[ccp4bb] PhD studentship available

Dear all, If you have any promising undergraduate or masters level students I would be grateful if you could point them to the following, funded, PhD opportunity in my laboratory. They are welcome to send me an email for an informal chat prior to an application. "Molecular basis of C-reactive

Re: [ccp4bb] 3D printing format

If it helps an academic colleague of mine has been developing hi-res full-colour 3D printed molecule models for the last 6 months or so and is very happy to help design and make any molecules of interest. These can include mini-magnets to click pieces together (ligand binding etc). I’ve

[ccp4bb] PhD studentships available

Dear colleagues, A number of PhD bursaries have become available at my institution. I would be grateful if you could direct any UK/EU students who might be looking for such opportunities to the following link: http://www.port.ac.uk/postgraduate-research/funding/phd-biomedical-and-biomolecular/

[ccp4bb] Opportunity for Object-Recognition and Augmented Reality Programmer

Posted on behalf of a colleague: Opportunity for Object-Recognition and Augmented Reality Programmer: - University of Portsmouth - Six-month Postdoctoral Research Fellow, Grade 7 (spine-point 35) - £18k for 6 months - Starts 5th January 2015 - Based in the School of Creative Technologies, in

[ccp4bb] Space group numbers

Dear ccp4bb, Could someone either provide, or point me to, a list of space-groups relevant to protein crystallography just by space group number? I can find lots of tables that list them by crystal system, lattice etc. but no simple list of numbers. Thanks, Simon

Re: [ccp4bb] Space group numbers

Hi all, Thanks for your help. CORRECT.LP includes precisely the information I was after. Also Ian Tickle’s article on http://www.ccp4.ac.uk/html/alternate_origins.html is very helpful. Simon

[ccp4bb] Structural Biology post-doc position, Portsmouth UK

on the following link (job reference 10012179 under external vacancies (EU only)): https://port.engageats.co.uk Closing date is 27th July with interviews aimed for 11th August. I am happy to be contacted informally for further information. Thanks! Simon -- Dr. Simon Kolstoe Institute of Biomedical

[ccp4bb] Script problem

Hi there, I've got a text file with multiple conformations of a ligand that has been docked to a protein using autodock, which I am trying to split into separate pdb files in order to visualise in pymol/coot etc. Previously I've used the script pasted below, but it is now falling over just

Re: [ccp4bb] Linux vs MacOS for crystallographic software

I am routinely having the Mac vs Linux conversation with crystallographers and new students, especially given the price of Macs. Generally I think that the extra money spent on a Mac pays for less time spent messing around installing software, sorting out dependencies, swearing at the less

[ccp4bb] Finding obsolete pdb entries

Dear ccp4bb, About 6 years ago I noted a couple of structures I was interested in were removed from the pdb. I saw in a recent email discussion that it is possible to access obsolete entries, however unfortunately I do not have the pdb code of the structure I am interested in - and neither

[ccp4bb] Homology modelling

Dear ccp4bb, One of my colleagues is interested in how a certain protein differs between species. He's done a blast search, collected all the aligned sequences, and emailed them to the crystallographer to tell him the implications of the sequence changes. Although I am not at all confident

[ccp4bb] xds question

Dear ccp4bb, I am quite a fan of XDS and have just upgraded to the latest version. Normally, to assess the quality of my data, I look at the tables in CORRECT.LP and especially the table SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = 0.0 AS FUNCTION OF RESOLUTION. However in my latest run

[ccp4bb] Low resolution MR

Dear CCP4bb, I've just started on a new project and was rather excited to see protein spots for my first few crystals at Diamond the other day. The only problem is that the reflections only went out to 8.5A. As it should be possible to get a solution using molecular replacement (and

[ccp4bb] Corrections in Sherwood Cooper

One of my colleagues asked if I could post the following to the ccp4bb: Thanks to very helpful feedback, there is now a fairly comprehensive set of curations for the new 'Crystals, X-rays and Proteins' (Sherwood and Cooper) at the following link: http://www.ucl.ac.uk/~rmhajc0/ The first

Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

?. It is whilst asking these two questions that rules of thumb become somewhat handy, especially when they coincide with the rules of thumb used by the referees. Simon On 28 Oct 2010, at 10:28, Eleanor Dodson wrote: Oh cynic! Eleanor On 10/27/2010 09:01 PM, Simon Kolstoe wrote: Surely

Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

Surely the best model is the one that the referees for your paper are happy with? I have found referees to impose seemingly random and arbitrary standards that sometime require a lot of effort to comply with but result in little to no impact on the biology being described. Mind you

[ccp4bb] CIF format frustrations

Dear all, What's the best way to convert a coordinate cif file to a pdb (without compiling a program, installing new utilities, writing script files...)? Cif2mtz works for the reflection file however coordconv doesn't have a cif option. If I try using Coot I get a mangled pdb file that

Re: [ccp4bb] Beginning crystallography text

Gomis-Rüth wrote: Could you please let us know when it appears ? A message to the ccp4bb would be really very much appreciated. Best, Xavier Simon Kolstoe escribió: FYI an updated version of the Sherwood book will hopefully be published in the next few months. Simon On 10 Jul 2010, at 18:04

Re: [ccp4bb] Beginning crystallography text

FYI an updated version of the Sherwood book will hopefully be published in the next few months. Simon On 10 Jul 2010, at 18:04, Vineet Gaur wrote: Hi, I found Crystal, X-rays and Proteins by Dennis Sherwood very helpful in understanding the basic concepts of crystallography. However,

[ccp4bb] Another scaling question

Dear CCP4bb, I am still playing around scaling two datasets together and have noticed another interesting behavior in scala. If I scale all my data (from 1.5A to 51A) I get 100% completeness in my outer shell, 98% in my inner shell and 99.9% overall, stats that I am normally quite happy

Re: [ccp4bb] Scaling question

: this is not normally recommended since they are pretty inaccurate (look in the Excluded data tab of ccp4i/Scala) If you are merging strong weak datasets it should do the right thing, I think. Phil On 7 Jun 2010, at 15:09, Simon Kolstoe wrote: Dear CCP4bb, I was wondering if someone

[ccp4bb] Scaling question

Dear CCP4bb, I was wondering if someone could tell me how mosflm and scala deal with overloaded reflections. From my understanding mosflm extrapolates the overloaded peaks but then scala throws them out completely - is this right? If so am I right to not worry about contamination from

[ccp4bb] Cavity filling

Dear ccp4bb A structure I have recently finished has a cavity with four waters in it. I am wondering if I might be able to fit a small molecule in the same place. Does anyone know a way of making some type of map of this cavity and then searching through a small molecule library to see

[ccp4bb] Map averaging question

Hi, I have 20 identical monomers in my asu of a 2.5A structure. We have previously model built all twenty monomers and used strict NCS in the refinement, however I would like to compare this with the maps generated by building one monomer into an averaged map and then replicating it nineteen

[ccp4bb] Phaser question

Dear all, In the phaser .sol file what do the two LLG's correspond to on the SOLU SET line eg SOLU SET RFZ=20.7 TFZ=35.4 PAK=0 LLG=1699 LLG=2821 Do they show an initial and a refined LLG or do they correspond to the rotation and translation function as in the Z scores? I checked the

Re: [ccp4bb] Hanging vs. Sitting

It's also easier to fish the crystals out of the solution with a hanging drop. Simon On 1 May 2009, at 06:35, Debajyoti Dutta wrote: Hi, From the experiance of mine I can tell you that the crystal size sometimes matters between these two methods. Hanging drop may yield bigger

Re: [ccp4bb] Computer hardware and OS survey

Hi Todd, I've found, in two institutions I have now worked for, that the tradeoff is between IT support and the hardware/software you want to use. When our group moved institutions recently our new IT department told us that they would only support managed desktops on windows machines.

