[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 protein (CRP) binding to the lipid bilayer – a flag for complement targeting and the generation of pro-inflammatory signals in the innate immune system" https://www.findaphd.com/search/ProjectDetails.aspx?PJID=81668=1286 Structural studies of biological macromolecules and their interactions underpin our understanding of function and guide the development of drug interventions to combat disease. The aim of this project is to define the structural detail of the interaction of the pentameric human acute phase C-reactive protein (CRP) with compromised lipid bilayers. This targets the innate immune system to resolve tissue damage, but also produces a monomeric variant of CRP that generates pro-inflammatory signals. The PhD project student will express and purify native and mutated forms of CRP from tissue culture cells, and crystallise the proteins in cubic lipid phase for structure analysis by X-ray diffraction methods. This will help to understand how CRP differentiates between sick and healthy cells. An experienced team working in the biophysics and crystallography of CRP will supervise the student. There will be opportunities to work at the Membrane Protein Laboratory (Harwell) and collect X-ray diffraction data at a synchrotron radiation source. In addition there will be access to a large number of training resources available through the graduate school including those geared toward improving presentation skills, time-management and project organisation skills, reviewing literature, thesis writing, data analysis and statistics, and related training modules. Portsmouth is a vibrant waterfront city on the south coast of England and is within easy reach of London. The city is compact and friendly with the university at its heart. More information about living in the city and working at the university can be seen here: http://www.port.ac.uk/virtualtour/ Funding Notes Home/EU applicants only. Please use the online application form and state the project code (BIOL2900217) and studentship title in the personal statement section. Funds will be provided for 3 or 4 years which will include: bursary (at current RCUK rates), University fees (UK/EU rate). Thanks, Simon
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 included a picture of one of his latest ones. His email address is: darren.gow...@port.ac.uk Simon On 15 May 2015, at 13:46, Christine Zardecki zarde...@rcsb.rutgers.edu wrote: The NIH 3D Print Exchange (http://3dprint.nih.gov/) has a collection of files for 3D printing, and can generate files based on PDB ID. Christine -- Twitter: http://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB
[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/ Thanks, Simon
[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 collaboration with Biological Sciences. We are seeking to appoint a talented and enthusiastic research fellow programmer to work on an exciting new interdisciplinary project funded by InnovateUK in the areas of Molecular Bioscience and Virtual and Augmented Reality. The project will involve software development of a new research tool to bring complex 3D molecular structures to life. You must have a PhD or equivalent industrial experience in one or more of the following areas: 3D modelling and programming for simulations or games; design of Virtual Reality applications; Augmented Reality programming; Serious Games design; Object recognition programming. You will be expected to have a strong practical knowledge of several industry-standard tools in these areas, such as Unreal, Unity, Vizard, PyMol, 3DS Max, Vuforia. A strong research profile in a related area is desirable. The successful candidate will be expected to contribute to funding applications to extend the project beyond this initial Phase I contract. Please contact Dr Darren Gowers on 02392 842057 or email darren.gow...@port.ac.uk
[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
Dear ccp4bb, I’ve just got my first grant from the BBSRC and need to recruit a post-doc. The project will involve protein expression using HEK293 followed by crystallisation/data collection and conducting binding assays (Biacore, ITC, AUC etc.). The details and how to apply can be found 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 and Biomolecular Science, School of Biological Sciences, University of Portsmouth, King Henry Building, Portsmouth. PO1 2DY, UK Tel: 023 9284 2058
[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
after it creates the pdb file with the error:
expr: syntax error
csplit: }: bad repetition count
./split_results.com: line 11: syntax error near unexpected token `('
./split_results.com: line 11: `foreach f ($outputname.[0-9][0-9][0-9])'
Can any of you wizzy programmers give me a hand with getting this to work
again? (it's on a mac just in the normal terminal)
Thanks,
Simon
The script:
#!
