Re: [ccp4bb] Van der waals force

jiri, VDW forces are always acting and between any pair of atoms the optimal distance (most favourable interaction energy) depends on the pair of atoms involved in the interaction, but is a big bitter than the sum of atomic radii all the best herman Herman van Tilbeurgh Professor structural

Re: [ccp4bb] Van der waals force

Hello, van der Waals interactions are very weak, this is why we usually speak about van der Waals contacts rather than interactions. These are usually in the range of 3.5-3.8/4 Å (smaller than that may indicate a close contact or steric clash of an atomic model under refinement),

Re: [ccp4bb] ITC data clarification.

hi dharma your ITC data suggest at least that your complex also exists in solution ITC never will answer to the question whether this is a “biological” interface one way getting around this, would be to check the response of your mutant versus WT in biological assay ALA substitutions

[ccp4bb] Van der waals force

Hi I just have a basic question if the Van der waals interaction will exist between the hydrophobic residues or it can also be contributed by the polar residues as well. What distance is required for the Van der waals interaction. best Jiri

[ccp4bb] ITC data clarification.

Hello CCP4 users, Based on the crystal structure of a two molecule protein complex, I have mutated (alanine substitutions) one of the putative binding interface. The mutant binds with much higher affinity than the wild type. However, the signature plot of ITC data reveals a decrease in the

[ccp4bb] Postdoctoral Fellow Position

Postdoctoral Fellow Position Parashar laboratory at University of Delaware College of Health Sciences, is currently seeking a Postdoctoral Fellow to perform structure-function studies of proteins regulating bacterial signaling.  Qualifications:·  Ph.D. in Biochemistry, Molecular Biology,

Re: [ccp4bb] covalent bond

Gerado John is correct that you can modify the restraints model to include a covalent bond. Also in more recent version of Phenix, if the input geometry is approximately correct, the bond can be automatically linked. If you send me the input file, I'll take a closer look. Cheers Nigel ---

Re: [ccp4bb] covalent bond

You can add a covalent bond by modifying this part of the PHENIX .def file via the gui: geometry_restraints.edits { excessive_bond_distance_limit = 10 bond { action = *add delete change atom_selection_1 = None atom_selection_2 = None symmetry_operation = None

Re: [ccp4bb] covalent bond

Is that format correct? Eleanor On 7 December 2017 at 17:32, gerardo andres < 130afa955101-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi everyone. I´m trying to make a covalent bond between a cystein residue > of a protein and its ligand, but always that I do the refinement by Phenix, > the

[ccp4bb] covalent bond

Hi everyone. I´m trying to make a covalent bond between a cystein residue of a protein and its ligand, but always that I do the refinement by Phenix, the ligand is placed outside of its electronic density. I edited the PDB file like this: LINK         SG  CYS A 215                 C02 LIG C   1

[ccp4bb] Open Research Positions: Structural Biophysics of Protein Allostery, in New York City

The Daniel Keedy Lab at the ADVANCED SCIENCE RESEARCH CENTER (ASRC) AT CUNY in New York City has available positions for a POSTDOCTORAL SCHOLAR and a RESEARCH ASSOCIATE starting in 2018. The lab’s goal is to elucidate the role of protein flexibility in allosteric regulation — and to use that

Re: [ccp4bb] secondary structure prediction

I'm fond of RaptorX ++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago pr...@uchicago.edu https://voices.uchicago.edu/phoebericelab/ From: CCP4 bulletin board

Re: [ccp4bb] secondary structure prediction

yes | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月07日 09:11，zheng zhou 写道： Thanks for many advices. I was not clear in the previous email. I know the close homologous protein (20% identity, total 500aa), but the fragment hits (30~40aa, identity 40~50%) are from other

[ccp4bb] Data analysis for Electron Microscopy, Machine Vision, and Team Leader positions at Diamond Light Source

Dear All, Please find enclosed details of positions with the Data Analysis Group at Diamond Light Source: Job Title: Data Analysis Scientist / Senior Software Scientist - Electron Microscopy Post Type: Full time / 3 year Fixed Term Contract Salary information: £32,805 to £38,593 (Discretionary

[ccp4bb] PostDoctoral Position in Structural Biology - Structural Studies of Ribosome Functional Complexes

Dear Colleagues, We ​ ​ have an open position for a P ost D oc ​ ​ in my laboratory ​ at the University of Illinois at Chicago, USA ​ ​ (https://bios.uic.edu/bios/people/faculty/yury-polikanov). ​ ​ The research in o ur laboratory is focused on understanding basic principles of protein synthesis

[ccp4bb] Problems with QT graphs in Aimless log files

Hi, I'm running CCP4 version 7.0.047 on a number of Linux PCs with OpenSUSE Linux as part of a course. I'm having problems with visualising Aimless log files, at least the graphical part. The graphs simply don't show up in the QT visualiser. Scala doesn't suffer from the same problem. Has

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

I see. Thanks Eleanor! On Thu, Dec 7, 2017 at 4:33 AM, Eleanor Dodson wrote: > Rf_used is the R factor for the non-free reflections. > > If you do the plot the 4SSQ/L**2 is converted to As.. > > E > > On 7 December 2017 at 11:50, Xiao Lei wrote:

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

Rf_used is the R factor for the non-free reflections. If you do the plot the 4SSQ/L**2 is converted to As.. E On 7 December 2017 at 11:50, Xiao Lei wrote: > Thanks Eleanor, yes, I looked at that table and tried to find out the > Rfree and R, I know the 4SSQ/LL means

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

Thanks Eleanor, yes, I looked at that table and tried to find out the Rfree and R, I know the 4SSQ/LL means column means resolution bins but I did not know what column means Rfac (The Rf_free means Rfree I guess). On Thu, Dec 7, 2017 at 2:58 AM, Eleanor Dodson <

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

This works. Thanks a lot Bernhard. On Wed, Dec 6, 2017 at 5:07 PM, Bernhard Rupp wrote: > You can find these numbers in the header of the output model coordinate > file. > > > > BR > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao >

[ccp4bb] Postdoctoral Fellowship in Structural Biology at TIFR Hyderabad, India

‘Postdoctoral Fellow’ position in structural biology at TIFR, Hyderabad, India A ‘Postdoctoral Fellow’ position in structural biology is available in the laboratory of Dr. Kalyaneswar Mandal at the Tata Institute of Fundamental Research Hyderabad, India. The position is funded by the Wellcome

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

Dont you look at the graphs from the log file? This table gives you all sorts of information including R and Rfree in resolution shells.. Eleanor Things for loggraph, R factor and others $TABLE: Cycle 11. Rfactor analysis, F distribution v resln :

[ccp4bb] Postdoc in structural biology of protein evolution and adaptation

Dear all, We are looking for a postdoc to work within a multidisciplinary project “Evolution of new genes and proteins” at Uppsala University, Sweden (http://uu.se/en/). The project is financed by the Wallenberg foundation and aims to understand how structure and function are intertwined in

[ccp4bb] structural biologist to work on cancer drug discovery

Please respond direct to Alex. Dear Colleagues, I have a 16 month postdoctoral position available immediately in my lab at the Astbury Centre, University of Leeds, for a versatile structural biologist to work on cancer drug discovery in a collaboration with the Northern Institute for Cancer