiled-coil "degree"
Dear Jorge, It sounds like you want to estimate the 'pitch' parameter of a coiled coil. You can extract that information from the structure using TWISTER program, a server is available here: https://pharm.kuleuven.be/apps/biocryst/twister.php The alpha-helical chains need to be in-register, i.e. the "parallel" residues need to have the same residue numbers (if that's not the case you'll need to renumber the chains before submitting). Kind regards, Dmytro. On Tue, Aug 28, 2018 at 6:03 AM, Jorge Iulek wrote: > Dear all, > > > I am working currently on a structure that, nicely, presents two > different orientations between its domains when one compares monomers of > the tetramer in the asymmetric unit. > > I notice, in this nature gift, that a helix, probably central (in its > role) for the relation (orientation) between the two domains, assumes > different relation to other one (helix, that belongs to one of the domains) > such that they are (significantly) more or less "coiled-coiled"one to > another, once the domains are in the "close" or "open" conformation. We > have already analyzed the hydrogen bonds and salt bridges that are > disrupted (or formed) due to the different (domain and helix) conformations. > > I wonder whether there is a metric (easy to evaluate) to characterize > how much the two helix are "around each other" (id est, how much > "coiled-coiled" they are) and, preferably, a software to calculate this > metric. > > Thank you, > > > Jorge > > State University of Ponta Grossa > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Fwd: Re: [ccp4bb] Structure comparison
Gert, There is nothing wrong with suggesting 45 softwares, as one of those may do exactly what a person needs and save loads of time. Besides, comparing protein structures locally need not involve any superposition method. I would say comparing torsion angles/distances between atoms is a more common solution to this problem. There are still cutoffs and weights to consider of course. Approaches vary on how to handle those (e.g. theoretical or through validation), but I seriously doubt your response constitutes 'case closed'. Kind regards, Dmytro. On 10/04/17 12:06, Gert Vriend wrote: Rather then now start mentioning yet 45 other 3D superposition softwares, I think a pointer to the Wikipedia should suffice: https://en.wikipedia.org/wiki/Structural_alignment The Russian Doll effect (if you align more residues the comparison stats get worse) is best explained (my opinion) by the CATH people (Orengo group), and Arthur Lest is the only one (still, I think) who has been thinking extensively about the cutoff question. Greetings Gert From: Reza Khayat Sent: Sunday, April 9, 2017 6:07 PM To: CCP4 bulletin board Subject: Structure comparison Hi, I have refined several structures of a protein from different space groups and would like to compare them to one another. Is there a program/software suite that would provide an objective comparison of the structures and identify regions where the structures are sufficiently different from one another to warrant a closer look? I think the most important aspect of the analysis would be defining a threshold (possibly based on resolution and structure statistics) that would identify sufficient difference between structures. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
Re: [ccp4bb] Structure comparison
Have a look at local distance difference test.https://swissmodel.expasy.org/lddt/ It's superposition-free and compares local atomic environment only. You will be able to see unusually different regions from the output. I am not aware of a similar structure comparison method that would also take into account the underlying data, you'll probably need to come up with something here. E.g. place one structure instead of another in its crystal and evaluate local electron density correlations along the sequence (sfcheck can do that I think) at different resolution levels. Then compare changes in local correlation (replaced-original) vs. lddt plot. If both plots go down in the same region, then it warrants a closer look. Kind regards, Dmytro. On 10/04/17 01:37, Reza Khayat wrote: Hi, My initial e-mail may have been a bit vague so I'll try to be more specific. Superposing the structures and comparing them against one another, while appropriate, is a subjective way to do the analysis as I would have to subjectively define a threshold that would indicate a difference between the structures. My threshold may be grossly different than someone else's threshold. I am interested in an objective criterion. One where strong emphasis has been put on error analysis and error modeling in terms of both the refined structure and the underlying data. I realize that defining such criterion is by no means trivial. Thanks again for the help. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: Reza Khayat Sent: Sunday, April 9, 2017 6:07 PM To: CCP4 bulletin board Subject: Structure comparison Hi, I have refined several structures of a protein from different space groups and would like to compare them to one another. Is there a program/software suite that would provide an objective comparison of the structures and identify regions where the structures are sufficiently different from one another to warrant a closer look? I think the most important aspect of the analysis would be defining a threshold (possibly based on resolution and structure statistics) that would identify sufficient difference between structures. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031