grep '^DOCKED' output.dlg | cut -c9- my_docking.pdbqt
cut -c-66 my_docking.pdbqt my_docking.pdb
# csh to split pdb files from autodock output.
# edit outputname.
#
set outputname=output
set a=`grep ENDMDL my_docking.pdb | wc -l`
set b=`expr $a - 2`
csplit -k -s -n 3 -f $outputname. my_docking.pdb '/^ENDMDL/+1' '{'$b'}'
foreach f ($outputname.[0-9][0-9][0-9])
mv $f $f.pdb
end
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 than effective office software etc. that plagues Linux which is more of a computer experts platform. I'd say if your interest is in solving structures with the least hassle get a Mac, but if you want to develop software get Linux. Meanwhile I think windows is slowly improving as a crystallography platform - and Microsoft is perhaps no longer hated in principle - however the one student in our lab who opted to go the windows route seems very limited in the software he can run. Of course getting the highest spec machine one can afford at the time applies to all platforms. Mind you I've been using mid range MacBook Pro's for the last few years which work fine, with the added bonus that you can keep your coffee warm by placing it near the processor during MR! Simon On 29 Sep 2011, at 01:26, Jacqueline Vitali wrote: Dear colleagues, I need some advice for a new computer. (1) I have the option of an HP Z210 8 GB with a low end Quadro Nvidia 400 512 MB. --How does Coot run with this card? --I am happy with any Linux. However, the system needs updates for security purposes (the University requires it). Do I have to remake the NVidia driver every time there is a kernel update or is there a way around it for this NVidia card? Do you suggest another NVidia card (inexpensive) that is good for coot and automatically updates when the kernel is updated? (2) Second option is an IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB GDDRS. --How does Coot work with this graphics card? --Should I get more memory for Lion? --Is this platform advisable for crystallographic software for the next four years? Thank you in advance for any advice. Jackie Vitali Cleveland State University
[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 does the original publication list the pdb code. Is there a way of searching withdrawn/obsolete entries for author name, macromolecule etc. or are structures that were withdrawn over 5 years ago lost for good? Thanks, Simon
[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 that I can predict any implications based upon sequence differences, I thought I could at least have a try by mapping the different species sequences onto the existing structure and then regularising it just to see what happens (and then perhaps looking at buried surface area, electrostatics, subunit interfaces etc.). I know the program chainsaw can mutate the sequence based on an alignment, however I can't stop it pruning non-conserved residues. Does anyone know of another program that I could use to do this step? Similarly if anyone knows other software tools/methods I could use to try and work out the implications of sequence changes I would be grateful for advice. Thanks, Simon
[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 I only get a single table for all the data i.e. for signal/noise = -3.0. Is there a command I can put in my XDS.INP that will give me all the other tables or has the CORRECT.LP logfile been altered in the most recent version of XDS? (FYI my xds.inp obtained from the ESRF last week is copied below) Thanks, Simon !=== File Automaticaly generated by mxCuBE !=== X-Ray data collected at: ESRF_ID14-1 !=== Detector type: ADSC Quantum Q210 !=== Date: Fri Feb 04 03:39:09 2011 !=== User comments: JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !JOB= DEFPIX XPLAN INTEGRATE CORRECT DATA_RANGE= 1 190 SPOT_RANGE= 1 20 SPOT_RANGE= 1 4 !SPOT_RANGE= 187 190 BACKGROUND_RANGE= 1 4 SECONDS=60 MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 6 STRONG_PIXEL= 6.0 OSCILLATION_RANGE= 1.000 STARTING_ANGLE= 0.000 STARTING_FRAME= 1 X-RAY_WAVELENGTH= 0.93340 NAME_TEMPLATE_OF_DATA_FRAMES= ./data/sk1_1_???.img !STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 180 10 !TOTAL_SPINDLE_ROTATION_RANGES= 60 180 10 DETECTOR_DISTANCE= 298.55 DETECTOR= ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000 ORGX= 1014.79ORGY= 1029.10 NX= 2048 NY= 2048 QX= 0.10200 QY= 0.10200 VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 7000 3 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 ROTATION_AXIS= 1.0 0.0 0.0 INCIDENT_BEAM_DIRECTION= 0.0 0.0 1.0 FRACTION_OF_POLARIZATION= 0.98 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !== Default value recommended !AIR= 0.00026895 SPACE_GROUP_NUMBER= 0 UNIT_CELL_CONSTANTS= 0 0 0 0 0 0 INCLUDE_RESOLUTION_RANGE= 50.0 2.4 RESOLUTION_SHELLS= 15.0 8.0 4.0 3.0 2.8 2.6 2.5 2.4 FRIEDEL'S_LAW= FALSE !FRIEDEL'S_LAW= TRUE TRUSTED_REGION= 0 1.40 REFINE(INTEGRATE)= BEAM ORIENTATION CELL !== Default value recommended !DELPHI= 3.000 MAXIMUM_NUMBER_OF_PROCESSORS= 16 !MAXIMUM_NUMBER_OF_JOBS= 16
[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 whilst I am waiting for new and hopefully better crystals to grow) will MR work with only 8.5A data (100% complete)? I've spent the last couple of days playing with phaser and molrep but not had much luck so far, so was wondering if 8.5A might be a lost cause for MR? Thanks, Simon
[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 6 are the most important!
Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)
It can sometimes be struggle to find the boundary between cynicism and pragmatism! I was, however, rather bemused by Dr Joosten's 7 rules of thumb - probably all of which I use and have seen used by referees. Of course I wouldn't want to blindly advocate any of them, however their use does make life somewhat easier for those of us who use crystallography to discover things about biology compared with their use by the (rather impressive!) members of this community who are involved in theoretical/methodological development. A time comes on my projects where you have to say two things - 1) my structure is telling me x and although I can spend the next six months performing minor tweaks these will not add (or subtract) from the conclusions I am interested in and 2)when I submit this to referees will they think my structure is appropriate to draw these conclusions?. 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 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 discussions on this email list can be a useful resource for telling referee's why you don't think you should comply with their rule of thumb. Simon On 27 Oct 2010, at 20:11, Bernhard Rupp (Hofkristallrat a.D.) wrote: Dear Young and Impressionable readers: I second-guess here that Robbie's intent - after re-refining many many PDB structures, seeing dreadful things, and becoming a hardened cynic - is to provoke more discussion in order to put in perspective - if not debunk- almost all of these rules. So it may be better to pretend you have never heard of these rules. Your crystallographic life might be a happier and less biased one. If you follow this simple procedure (not a rule) The model that fits the primary evidence (minimally biased electron density) best and is at the same time physically meaningful, is the best model, i. e., all plausibly accountable electron density (and not more) is modeled. This process of course does require a little work (like looking through all of the model, not just the interesting parts, and thinking what makes sense) but may lead to additional and unexpected insights. And in almost all cases, you will get a model with plausible statistics, without any reliance on rules. For some decisions regarding global parameterizations you have to apply more sophisticated test such as Ethan pointed out (HR tests) or Ian uses (LL-tests). And once you know how to do that, you do not need any rules of thumb anyhow. So I opt for a formal burial of these rules of thumb and a toast to evidence and plausibility. And, as Gerard B said in other words so nicely: Si tacuisses, philosophus mansisses. BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Robbie Joosten Sent: Tuesday, October 26, 2010 10:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree) Dear Anthony, That is an excellent question! I believe there are quite a lot of 'rules of thumb' going around. Some of them seem to lead to very dogmatic thinking and have caused (refereeing) trouble for good structures and lack of trouble for bad structures. A lot of them were discussed at the CCP4BB so it may be nice to try to list them all. Rule 1: If Rwork 20%, you are done. Rule 2: If R-free - Rwork 5%, your structure is wrong. Rule 3: At resolution X, the bond length rmsd should be than Y (What is the rmsd thing people keep talking about?) Rule 4: If your resolution is lower than X, you should not use_anisotropic_Bs/riding_hydrogens Rule 5: You should not build waters/alternates at resolutions lower than X Rule 6: You should do the final refinement with ALL reflections Rule 7: No one cares about getting the carbohydrates right Obviously, this list is not complete. I may also have overstated some of the rules to get the discussion going. Any addidtions are welcome. Cheers, Robbie Joosten Netherlands Cancer Institute Apologies if I have missed a recent relevant thread, but are lists of rules of thumb for model building and refinement? Anthony Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 =
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 discussions on this email list can be a useful resource for telling referee's why you don't think you should comply with their rule of thumb. Simon On 27 Oct 2010, at 20:11, Bernhard Rupp (Hofkristallrat a.D.) wrote: Dear Young and Impressionable readers: I second-guess here that Robbie's intent - after re-refining many many PDB structures, seeing dreadful things, and becoming a hardened cynic - is to provoke more discussion in order to put in perspective - if not debunk- almost all of these rules. So it may be better to pretend you have never heard of these rules. Your crystallographic life might be a happier and less biased one. If you follow this simple procedure (not a rule) The model that fits the primary evidence (minimally biased electron density) best and is at the same time physically meaningful, is the best model, i. e., all plausibly accountable electron density (and not more) is modeled. This process of course does require a little work (like looking through all of the model, not just the interesting parts, and thinking what makes sense) but may lead to additional and unexpected insights. And in almost all cases, you will get a model with plausible statistics, without any reliance on rules. For some decisions regarding global parameterizations you have to apply more sophisticated test such as Ethan pointed out (HR tests) or Ian uses (LL-tests). And once you know how to do that, you do not need any rules of thumb anyhow. So I opt for a formal