Re: [ccp4bb] how to calculate the volume of a small molecule
Dear all, Is there a way to calculate or estimate the volume of a small molecule within CCP4 or with other programs? Thanks, Kemin To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
[ccp4bb] Log graphs not opening with CCP4i and Windows 10
Anyone run into the loggraph utility not opening on Windows 10? If not then any ideas what to check if it does not open? Mark To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] scale and merge suggestions
Hi Almudena, did you cut the res. after the merge of your "individual" datasets ? or you cut for each and then you merged? Because I will probably go for the first, I merge and then I decide where to cut. If you cut for each, maybe you "miss" the gain provide by the redundancy you have cumulated using all the data. If I mis understood what you did, and return a bad answer, sorry. And to really answer your question, I will say : I stick to a combination of the "standard" stats, CC 1/2 mainly, I/sig and if you expect anomalous, CC Ano and SigAno. My choice would be conditioned also by the strategy for the phasing. Hope to help. De: "Almudena Ponce Salvatierra" À: "CCP4BB" Envoyé: Mercredi 4 Novembre 2020 17:30:29 Objet: [ccp4bb] scale and merge suggestions Hello everyone, I have collected 6 small datasets from a crystal, each from a different point on the crystal to avoid radiation damage, and there is some overlap among them, as follows: - dts1: 0-90 degrees - dts2: 60-150 degrees - dts3: 120-210 degrees - dts4: 180-270 degrees - dts5: 240-330 degrees - dts6: 300-390 degrees Diffraction is very poor and, after processing, I've cut resolution at around 5 Angstroms for all of them. The space group is C2. Feeding the 6 of them to scale_and_merge in Phenix gives the attached output. Does anybody who has merged such low-resolution anomalous data before know whether this is a "good" indicator (meaning there's a tiny light at the end of the tunnel) or rather not? Any suggestions? (besides the obvious "go back to the lab and grow new crystals") My aim is to combine these phases with a partial molecular replacement solution and a native dataset at 3.5 Angstroms. Hopefully, then I would be able to finish building the model. Thanks a tone in advance! Best, Almudena To unsubscribe from the CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] scale and merge suggestions
Hello, it would be useful to see how the merging of the normal data looks in addition to the anomalous, which could be a bit better, I fear. Are you expecting significant anomalous differences e.g. Se-Met, S with long wavelength, H-atom, etc? You should have quite high redundancy with all that data even with monoclinic. HTH a bit. Jon Cooper Sent from ProtonMail mobile Original Message On 4 Nov 2020, 16:30, Almudena Ponce Salvatierra wrote: > Hello everyone, > > I have collected 6 small datasets from a crystal, each from a different point > on the crystal to avoid radiation damage, and there is some overlap among > them, as follows: > > - dts1: 0-90 degrees > - dts2: 60-150 degrees > - dts3: 120-210 degrees > - dts4: 180-270 degrees > - dts5: 240-330 degrees > - dts6: 300-390 degrees > > Diffraction is very poor and, after processing, I've cut resolution at around > 5 Angstroms for all of them. The space group is C2. Feeding the 6 of them to > scale_and_merge in Phenix gives the attached output. Does anybody who has > merged such low-resolution anomalous data before know whether this is a > "good" indicator (meaning there's a tiny light at the end of the tunnel) or > rather not? > > Any suggestions? (besides the obvious "go back to the lab and grow new > crystals") > > My aim is to combine these phases with a partial molecular replacement > solution and a native dataset at 3.5 Angstroms. Hopefully, then I would be > able to finish building the model. > > Thanks a tone in advance! > > Best, > > Almudena > > --- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
[ccp4bb] PostDoc position DNAorigami and cryoTEM, France
Dear all, I would like to bring your attention to the open postdoctoral position at the Centre de Biochimie Structurale in Montpellier, France ( www.cbs.cnrs.fr ). This will be a full-time, 34-months appointment focused on the development and implementation of new DNA nanotechnology based tools for protein structural biology. The project is funded by The French National Research Agency and will be carried out under the supervision of Gaëtan Bellot. We are seeking a highly motivated candidate with expertise in Biochemistry and Structural Biology, ideally in the area of Electron Microscopy, with a keen interest in applying this knowledge to Membrane Biology. Our EM facility hosts a 200 keV microscope equipped with energy filters and direct electron detector. In addition, a 120 keV microscopes will be available soon for screening. Specifically, our laboratory develops functional DNA origami