Re: [ccp4bb] suggestion for structure solution of a protein with low sequence identity
Hi Vikram, Try Buccaneer, it works much better at such resolution than Arp/Warp. Launch it several times with different parameters (e.g. use original structure as seed/initial/nothing), then open the results together and merge the pieces that look best and have lowest b-factors. Use Buster for refinement of the merged model and iterate with Buccaneer again. That's what worked for me once to bootstrap a poor MR solution (~20% of the structure originally) to a near-complete model at 2.7A. You are in a sense replicating what phenix.autobuild attempts to do, but you'll be able to do it better (and probably faster) manually. Kind regards, Dmytro. On 25/10/16 14:16, Vikram Dalal wrote: Hi everyone, We are trying to solve a protein structure of 2.6 A. We have processed it with HKL2000. We have even tried processing with mosflm and xia2. It is in C2221 space group (checked by pointless) and data is not twinned. It has 31% identical with a search model and has 57% sequence coverage. There are 2 subunits in asu. I did not get proper phases with MOLREP and phaser. I have tried Balbes (R free 50) and Mr BUMP (R free 54).But, density from balbes look some reasonable. So i have refined it in ccp4i and phenix differently and then model build it by coot. My protein has 377 Amino acid. But, I stucked at R free 41 and now i have amino acid 50 to 369 in both chains, still 49 amino acid at N terminal and 8 amino acid at C terminal are missing and some loops are missing in between too. *I have tried the ARP/wARP, but it does not work for it. * * * *I have even tried phase and build of phenix but condition remain same. i got stuck at R free at 42 and same around 49 amino acids at N terminal and 8 amino acids at C terminal and some internal loops still absent.* * * *Thank you in advance.* * *
Re: [ccp4bb] OT: Who's Afraid of Peer Review?
Hi Folmer, I was hoping to see what kind of science was behind the computer program that generated the unique papers. Combinatorics in this case. The article was pre-written, he just replaced some names. Typically for hard science texts you would use a formal grammar with random production rules instantiation. To generate a philosophic text you could apply a Markov chain trained on existing papers. Kind regards, Dmytro. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Folmer Fredslund Sent: Wednesday, October 09, 2013 9:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] OT: Who's Afraid of Peer Review? Hi Navdeep, I feel disappointed. (not your fault) I was hoping to see what kind of science was behind the computer program that generated the unique papers. That doesn't seem to be contained in the linked article. The article does, however, seem to be lacking in peer review itself? Or can anything be done in the name of journalism? Why were only open-access journals selected? I guess I'm just repeating the questions that many others have asked since the publication. Best regards, Folmer 2013/10/9 Navdeep Sidhu nsi...@shelx.uni-ac.gwdg.demailto:nsi...@shelx.uni-ac.gwdg.de John Bohannon wrote about his experience writing a computer program to generate hundreds of unique papers. Thought some of you might find it of interest: John Bohannon. Who's Afraid of Peer Review? Science 342 (Oct. 4, 2013) 60-65. DOI: 10.1126/science.342.6154.60 http://www.sciencemag.org/content/342/6154/60.full Best regards, Navdeep --- Navdeep Sidhu University of Goettingen --- -- Folmer Fredslund
Re: [ccp4bb] stereo monitor for DELL T7600
Hi JI, Just FYI: we have a working setup of Nvidia 3D Vision on Quadro FX 3700 with Acer GD235HZ under Ubuntu 12. Quadro FX 3450/4000 was also tested (not officially supported by NVidia, but has all the capabilities) - although it works in principle, there was an annoying flickering effect I could not get rid of. In addition to what was already told here, I would recommend checking the monitor for backlight irregularities on 100% brightness before buying. This is the mode you are typically working in with the glasses (in fact, GD235HZ locks it at 100% when stereo is enabled), and the defects might not be noticeable on normal brightness. Kind regards, Dmytro. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of jlliu liu Sent: Friday, March 01, 2013 12:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] stereo monitor for DELL T7600 Hi All, I am ordering a Dell workstation (Dell Precision,T7600n,MT,1300W) with 2GB nVIDIA Quadro 4000. Can anyone recommend to me which stereo monitor would be compatible with this model? I have some stereo models mentioned in previously ccp4bb email: - Zalman ZM-M215W 21.5in - Zalman ZM-M240W 24in - Samsunghttp://proteincrystallography.org/ccp4bb/message29933.html SyncMaster S27A750D 27in - LG D2342P 23in / LG D2542P 25in Any advice will be highly appreciated. Thanks so much in advance! Jl