burial of these rules of thumb and a toast to evidence and plausibility. And, as Gerard B said in other words so nicely: Si tacuisses, philosophus mansisses. BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Robbie Joosten Sent: Tuesday, October 26, 2010 10:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree) Dear Anthony, That is an excellent question! I believe there are quite a lot of 'rules of thumb' going around. Some of them seem to lead to very dogmatic thinking and have caused (refereeing) trouble for good structures and lack of trouble for bad structures. A lot of them were discussed at the CCP4BB so it may be nice to try to list them all. Rule 1: If Rwork 20%, you are done. Rule 2: If R-free - Rwork 5%, your structure is wrong. Rule 3: At resolution X, the bond length rmsd should be than Y (What is the rmsd thing people keep talking about?) Rule 4: If your resolution is lower than X, you should not use_anisotropic_Bs/riding_hydrogens Rule 5: You should not build waters/alternates at resolutions lower than X Rule 6: You should do the final refinement with ALL reflections Rule 7: No one cares about getting the carbohydrates right Obviously, this list is not complete. I may also have overstated some of the rules to get the discussion going. Any addidtions are welcome. Cheers, Robbie Joosten Netherlands Cancer Institute Apologies if I have missed a recent relevant thread, but are lists of rules of thumb for model building and refinement? Anthony Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 =
[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 gives lots of errors when I read it into pdbset, and I have the same problem with babel. Also if the pdb has decided that cif files are the best format, are the program developers working on phasing out pdb and mtz files, and if not why not? Thanks, Simon
Re: [ccp4bb] Beginning crystallography text
For all those who asked about the new edition of the Sherwood book, it is available for pre-order on Amazon (at least on the UK version, search for Crystals, X-rays and Proteins: Comprehensive Crystallography). Simon PS Jon - do I get a commission? On 12 Jul 2010, at 11:28, F.Xavier 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, Vineet Gaur wrote: Hi, I found Crystal, X-rays and Proteins by Dennis Sherwood very helpful in understanding the basic concepts of crystallography. However, it seems that the book is out of print. It would be great, If anyone here is having an E-copy of this book and can share with us. Thanks, Vineet -- fxgr_signa.jpg
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, it seems that the book is out of print. It would be great, If anyone here is having an E-copy of this book and can share with us. Thanks, Vineet
[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 with. I tend to also look at the table in the log file which in this case reports above 98% completeness in all shells between 1.5 and 4.7A. Rmerges are 0.054 overall with 0.29 in the outer shell, which again I think is OK. However I then ran scala again in an attempt to scale with the strongest overlapping reflections in my two datasets, so limited the resolution to between 15A and 4A. Now when I look at my completeness I get 97% overall, but only 32% in the highest 15-12A shell! Is something funny going on in the program or am I really missing 70% of my data in this resolution, and if so how come the scala run with all the data doesn't report this? I am now worrying that all the data I previously thought was complete might be lacking many lower resolution reflection! Thanks, Simon
Re: [ccp4bb] Scaling question
Thanks Tim, Phil and Andrew for your answers. Just one further related question: Why is it that mosflm seems to report higher completeness than XDS on the same data (I've seen this on about 50 datasets)? I always thought it was due to mosflms peak extrapolation but it seems this isn't the answer if SCALA throws those reflections out. Thanks, Simon On 7 Jun 2010, at 15:35, Phil Evans wrote: Mosflm integrates them (profile-fitted overloads) but flags them. Pointless uses them for systematic absence tests. Scala by default ignores them, but you can include them if you want: 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 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 extrapolated peaks when combining high and low resolution datasets from the same crystal? Thanks Simon
[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 extrapolated peaks when combining high and low resolution datasets from the same crystal? Thanks Simon
[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 what might fit in it (I'm guessing there is commercial software that will do this however I am after something without large financial commitments!)? Thanks, Simon
[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 times for the refinement. On a previous structure with just two monomers I did this to good effect using coot to make my average map and then pymol to replicate the second monomer, however with twenty monomers things are a bit more complicated. So: 1. Can the map averaging function in coot cope with averaging across twenty monomers or is there another better program to use? 2. What program can I use to generate the nineteen NCS symmetry operators and then apply them to the monomer I am building? I'm guessing I'll need a script to do this - is there a webpage/tutorial that explains how to do what I imagine must be a fairly common procedure? Thanks, Simon
