[ccp4bb] Conference in Structural Bioinformatics, Prague, November 15-17, 2023
Dear Colleague! it is a pleasure to invite you to the upcoming conference of ELIXIR 3D-BioInfo community, 3D-SIG of Intl. Soc. for Computational Biology, and Czech ELIXIR https://www.xray.cz/3D-bio-2023/ (apologies for multiple posting) This structural bioinformatics event will be held in the Prague Congress Center, Czech Republic, in November 15-17, 2023. We encourage you to present your results in person; there are still a few slots available for talks. Deadline for submission of abstracts for talks is extended till Thursday, September 21 and will not be extended further. However, you can keep sending abstracts for your posters after this deadline. Your abstract can be uploaded after the registration at https://www.conftool.com/3d-bio-2023/ The fee can be paid at the time of registration or later. See you in Prague in November! Best regards, The Organizers To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] how to get mol files from PDB and restraint CIF?
apologies for a brief note: mmCIF is the default for structural biology data and the ways to avoid its use are just improvisations leading to more improvisations. Bohdan, bs.structbio.org On 2023-05-19 11:48, Frank von Delft wrote: Really, no CIF needed? As far as I know, it's only in the CIF file that the precise atom identities can be found. You can infer them from the PDB lines, but that rather misses the point. Frank On 19/05/2023 10:42, Fred Vellieux wrote: Hello Frank, We have to convert betwen file formats very frequently (usually several times daily) and: 1) we didn't need any restraints CIF file for that; 2) the tools we are using are http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html https://datascience.unm.edu/tomcat/biocomp/convert Sometimes the conversion doesn't take place and I have no idea why. HTH, Fred. On 5/19/23 11:28, Frank von Delft wrote: Hello - as in the subject line, does anybody know of, or have, code that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the restraints CIF file used in refinement, and generate a .mol (or .sdf) file? OpenBabel apparently does not. I thought the PDB processing tools would, but my collaborator couldn't find them. Any pointers welcome. (To save us time.) Thanks! Frank To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Lower b-factors with increasing T
Hello: this may not be 100% relevant to the discussed issue but to add a data analysis perspective: to be able to compare B factors in different structures, they need to be scaled. We used primitive but in my opinion functional linear scaling from 1 to 100 (Schneider et al. Acta Cryst D, D70: 2413 (2014)). We observed clear correlation between B factor distributions and resolution. At "high resolution" (<1.9 Å) Bs correlate with the expected physical behavior of atoms (Bs of the AAs in hydrophobic core << solvent exposed AAs < solvent at the interfaces < solvent at the surface). In "low resolution" structures, 2.5-3.0 Å, all atoms have indistinguishable behavior. We analyzed only structures determined at cryo conditions. Bohdan, bs.structbio.org On 2022-09-08 09:17, Gerard Bricogne wrote: In a similar vein, there could be effects of variation in humidity. How is humidity controlled at these different temperatures? It can drastically affect crystal ordering, which is of course a key determinant of the eventual Wilson B of a dataset and should be distinguished from a property of the individual atoms when interpreting their refined B-factors. Gerard. -- On Thu, Sep 08, 2022 at 08:11:08AM +0200, Jan Dohnalek wrote: There could be a release of sum stress in the crystal with increasing temperature which could even lead to better ordering I can imagine. But that would need a very close inspection and mainly - are the structures completely isomorphous?? I.e. are there changes at all? If not then I am puzzled. Jan On Thu, Sep 8, 2022 at 3:03 AM Tom Peat wrote: I think the basic question being asked is why are the B-factors going the 'wrong' way? That is, as the temperature