nanodevices. You will develop two main projects: i) Structural analysis of membrane protein (G-Protein Coupled Receptors) by single particle electron microscopy. This work is part of an ongoing collaborative research projects with the team of Sebastien Granier at IGF, Montpellier ( https://www.igf.cnrs.fr/index.php/fr/h-teams- fr/h-granier-fr ). ii) New DNA-based nanostructures methods for biophysics studies and structural elucidation of proteins by Cryo-Electon Microscopy. Applicants must have a Ph.D. and should have a strong background in Biochemistry/Chemistry or in Biophysics/Structural-Biology. Experience in the field of Cryo-Electon Microscopy is highly desirable. Candidates should send an inquiry with CV and have one or two references send letters of recommendation to gaetan.bel...@cbs.cnrs.fr -- __ Gaëtan Bellot, Ph.D. INSERM gaetan.bel...@cbs.cnrs.fr Centre de Biochimie Structurale www.cbs.cnrs.fr ___ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] R free rising
Dear Nika, XDS probably did what you asked it to do ;-) This is, however, not a problem. You only need to refine for a couple of rounds longer to gain independence of your Rfree set. No need to reassign them. Depending on the refinement program, it may take many rounds. With Refmac (or shelxl), it does not take very long. Wenn you plot the LLgain, listed at the end of the refmac log-file, and its curve flattens out, your Rfree reflections should be independent and not model-biased anymore. Best regards, Tim On Wed, 4 Nov 2020 13:18:06 + Nika Žibrat wrote: > Hello, > > Two days ago I was asking about R free rising. The problem was xds > adds R free flags already and then re-introduced them in Phenix, > causing R free to rise. I would like to thank you for your answers, > they were most helpful. > > Best, > Nika > > > From: Nika Žibrat > Sent: ponedeljek, 02. november 2020 11:26 > To: ccp4bb@jiscmail.ac.uk > Subject: R free rising > > > Hello, > > > > I am trying to solve an X-ray structure of a protein of which the > structure is already known. My aim is to only seek for ligands > (soaking) and interpret any conformational changes. Since I am using > a model with 100% sequence identity from PDB I am not doing Autobuild > after Molecular phasing and continue directly with phenix.refine > according to reccomendations (10 rounds). In accordance with X-triage > I am also using NCS default settings in the refinement. > > > > This refinement produces solid R free and R work values around 0.29 > and 0.22. The problem becomes when I want to manually edit the > structure, correct the loops which are changed upon binding of the > ligand, and correct any outliers. This results in R free slightly > lower than R work. Upon refining, R work drops normally while R free > rises significantly (for 0.2 -0.3). I have been trying to crack this > for a few days with no success. > > > > I read that slightly lower R free can be normal in such cases but > nevertheless both R values should drop, and haven't found anything > about the big rise of this value after refinement. It feels like I am > missing something, since this is my first time solving a structure. > Any advice? > > > > Thank you, > > Nika > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ pgpQENZ1hSHVf.pgp Description: OpenPGP digital signature
Re: [ccp4bb] R free rising
Hello, Two days ago I was asking about R free rising. The problem was xds adds R free flags already and then re-introduced them in Phenix, causing R free to rise. I would like to thank you for your answers, they were most helpful. Best, Nika From: Nika Žibrat Sent: ponedeljek, 02. november 2020 11:26 To: ccp4bb@jiscmail.ac.uk Subject: R free rising Hello, I am trying to solve an X-ray structure of a protein of which the structure is already known. My aim is to only seek for ligands (soaking) and interpret any conformational changes. Since I am using a model with 100% sequence identity from PDB I am not doing Autobuild after Molecular phasing and continue directly with phenix.refine according to reccomendations (10 rounds). In accordance with X-triage I am also using NCS default settings in the refinement. This refinement produces solid R free and R work values around 0.29 and 0.22. The problem becomes when I want to manually edit the structure, correct the loops which are changed upon binding of the ligand, and correct any outliers. This results in R free slightly lower than R work. Upon refining, R work drops normally while R free rises significantly (for 0.2 -0.3). I have been trying to crack this for a few days with no success. I read that slightly lower R free can be normal in such cases but nevertheless both R values should drop, and haven't found anything about the big rise of this value after refinement. It feels like I am missing something, since this is my first time solving a structure. Any advice? Thank you, Nika To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