[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 appropriate web page and didn't see anything immediate. http://www-structmed.cimr.cam.ac.uk/phaser/documentation/phaser-2.1_key.html#MR_solved_it Thanks, Simon
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 crystals than sitting drop, that may be due to the evaporation rate(surface area). Hanging drop allow us to set different protocols also like free interface diffusion, area covered by the drp etc. These informations are gained purely by experiance. cheers Deb On Thu, 30 Apr 2009 20:40:35 +0530 wrote I have noticed that a significant majority of crystallizations are done in hanging- rather than sitting-drop configuration, and considering the significant extra labor involved in hanging drops, can only understand this preference as a historical bias. I understand that sometimes one technique works and not the other, but all things being equal, why is hanging drop still hanging around? Any insights appreciated... Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
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. We told them that wasn't good enough so they said fine run your own network which we now do. The downside is that we have to fix all problems ourselves, but the upside is that we have almost complete freedom. This is slowly leading to people getting apple laptops (through the apple educational store) and then configuring the crystallography software themselves. The bottom line is that Linux is just slightly too complicated for someone who is only a part time computer geek whereas both the flexibility and ease of use offsets the price penalty of using OSX. Mind you the only money we have for computers is from grants which probably gives us a bit more flexibility than any arrangement where the institution provides the machines. But again, I am not certain that a free $500 Linux box from my university would convince me to spend hours battling with dependencies! Simon On 1 May 2009, at 17:50, mjvdwo...@netscape.net wrote: Todd, Once upon a time I studied at an institution of higher learning. Its specialty is (and was) the education of and participation in medical sciences (I guess that could be an oxymoron, sorry). With that comes the securely keeping and sharing (as needed) of patient data. The institutional bureaucrats decided that Novell token ring networks were the best suited for that purpose and that, on the other hand, TCP/IP was inherently insecure, so they were going to do away with TCP/IP networks. Shock was on the face of the workers. All academic and scientific networks need TCP/IP. The same thing was done as Bill says: we had to go in and argue that we didn't work for the computer and network people, but they worked for us. I can't remember if we did this - this was long before the time of ssh and sftp- long ago, but today I would bring up the argument of how much grant money and overhead money (which pays for the computer and network people) scientists bring in and that without the proper tools, these things cannot be perpetuated. It would seem to me that you cannot run crystallography efficiently (!) on one platform alone (no matter which one you choose). Some tasks, like grant writing, are easily done on some platforms (windows or Mac, but not Unix/Linux) etc. So the driving force should be what needs to be done and how to best do it. With that should come the realization that making you as a scientist less efficient will translate into less ability to attract funds (because funds are competitive), which does not affect only you, but the entire institution. Things should not be and are not all about money, but that argument always works - hit them in the pocket book and they will reconsider. There are ways of cutting costs without doing away with capabilities. You can have groups of people who use Windows and have support for that. At the same time you can have other groups of people who use Macs with support for that. And you can make a rule that if you want to be different from everyone in your group, you will belong (for computing needs only) to the other group. That is how our University tries to run things. Mark -Original Message- From: William G. Scott wgsc...@chemistry.ucsc.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Fri, 1 May 2009 9:39 am Subject: Re: [ccp4bb] Computer hardware and OS survey Hi Todd: One option on Windows is to install Ubuntu in a mode that lets it run nested as a guest in a window within the host operating system. This is now one of the options on the (free) Ubuntu install CD. I've actually not tried it, so I can't tell you how good it is, but my guess is that it works in a way that is very similar to VMware of Parallels on OS X. But if you already have made the investment in OS X hardware, I really would recommend standing your ground on this. The main arguments to make, I believe, are the following: 1. Scientists really need to have ready access to unix-based operating systems. OS X and Linux are two such variants, but the main arguments in favor of each are the same. I'm flattered you liked my website, but frankly I don't think its existence is a compelling argument. (In fact, I made the thing originally as a publicly accessible log/whine of my trials and tribulations in a do- it-yourself sys admin environment. You could point out that if an idiot like me can do this, anyone can.) You could probably get by with work-around solutions on Windows, but why should you be forced to hobble yourself. 2. Your institutional bureaucrats should not, as a matter of principle, dictate to you what your computer or other equipment needs are.