increases, one might expect higher B-factors (at least that is what we are taught) whereas what Matt is seeing is the opposite- decreasing B-factors as one goes up in temperature (which I also think is a little strange and I don't have an explanation). cheers, tom -- *From:* CCP4 bulletin board on behalf of Phoebe A. Rice *Sent:* Thursday, September 8, 2022 10:48 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Lower b-factors with increasing T I guess the big question is what is the question that you’re trying to address from those numbers? I’d be nervous about making conclusions about trends in B factors from just 1 data set per temperature. As you probably know, the B factors will reflect static differences in atomic position across asymmetric units as well as thermal motion, and it can be difficult to control variables such as exactly how fast a crystal freezes or how much trauma it experiences in its journey from sitting happily in a drop to the frozen state. *From: *CCP4 bulletin board on behalf of Matt McLeod *Date: *Wednesday, September 7, 2022 at 1:57 PM *To: *CCP4BB@JISCMAIL.AC.UK *Subject: *[ccp4bb] Lower b-factors with increasing T Hi everyone, I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), 313K (2.2A) and I am curious as to the details in determining B-factors. I have treated these datasets more-or-less identically for comparison's sake. I used DIALS to index, integrate, and scale the data. I scaled the data to a ~0.6 CC1/2 cutoff. After fully refining the datasets, there is an odd trend with respect to temperature (from what has been previously published) and I assume that this is because of "behind-the-scenes" computation rather than a biophysical observation. The B-factors slightly decrease from 252-293K, and then significantly drop at 313K. The maps look pretty well identical across the datasets. 253K - 53.8 A^2 273K - 48.4 A^2 293K - 45.5 A^2 313K - 18.6 A^2 I compared the wilson intensity plots from DIALS scaling for 273K and 313K and they are very comparable. I am looking for suggestions as to where to look at how these b-factors are selected or how to validate that these B-factor are or are not accurate. Also, any relevant literature would be welcomed. From what I have read, there is a general trend that as T increase, the atoms have more thermal energy which raises the b-factors and this trend is universal when comparing datasets from different temperatures. Thank you and happy to supply more information if that is helpful, Matt To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- To unsubscribe from the CCP4BB list, click the following link:
Re: [ccp4bb] [External] Re: [ccp4bb] phenix refinement for bent DNA
Dear Dhiraj, you may want to check our web service dnatco.datmos.org where you can also generate 3D constraints for refinement in Phenix. Best regards, Bohdan, bs.structbio.org On 2021-03-30 3:52, Srivastava, Dhiraj wrote: Thank you everyone for the help. I am sorry about phenix related question. But since the question was refinement related I thought it will be ok to ask on ccp4bb. Thank you Dhiraj - *From:* Oleg Sobolev *Sent:* Monday, March 29, 2021 6:18 PM *To:* Srivastava, Dhiraj *Cc:* CCP4BB@jiscmail.ac.uk *Subject:* [External] Re: [ccp4bb] phenix refinement for bent DNA Hi Dhiraj, I have structure with bent DNA. I am trying to refine the structure using phenix. do I need to turn off the DNA secondary structure restraints during refinement? Application of secondary structure restraints depends on the quality of the experimental data. The most basic parameter to consider would be a resolution. For lower-resolution SS restraints might help to keep a reasonable geometry of the structure. The bent DNA should also work fine with SS since they are restraining base pairs and stacking pairs which normally don't distort too much. P.S. There is a separate bulletin board for Phenix-specific questions: http://www.phenix-online.org/mailman/listinfo/phenixbb Best regards, Oleg Sobolev. Thank you Dhiraj To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [3dem] Which resolution?