[ccp4bb] Refmac dictionary problem

Dear ccp4bb, I've finally gotten around to updating my ccp4 to version 6.1.1 with the default refmac 5.5.0072 that comes with this from the ccp4 downloads site. I am working on relatively high resolution structures with a number of alternate conformers for certain amino acids which I put

Re: [ccp4bb] Refmac dictionary problem

Thanks to Robbie Joosten who suggested updating to refmac 5.5.0090 which seems to be happy with alternate conformation again. I thought it was probably worth mentioning on the list that the ccp4 bundled refmac has this bug. Simon On 17 Apr 2009, at 14:07, Simon Kolstoe wrote: Dear

Re: [ccp4bb] CCP4 tcl installation problem (mac)

Dear ccp4bb, Thanks for the help. To summarise: 1) CCP4's tcl/tk installs into /usr/local/X11/bin 2) To point imosflm to this version of Tcl/Tk the line export MOSFLM_WISH=/usr/local/X11/bin/wish8.4 needs to be in a file called .bash_profile NOT .profile for some reason (but not if you are

[ccp4bb] CCP4 tcl installation problem (mac)

Dear ccp4bb, I'm trying to update Tcl/Tk on a mac running OSX5.6 as my version of mosflm has suddenly started crashing when trying to autoindex, so I figured the best thing to do was to reinstall both mosflm and its dependencies. So I went to the CCP4 download page and used the Daresbury

[ccp4bb] RMSD's authority

Dear ccp4bb, Can anyone point me to a table/paper that gives acceptable RMSD's for bond lengths and angles against resolution? We have had two different referees for a paper contradict each other and I am not sure what to use as a good authority for this. Thanks, Simon

Re: [ccp4bb] Crystallographic computing platform recommendations?

I've gone off computers completely after finding that if I stare hard enough at my diffraction pattern I can sketch the density by hand :-)! Actually it's OSX for me because I view myself as a scientist who uses computers rather than a computer expert who uses science. Linux is just that

[ccp4bb] New XDS question

Hi, I am trying to process data with the new XDS version (June 2nd) however the new space group determination sub-routine is picking the wrong space group. Can I simply run CORRECT after the INTEGRATE step as in the old version putting in the space group I want? If so is there no longer

[ccp4bb] Validation Question

Dear ccp4bb, I have heard from many people that molprobity is the gold standard as far as validation is concerned. As I am just about to deposit a structure I therefore figured it was best to use molprobity in guiding the final stages of my refinement. I do not have enough data to

[ccp4bb] Coot problems on mac...

Has anyone found a solution to the X window problem on macs running 10.5.2? Both Coot and pymol are becoming almost unusable by freezing frequently because of X11 not responding. I've upgraded my X11 to 2.1.4 from the webpage http://trac.macosforge.org/projects/xquartz/ wiki/ but the

[ccp4bb] Missing reflections

Dear CCP4bb, I was looking through the REFMAC manual today and found the following advice: Completing the data to include all possible hkls. Should do this after data reduction, and certainly before using REFMAC. This is now done with the uniqueify script. It is best done using CCP4i.

Re: [ccp4bb] Missing reflections

phenix.refine does. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Wed, 12 Mar 2008, Simon Kolstoe wrote: Dear CCP4bb, I was looking through the REFMAC

Re: [ccp4bb] XDS and overlaps

, Herman -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kay Diederichs Sent: Thursday, February 21, 2008 3:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] XDS and overlaps Simon Kolstoe schrieb: Whilst we are on the subject of XDS... I had

Re: [ccp4bb] XDS and overlaps

or wrong. Simon On 21 Feb 2008, at 17:32, Michele Lunelli wrote: Simon Kolstoe wrote: I converted the resulting XDS_ASCII.HKL using xdsconv and then f2mtz ready for phaser and refmac. Sorry if this is obvious, but you should also run CAD after f2mtz, as reported at the end of the log file