Re: [ccp4bb] ccp4i:buccaneer+refmac curiosity on Intel mac osx only

Dear Bryan, are there any differences when you look at the input scripts for the differing jobs? Tim On Wed, May 11, 2011 at 06:54:38PM -0400, Bryan Lepore wrote: it seems that shift-double-clicking on a buccaneer+refmac job in ccp4i and rerunning it with everything the same (except output

[ccp4bb] Macromolecular Crystallographer Post in the Industrial Liaison office at Diamond

Dear All, we have a permanent post available for a Macromolecular Crystallographer in the Industrial Liaison Group at Diamond. Full details and how to apply can be found at http://www.diamond.ac.uk/Home/Jobs/Current/DIA0619-TH.html. (Closing date for receipt of applications is the 17th June

[ccp4bb] Technician Position available in Milan

Dear all, a technical position is available to work in the Crystallography Unit of the IFOM-IEO-Campus in Milan. (http://www.ifom-ieo-campus.it/joinus/detail_jobs.php?docuID=1566) The position is available immediately, and will be granted until March 2012. We are looking for a person who will

[ccp4bb] Bug in Pointless version 1.5.19

If anyone has picked up a very recent version of Pointless from our web site here, they should note that version 1.5.19 was seriously broken [1]. Versions 1.5.17 and earlier are OK, as is the very latest 1.5.21 which I've just put there [2] I don't think the broken versions have got into any

[ccp4bb] mutation and minimization

Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Thanks. Andreas --

Re: [ccp4bb] mutation and minimization

Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. PyMOL has a Mutagenesis wizard but

Re: [ccp4bb] mutation and minimization

You can try Swiss-PDB viewer.. 2011/5/12 Thomas Holder thomas.hol...@tuebingen.mpg.de Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple

Re: [ccp4bb] mutation and minimization

Hi Andreas Without the x-ray data, phenix.pdbtools might do this (http://www.phenix-online.org/version_docs/dev-712/pdbtools.htm) From the website: [phenix.pdbtools can] Perform model geometry regularization. Minimize geometry target to idealize bond lenghths, bond angles, planarities,

Re: [ccp4bb] mutation and minimization

Or try SCWRL from Dunbrack's lab... --- On Thu, 5/12/11, gauri misra kamga...@gmail.com wrote: From: gauri misra kamga...@gmail.com Subject: Re: [ccp4bb] mutation and minimization To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, May 12, 2011, 12:52 PM You can try Swiss-PDB viewer.. 2011/5/12 Thomas

[ccp4bb] Graduate Teaching Assistants- Birkbeck University of London

There are two graduate teaching assistant available for October 2011 in the Dept of Biological Sciences, Birkbeck University of London. These positions require you to teach and support teaching for up to 50% (17.5 hours a week) of your time during term and to undertake a Ph.D with a member of

Re: [ccp4bb] mutation and minimization

Hi If you are familiar with turbo-frodo, you can use it for mutagenesis and refinement . Just go inside the editing menu, replace the residue, save the file and REFINE the residue. You can also select the stretch of residues by picking the first and last residues so you will get the

[ccp4bb] B factor

Hey all, I would like to make one ribbon diagram of the structure showing the B factor in different colors (contour levels). I am using pymol but it is not representing the perfect contour level of B factor. Is any other program where I can change the color according to B factor? Thanks

[ccp4bb] how convert SF to intensities

Dear ccp4 users, I need to generate intensities from a model (.pdb). That is, I think that a correct procedure could be to convert model to structure factor and then obtain intensities squaring the SF.Does anyone know how can I do?Thanks in advanceFulvio Saccoccia

Re: [ccp4bb] how convert SF to intensities

Hi Fulvio, a possible option that will do what you want (almost - you will get SF that you will have to square): http://phenix-online.org/documentation/fmodel.htm Pavel. On Thu, May 12, 2011 at 12:13 PM, Fulvio Saccoccia fulvio.saccoc...@uniroma1.it wrote: Dear ccp4 users, I need to

Re: [ccp4bb] how convert SF to intensities

That is, I think that a correct procedure could be to convert model to structure factor and then obtain intensities squaring the SF. Does anyone know how can I do? Use sftools -- Hurry up before we all come back to our senses! Julian, King of Lemurs

[ccp4bb] Detecting and dealing with Pseudotranslation and/or twinning

I’ve been working on a troublesome protein structure. The native protein forms crystals that diffract to 2.75A and belong to P212121 (55.179 64.316 233.748 90.000 90.000 90.000) with 4 molecules in the ASU. I have 3 versions of the same protein where selenomethionine mutations are

Re: [ccp4bb] how convert SF to intensities

Hi, Use SFALL to convert coordinates to structure factors...and then use mtz2various to convert to intensities...use the scalepack format under mtz2various. On Thu, May 12, 2011 at 3:13 PM, Fulvio Saccoccia fulvio.saccoc...@uniroma1.it wrote: Dear ccp4 users, I need to generate intensities

Re: [ccp4bb] B factor

hello sir , in chimera its available in module Render by Attribute. go through this link http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html . regards On Fri, May 13, 2011 at 12:01 AM, Luthra,Amit alut...@uchc.edu wrote: Hey all, I would like to make