Hello, B-factors actually do have a physical meaning which is at least to some extent reflected by the crystal structures as refined. This can be demonstrated at higher resolution structures: when we created three tiers of structures, better than 1.9 Å, 1.9-2.4 Å, and 2.4-3.0 Å, structures in the first one showed distinct distributions of B factors for the amino acid side chain/main chain atoms inside and outside the protein, for DNA bases, and phosphates, and for water at the interface, and on the biomolecule surface. The distinction is less clear for the 1.9-2.4 Å structures and is lost completely below that resolution limit. We think that the distributions for the high resolution structures can be developed into meaningful set of constraints and/or validation criteria. If interested, you can read more in our open access paper Acta Cryst. (2014). D70, 2413–2419 (doi:10.1107/S1399004714014631). Best regards, Bohdan, bs.structbio.org On 2020-03-11 16:41, Gerard DVD Kleywegt wrote: If this is the case, why can't we use model B factors to validate our structure? I know some people are skeptical about this approach because B factors are refinable parameters. Rangana It is not clear to me exactly what you are asking. B factors _should_ be validated, precisely because they are refined parameters that are part of your model. Where have you seen skepticism? Rangana said that B-values should not be used *to validate structures*, NOT that B-values themselves shouldn't be validated themselves. I suppose I am at least in part to blame for the former notion and the reason for this (at least circa 1995 when the Angry Young Men from Uppsala first starting harping on about this) was that B-values tend(ed) to be error sinks which could "absorb" all sorts of errors and phenomena in addition to modelling atomic displacement (e.g., unresolved disorder, unresolved NCS differences, incorrect restraints, incorrect atom types modelled, partial ocupancies, etc.). --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let "z" be the radius and "a" the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! ** 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] Reg: water pentagon at dimer interface
Dear All, pentagons of water are one of the old myths from the past millennium: everyone talks about them, nobody has seen them. How many cases do you have in your structure, how many have you analyzed in the PDB? In other words, anecdotal evidence is fine, but what is their statistical significance? The first shell of waters around biomolecules is ordered, in proteins as well as nucleic acids. The positions of these waters are a function of the local geometry of the amino acid or nucleotide which is however significantly modulated by the neighboring residues. The geometry of the above mentioned first hydration shell of waters around say guanosine phosphate is different in the B and A forms of DNA. Another example, asparagine has different hydration sites in the alpha-helical or beta sheet environments, of course on top on differences depending on the asparagine conformation. You may look at https://www.dnatco.org/watAA/atlas.html for more examples. I believe that in your case, Vijaykumar, the meaning of the pentagon(s) is that you see five waters at the interface as other people see three, four or seven. Best regards, Bohdan, bs.structbio.org On 2019-09-27 14:28, Jon Cooper wrote: Pentagons of water are quite common in ordered water structure. Is it isolated or do the waters H-bond to other waters?The dimer interface looks, if I may say, a bit borderline to me. How does it fare in Pisa? Best wishes. On 27 Sep 2019 12:33, Vijaykumar Pillalamarri wrote: Dear Community, I solved the structure of a protein from vibrio. There are two molecules in the asymmetric unit of this protein. At the dimer interface, the C-termini of both the chains interact with each other with the help of five water molecules that form a pentagon. I have attached an image showing both the chains and stereo image of dimer interface in the inset. I was wondering if there is any significance to this or if there is any relevant literature that explains this behavior. Thank you Vijaykumar Pillalamarri C/O: Dr. Anthony Addlagatta Principal Scientist CSIR-IICT, Tarnaka Hyderabad, India-57 Mobile: +918886922975 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Thoughtful remark...
what is this discussion about? please, try to be reasonable Bohdan, structbio.org/bs On 2019-02-01 10:05, vincent Chaptal wrote: Hi Leo, are you asking the question from the point of view of the user, or from the beamline scientist allocating beamtime? different answers then! best Vincent On 01/02/2019 09:42, CHAVAS Leonard wrote: Dear all I had one interesting comment today at the beamline, that I would like to share with you for your advice on how to answer this... Is it better to have no diffraction from a crystal you shoot, or to have no crystal in the loop? Hum, difficult one... Cheers, leo - Leonard Chavas - Synchrotron SOLEIL Proxima-I L'Orme des Merisiers Saint-Aubin - BP 48 91192 Gif-sur-Yvette Cedex France - Phone: +33 169 359 746 Mobile: +33 644 321 614 E-mail:leonard.cha...@synchrotron-soleil.fr - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://mmsb.cnrs.fr/en/ 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