[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 in using the mac version of Coot 0.6-pre-1, something else I updated last week. However, when I now run refmac on a pdb file with two conformers for certain amino acids it seems that refmac doesn't recognise them and distorts the bond angles/lengths. I've checked the format of the pdb file outputted by coot and this seems normal (see below), which suggests to me that the new refmac doesn't like the A and B suffix on the residue name. Is this a known bug, and if so is there an easy fix? Thanks, Simon ATOM860 N ASER A 107 -1.909 -4.393 -14.018 0.50 10.31 N ATOM861 N BSER A 107 -1.942 -4.416 -14.064 0.50 8.93 N ATOM862 CA ASER A 107 -0.633 -3.962 -14.010 0.50 6.64 C ATOM863 CA BSER A 107 -0.669 -4.036 -13.974 0.50 5.74 C ATOM864 CB ASER A 107 -0.549 -2.697 -13.710 0.50 7.45 C ATOM865 CB BSER A 107 -0.505 -2.657 -13.639 0.50 6.94 C ATOM866 OG ASER A 107 -0.877 -1.986 -12.787 0.50 16.90 O ATOM867 OG BSER A 107 -0.869 -1.863 -14.924 0.50 3.17 O ATOM868 C ASER A 107 -0.612 -4.590 -12.892 0.50 15.50 C ATOM869 C BSER A 107 -0.533 -4.683 -12.889 0.50 12.17 C ATOM870 O ASER A 107 -0.999 -5.055 -11.781 0.50 7.08 O ATOM871 O BSER A 107 -1.003 -5.114 -11.813 0.50 7.22 O
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 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 in using the mac version of Coot 0.6-pre-1, something else I updated last week. However, when I now run refmac on a pdb file with two conformers for certain amino acids it seems that refmac doesn't recognise them and distorts the bond angles/ lengths. I've checked the format of the pdb file outputted by coot and this seems normal (see below), which suggests to me that the new refmac doesn't like the A and B suffix on the residue name. Is this a known bug, and if so is there an easy fix? Thanks, Simon ATOM860 N ASER A 107 -1.909 -4.393 -14.018 0.50 10.31 N ATOM861 N BSER A 107 -1.942 -4.416 -14.064 0.50 8.93 N ATOM862 CA ASER A 107 -0.633 -3.962 -14.010 0.50 6.64 C ATOM863 CA BSER A 107 -0.669 -4.036 -13.974 0.50 5.74 C ATOM864 CB ASER A 107 -0.549 -2.697 -13.710 0.50 7.45 C ATOM865 CB BSER A 107 -0.505 -2.657 -13.639 0.50 6.94 C ATOM866 OG ASER A 107 -0.877 -1.986 -12.787 0.50 16.90 O ATOM867 OG BSER A 107 -0.869 -1.863 -14.924 0.50 3.17 O ATOM868 C ASER A 107 -0.612 -4.590 -12.892 0.50 15.50 C ATOM869 C BSER A 107 -0.533 -4.683 -12.889 0.50 12.17 C ATOM870 O ASER A 107 -0.999 -5.055 -11.781 0.50 7.08 O ATOM871 O BSER A 107 -1.003 -5.114 -11.813 0.50 7.22 O
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 using an X terminal in which case you need to use .bashrc)! Can any mac experts explain why there are so many options? 3) Thanks to everyone who suggested I forget trying to install it myself and just use Bill Scott's fink installation, BUT what happens if someone like Apple offers Bill a large crate of beer and he decides to work for them instead of maintaining his crystallography software support? It has concerned me slightly how much mac users seem to rely on just one member of the community... Simon
[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 ftp site to get the file Tcl-Tk++-osx-universal.dmg.gz which I then unzip, mount and run without a problem. HOWEVER when I open a new terminal and type wish my previous version (Tcl 8.4.10) opens instead of the new version, 8.4.18. I'm guessing that I need to point the soft-link in my /usr/local/bin directory to the new version, but I can't find where it has installed on my machine! If anyone could give me a hand and tell me where CCP4's Tcl installs itself I would be grateful. Thanks, Simon
[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 bit too complicated and windows still lacks function. Simon On 18 Nov 2008, at 16:09, Warren DeLano wrote: They're all great! - Linux offers limitless possibility with its concomitant complexity and chaos. - Mac OS X offers the design integrity, consistency, and efficiency of centralized control. - Windows guarantees lowest common denominator functionality for a rock bottom price. So why not buy hardware software that can run all three? ...with native-like performance. ...simultaneously. -Original Message- From: CCP4 bulletin board on behalf of William G. Scott Sent: Tue 11/18/2008 7:37 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Crystallographic computing platform recommendations? On Nov 18, 2008, at 7:01 AM, Mischa Machius wrote: For linux, I would recommend a commercial solution, For linux, I actually ditched the commercial solution for Ubuntu, because it was vastly easier as a non-expert to maintain. Having said that, like you, I have found running Mac OS X to be the most cost-effective in terms of time and utility. Bill
