[ccp4bb] Postdoctoral position
We are seeking a highly motivated postdoctoral fellow to investigate novel regulation mechanisms of ubiquitinating enzymes. Our lab at the Hebrew University of Jerusalem combines cutting-edge structural biology, biochemistry, cell biology and molecular biology techniques to study the molecular mechanism of protein ubiquitination and ubiquitin-like modification. Applicants should possess a strong background in molecular biology and biochemistry with emphasis on protein purification. Experience in X-ray crystallography is advantageous but not mandatory. Prospective applicants are invited to send CV and contact information of three referees to Dr. Reuven Wiener at reuv...@ekmd.huji.ac.il . -- Reuven Wiener, PhD Department of Biochemistry and Molecular Biology The Institute of Medical Research Israel-Canada Hebrew University, School of Medicine Ein-Kerem, Jerusalem, 91120 Israel E-mail: reuv...@ekmd.huji.ac.il Phone: 972-2-675-7327
Re: [ccp4bb] RMSD between superposed structures without moving
Hi Johannes, Did you read the PymoWIKI entry on the align command? https://pymolwiki.org/index.php/Align#RMSD I think this should give you what you want within PyMOL. Btw, there is a nice dedicated PyMOL mailing list https://pymolwiki.org/index.php/PyMOL_mailing_list It is rather low traffic, but the replies are generally from the developers or very knowledgeable users. Hope this helps, Folmer Fredslund On 2017-08-27 13:09, Johannes Sommerkamp wrote: Hello everybody, I have superposed two structures based on the central beta-sheet CA atoms with the "super" command in Pymol. Now, I want to calculate the RMSD between ALL atoms or ALL CA atoms without moving the structures again. The rms_cur command in Pymol would do that, but only works if all atom identifiers match. Adding "transform=0" to the super, oder align command still does the alignment and moves the structure but does not show the movement. Is there an easy way to just calculate the all atom RMSD between two already superposed structures in pymol or any other programm? Thanks in advance! Johannes
Re: [ccp4bb] RMSD between superposed structures without moving
May be you should try pdbefold server. It provides rmsd between equivalent CA atoms of superimposed structures. All the best. Vipul Panchal, Ph.D. student CSIR-IGIB (M)- 091 7678617949 On 27-Aug-2017 4:50 PM, "Johannes Sommerkamp" < 155b9e78396e-dmarc-requ...@jiscmail.ac.uk> wrote: > Hello everybody, > I have superposed two structures based on the central beta-sheet CA atoms > with the "super" command in Pymol. > Now, I want to calculate the RMSD between ALL atoms or ALL CA atoms > without moving the structures again. The rms_cur command in Pymol would do > that, but only works if all atom identifiers match. Adding "transform=0" to > the super, oder align command still does the alignment and moves the > structure but does not show the movement. > > Is there an easy way to just calculate the all atom RMSD between two > already superposed structures in pymol or any other programm? > > Thanks in advance! > Johannes > > -- > Johannes Sommerkamp > Ruhr-Universität Bochum > AG Röntgenstrukturanalyse an Proteinen, LS Biophysik, ND04/396 > Universitätsstraße 150 > 44801 Bochum > Tel: +49-(0)234/32-25754 >
[ccp4bb] RMSD between superposed structures without moving
Hello everybody, I have superposed two structures based on the central beta-sheet CA atoms with the "super" command in Pymol. Now, I want to calculate the RMSD between ALL atoms or ALL CA atoms without moving the structures again. The rms_cur command in Pymol would do that, but only works if all atom identifiers match. Adding "transform=0" to the super, oder align command still does the alignment and moves the structure but does not show the movement. Is there an easy way to just calculate the all atom RMSD between two already superposed structures in pymol or any other programm? Thanks in advance! Johannes -- Johannes Sommerkamp Ruhr-Universität Bochum AG Röntgenstrukturanalyse an Proteinen, LS Biophysik, ND04/396 Universitätsstraße 150 44801 Bochum Tel: +49-(0)234/32-25754
