Re: [ccp4bb] Refining Metal Ion Occupancy

Straightforward in Refmac...(a CCP4 package)... >From my iPhone On 6 May 2014, at 18:02, "Chris Fage" wrote: > Hi Everyone, > > In my 2.5-angstrom structure, there is negative Fo-Fc density > surrounding a metal ion after refining in Phenix. From anomalous > diffraction I am certain of the met

Re: [ccp4bb] Refining Metal Ion Occupancy

I have used CNS before, but not for this sort of refinement. I see in the bindividual.inp file that I can "select atoms to be included"--it is defaulted at "known and not hydrogen". Do you know the proper nomenclature for selecting a Zn ion in chains A and B? Thanks, Chris On 5/6/14, Steven Herro

Re: [ccp4bb] Refining Metal Ion Occupancy

Refining the occupancy will help your R-factor and flatten your density, but you need to be careful to also refine the B-factor of the metal ion. Don't refine both the occupancy and the B-factor during the same run (the two are correlated at this resolution), refine the occupancy of just the m

Re: [ccp4bb] Script for Comparing Structurally-Similar Proteins

Hi, I love using the ESCET algorithm developed by Thomas R. Schneider, it calculates error-scaled difference distance matrices, identifies domains very precisely, generates pml of aligned and coloured molecules... I just love it. More info: http://www.ncbi.nlm.nih.gov/pubmed/10818348 http://www

Re: [ccp4bb] SOS from last century!

Dear Charlie, I still use molscript quite a bit, it is not so old fashioned as you might think. Raster3D is even in the standard repository of Debian. You need to use the command line option '-r' in order to create Raster3D output. You can use the pipe molscript -r -in your_molscipt.inp | render

[ccp4bb] SOS from last century!

I need help with a problem whose dimensions I perceive, but cannot surmount. It appears to be very important for me to re-make an illustration I made long ago using molscript. For various reasons, I cannot think of a way to do this with Pymol. I want to highlight active site residues by showing

Re: [ccp4bb] Refining Metal Ion Occupancy

Hi Chris, > In my 2.5-angstrom structure, there is negative Fo-Fc density > surrounding a metal ion after refining in Phenix. From anomalous > diffraction I am certain of the metal's identity and position in each > monomer. Also, the ion is appropriately coordinated by nearby side > chains. Shoul

Re: [ccp4bb] Script for Comparing Structurally-Similar Proteins

I would also be very interested in acquiring such a script, if one exists and the savvy author is willing to share it. Jaime __ Jaime L. Jensen GRA Department of Chemistry and Biochemistry North Dakota State University email: jaime.jen...@ndsu.edu

[ccp4bb] Refining Metal Ion Occupancy

Hi Everyone, In my 2.5-angstrom structure, there is negative Fo-Fc density surrounding a metal ion after refining in Phenix. From anomalous diffraction I am certain of the metal's identity and position in each monomer. Also, the ion is appropriately coordinated by nearby side chains. Should I be r

Re: [ccp4bb] project and literature organization software (laboratory information management software)

Hi Tobias, We use LabTrove: http://www.labtrove.org/ Pros: Relatively easy local install Revision control Ability to attach any file Cons: clumsy blog formatting does not lay eggs. Regards, Dmitry It is a bit clumsy being based on a blog engine and does not lay eggs… But it works fin

Re: [ccp4bb] books to go

Thank you all for your interest in my books - the response was overwhelming! All books have found a new home and were sent to their destination with the addressee informed by mail. Sorry if it wasn't you - I have tried to help people who are starting up or who are teaching and do not have resour

[ccp4bb] Script for Comparing Structurally-Similar Proteins

Dear Crystallographers, In a former lab we had a script which would read DALI output, automatically download the structurally-similar proteins, superimpose them, and color by regions superimposed. That was in the days of O. Does anyone have a similar-functioning script for CCP4MG, pymol, or oth

[ccp4bb] PhD Bayesian protein structure prediction

Hi everybody, One PhD position is available in the group of Assoc. prof. Thomas Hamelryck, Copenhagen, Denmark. The subject is inference of protein structure using state of the art probabilistic methods. Knowledge of Bayesian probabilistic modelling, machine learning and C++ is a strong plus. Know

[ccp4bb] Position at Diamond Light Source

Can I please draw your attention to a post we have for a software scientist at Diamond Light Source: http://www.diamond.ac.uk/Careers/Vacancies/All/DIA0919_CH.html Closing date is 25th May. Informal enquiries to myself but please follow the instructions on the web page to apply. Best regards