[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 need for REIDX as I note the parameters are not in IDXREF.LP anymore? Alternatively, if the data has been integrated in the wrong space- group, do I need to reintegrate in P1 and if so how do I stop the new sub-routine? Thanks, Simon
[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 justify adding hydrogens in my refinement, however as molprobity suggests adding hydrogens for validation purposes I obediently did so and (surprise surprise) found that I had a number of clashes (clashcore 17.6). Just as an experiment I re-ran refmac including hydrogens and this time my clash score was much lower and apparently acceptable (6.27), whilst my R factors were pretty much identical to before. So my question is this - do I ignore the normal obs:params calculation and just refine my structure with hydrogens (resolution 1.9, 99.9% complete) as according to molprobity this gives me a better structure, or do I just ignore the clashscore targets in molprobity based upon not having enough data to justify refining this component? Thanks, Simon
[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 problem still persists. I know a couple others have commented on this problem, but have yet to see an answer. Simon
[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. http://www.ccp4.ac.uk/dist/html/refmac5/usage/examples.html#exam0 Is it a good idea to always run uniqueify on data before running REFMAC - what about other refinement programs such as SHELX, CNS or phenix.refine? Simon
Re: [ccp4bb] Missing reflections
Thanks for the reply, Does this mean REFMAC/Coot does need the missing number flags (and thus you will get improved maps ONLY if uniqueify is run) or does REFMAC/Coot recognise when a reflection is missing and use DFc regardless (in which case there is no point running uniqueify)? Simon On 12 Mar 2008, at 16:00, George M. Sheldrick wrote: All these programs only refine against reflections that were actually measured. REFMAC, but not SHELXL, provides the 'Sigma-A' weight coefficients for Coot to use DFc instead of 2mFo-DFc for the reflections for which Fo is not known (or is reserved for the free R) to calculate a map. This will in general improve the appearence of the map at the cost of introducing a little model bias. As far as I know these 'unobserved' reflections are not used in calculating the difference map. CNS is probably like SHELXL, I'm not sure what 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 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. http://www.ccp4.ac.uk/dist/html/refmac5/usage/examples.html#exam0 Is it a good idea to always run uniqueify on data before running REFMAC - what about other refinement programs such as SHELX, CNS or phenix.refine? Simon
Re: [ccp4bb] XDS and overlaps
In the past I have used the USF program DATAMAN to pick my Rfree in thin shells. Thus my data goes XDS- XDSCONV- DATAMAN- F2MTZ in order to get a reflection file that refmac and phaser are happy with. Do I then need to run the UNIQUEIFY script selecting the option keep existing FreeR data in order to avoid the reciprocal asymmetric unit problem? If so this problem must only occur occasionally as I have had structures refining with R Rfree's in the very low 20s without performing the UNIQUEIFY step. Simon On 21 Feb 2008, at 15:32, Dirk Kostrewa wrote: Usually, I run CAD first after F2MTZ to make sure that the reflections are in the correct reciprocal asymmetric unit for CCP4 programs. I think, UNIQUE on its own doesn't do this, but the UNIQUEIFY script calls CAD, UNIQUE and FREERFLAG for setting a FreeR_flag column. The latter may or may not be wanted, depending on whether the test-set has been assigned by XDS/XSCALE, already. Best regards, Dirk. Am 21.02.2008 um 16:15 schrieb [EMAIL PROTECTED]: In my experience