Re: [ccp4bb] Resolution cut off
Thanks, Robbie, I will try this. -Vandna On Mon, Feb 12, 2018 at 3:00 PM, Robbie Joosten <robbie_joos...@hotmail.com> wrote: > Dear Vandna, > > > > Paired refinement is indeed the most reliable way to see whether the > higher resolution data help your refinement. It is done automatically on > the pdb-redo.eu server if the resolution of the data used in refinement > so far is lower than the resolution of your dataset (by at least 0.1A). We > get the resolution from your REMARK 3 stuff in the input pdb file header. > > Although it is not an ideal experiment, you can also cheat pdb-redo into > doing paired refinement by forging the header of your pdb file. > > > > HTH, > > Robbie > > > > Sent from my Windows 10 phone > > > > *From: *Graeme Winter <graeme.win...@diamond.ac.uk> > *Sent: *maandag 12 februari 2018 20:48 > *To: *CCP4BB@JISCMAIL.AC.UK > *Subject: *Re: [ccp4bb] Resolution cut off > > > > The most useful information for this can come from paired refinement, > which will tell you if the data in outer shell is improving the model. > > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/ > > For example > > On balance it’s unlikely throwing away measurements will make your model > better... > > Best wishes Graeme > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vands [ > vanx...@gmail.com] > Sent: 12 February 2018 19:27 > To: ccp4bb > Subject: [ccp4bb] Resolution cut off > > Hi, >I solved a crystal structure at 1.69 A resolution with R /R free > 18 / 20 i used 1.69 A data. > > Data completeness is 100 % and for the outer shell, it's 50 %. for i /Sig > I > 1. > > Do I need to cut resolution in refinement?? > > Vandna Kukshal > Postdoctral Research Associate > Dept. Biochemistry and Molecular Biophysics > Washington University School of Medicine > 660 S. Euclid > <https://maps.google.com/?q=660+S.+Euclid=gmail=g>, Campus > Box 8231 > St. Louis, MO 63110 > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > -- Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
[ccp4bb] Resolution cut off
Hi, I solved a crystal structure at 1.69 A resolution with R /R free 18 / 20 i used 1.69 A data. Data completeness is 100 % and for the outer shell, it's 50 %. for i /Sig I > 1. Do I need to cut resolution in refinement?? Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
Re: [ccp4bb] Non crystallography question
Yes thank you very much .. I used it two years back and just blanked out. :) -Vandna On Fri, Dec 8, 2017 at 3:55 PM, amin sagar <aamin.sa...@gmail.com> wrote: > Seems like you are looking for something like DARA. > > https://dara.embl-hamburg.de/ > > -Amin. > > On Sat, 9 Dec 2017 at 3:21 AM, Vands <vanx...@gmail.com> wrote: > >> Hi All, >>Is there any Web server available where I can input my SAXS >> profile and it will give all closely matched PDB structures from the all >> available PDB. >> >> >> -- >> Vandna Kukshal >> Postdoctral Research Associate >> Dept. Biochemistry and Molecular Biophysics >> Washington University School of Medicine >> 660 S. Euclid >> <https://maps.google.com/?q=660+S.+Euclid=gmail=g>, Campus >> Box 8231 >> St. Louis, MO 63110 >> > -- Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
[ccp4bb] Non crystallography question
Hi All, Is there any Web server available where I can input my SAXS profile and it will give all closely matched PDB structures from the all available PDB. -- Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
[ccp4bb] How to rotate subunits
HI all, I have a Structure of dimer where I would like to rotate one monomer with respect to other to know the interface surface area buried in different orientations. which software should I use to generate different orientation? thanks for the help. -- Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
[ccp4bb] How to determine Quaternary symmetry
Hi , I have a protein which has A4 stoichiometry. I am trying to find symmetry component which should be D2 but one axis looks like translated which does not make it perfect D2. I am wondering if there is any tool which I can use to determine Quaternary symmetry. thanks -- Vandna Kukshal Senior Scientist Dept. oncology Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
[ccp4bb] NCS axis detrmination
Hi every one , I am looking for a tool to perfectly determine the NCS axis. I have two forms of crystals where diamer is with NCS but on a comparison of both forms, it looks like NCS axis is little off when i superpose two forms, i would like to measure rotation or translation between axes . -- Vandna Kukshal Senior Scientist Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