when going from XDS via some intermediate file to mtz format, XDS uses in some cases a different reciprocal asymmetric unit as mtz uses, which may result in only half of the reflections being used and/or ccp4 programs getting confused. By using UNIQUE, one makes sure that the reflections are mapped to the correct asymmetric unit. It has nothing to do with missing reflections but is in many cases essential. Best regards, 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 difficulty processing a data-set in mosflm the other day so on the recommendation of a colleague switched to xds which, with a bit of tweaking, seemed to work really well. I converted the resulting XDS_ASCII.HKL using xdsconv and then f2mtz ready for phaser and refmac. We do it in the same way here. However, my colleague then told me that xds handled missing reflections differently from the usual mosflm/CCP4 route I have honestly not the slightest idea what your colleague was referring to. and thus I had to run the CCP4 program UNIQUE before I tried refinement as apparently refmac does not like reflection files originally processed with xds. As I couldn't In the case of a new project, one should run uniqueify or some other means of assigning reflections to the free set (thin shells come to mind; see earlier discussions on CCP4BB). In the case of an old project, one should transfer the free set of reflections from some master data set to the new dataset. None of this is specific to XDS. HTH, Kay find anything in the literature about this I was wondering whether this advice is still up to date? Thanks, Simon On 21 Feb 2008, at 09:44, Kay Diederichs wrote: Engin Ozkan schrieb: Hi everyone, I have been recently relying on XDS quite a bit, but at the same time worrying about how XDS treats overlaps. We had one dataset that both HKL2000 and Mosflm would show to have severe overlaps, as expected due to unit cell parameters and the unfortunate crystal orientation in the loop. We always ended up with completeness percentages in the 70's. XDS can find the same lattice, index and scale the data, but yields a 100% complete mtz (and a nice structure). Without the HKL/Mosflm-like GUI, it is difficult to assess the fate of the overlapped observations in XDS. What I could see with VIEW was that some observations were being divided into several ovals, probably different reflections, but I'm not very certain. So, the basic question is, how does XDS treat overlaps? I could not find in the documentation an answer to this question; the single mention of overlaps I could find tells me that XDS can recognize overlaps, but does not tell me if it rejects them, or divvies them up into separate reflections, and if that is the case, how does it divide them, and how reliable is that? Depending on how it divides the overlaps, could that affect commonly-used intensity stats and distributions? Thanks, Engin Engin, the basic answer is: a) each pixel of the detector is assigned to its nearest reflection in reciprocal space b) some of these pixels will mostly allow the background estimation, others will mostly contribute to the integration area (but as they are transformed into a local coordinate system there is not a 1:1 relationship). At this step, pixels which should be background but are higher than expected (due to overlap) are rejected. c) for each reflection, the background is estimated, and the 3D profile is assembled from the pixels contributing to it d) a comparison is made: for a reflection, is the percentage of its observed profile assembled in c) larger than some constant (called MINPK in XDS.INP
Re: [ccp4bb] XDS and overlaps
doh... of course I also run CAD - which means (according to XDSCONV.LP) that the data would have already been converted into the CCP4-asymmetric unit prior to me getting to DATAMAN to pick my Rfree set. In which case we have solved the reciprocal asymmetric unit problem and thus get back to my original question (which I think has already been answered) as to whether or not there is anything else one needs to do to the data regarding missing reflections before trying to refine the model - I think the consensus so far is no and thus my colleagues advice is either dated 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 XDSCONV.LP. Michele
