Re: [ccp4bb] High B factor

Sunanda, As "common people", ... "agreement" don't means for me "equals" ... So I hope I'm not so "incorrect" if I keep one mind the Wilson B as the model refinement goes and the average B factor changes with different strategies. If you are still worry about your Bfactor, you could try TLS,

Re: [ccp4bb] High B factor

> If you are still worry about your Bfactor, you could try TLS, > Or NCS, but SA with MLHL might be better. (A joke).

[ccp4bb] Travel bursaries to CCP4 Study Weekend 2017 - deadline for applications 31st October 2017

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[ccp4bb] Postdoc Protein Crystallographer position at MDC

[cid:image001.png@01D22625.583FB020] Protein Crystallographer The Macromolecular Structure and Interaction laboratory at the Max Delbrück Center for Molecular Medicine, Berlin, is recruiting a protein crystallo­grapher at the postdoctoral level. The position is available immediately and limi

[ccp4bb] Workshop "Challenges in Data Processing" Announcement

Dear all, we would hereby like to announce that on Dec 09, 2016 attached to the 2016 HZB Users Meeting, there will be a workshop on "Challenges in data processing". This workshop should be interesting for anybody who has to process some diffraction data sets now and then, with an obvious focus o

[ccp4bb] Antw: Re: [ccp4bb] High B factor

Picking up the mail of Pavel, Phenix refines occupancies.. If you expect the loops to be disordered, did you try to lower the occupancy of these residues, following Ethan Merritt statement that "general uncertainty [...] is represented better by occupancy <1 rather than an arbitrary large B fact

Re: [ccp4bb] High B factor

I agree that it would certainly be bad if your model was inconsistent with the Wilson B. When I first ran into people who were worried about this I recommended that they calculate the Wilson B of their model, not look at the average B as a proxy. You can calculate structure factors from your

[ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Dear All, our institution requires me to provide a reasoning not to buy a Windows computer (I want to buy a new MacOSX system), so I am looking for software that does not run or is limited on Windows. Not available: (Auto)SHARP ARPWARP Available on Windows but with significant limitations Phen

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Dear Mark, I think XDS (diffraction image processing) is the best example. It runs only on Mac and Linux machines 2016-10-14 18:14 GMT+03:00 Mark J van Raaij : > Dear All, > > our institution requires me to provide a reasoning not to buy a Windows > computer (I want to buy a new MacOSX system), s

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Dear Mark, XDS does not run on Windows, and even if you take your mtz-file home from the synchrotron nowadays, you sometimes may want to re-refine some data set. Windows also costs a lot of money, and if you do a lot of scripting, Windows may be cumbersome. WinCoot is also often mentioned with

Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

Interesting way to look at it. But those loop residues are really in the crystal with an occupancy of 1, so wouldn't letting the B factor fly give a clearer description of what's in the crystal? Especially as many people know to color the structure by B factors to get a feel for which bits are

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Windows 10 now allows a full Ubuntu within Windows. It actually works quite easily. There is a good rsync for windows. I use it to make back-ups of the pdb_redo databank. Windows has it own system of incremental backups which works well in my hands. There are two scripting systems in Windows ba

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Except for graphics-intensive programs (e.g., Coot, Pymol), it is possible to run Linux within a VM in windows, and you can even share files with the other OS. I actually do it the other way 'round, running Windows in Linux via wine to have a one-box solution for processing data from our Oxford

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

How about the ability to compile code? Are there decent compilers readily available for Windows? I like being able to write & compile the occasional fortran program {hic sunt dinosaurs}, and it’s easy to do this on a unix-based platform like OSX. If your reasoned arguments fail, I have found th

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Most software used for cryo-em analysis (e.g. EMAN2, Relion, Spider, Frealign etc) runs better or only in Linux. Best Hernando From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent: Friday, October 14, 2016 11:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Hi On this point, I have (for many years) built my Windows executables on a Mac with a cross-compiler; it is possible to install MinGW on a Windows box and have gcc, g++, gfortran available. If you want X windows & the compilers, you could install Cygwin. However, I'd prefer to use a proper Uni

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Just to add to Hernando’s comments BSOFT and EMAN2 runs on both Macs and LINUX. However its much easier to use them on Macs because of the library issues for different flavors of LINUX. Best Andy > On Oct 15, 2016, at 1:31 AM, Hernando J Sosa > wrote: > > Most software used for cryo-em an

Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

Quoting Dale from an older post "It's also true that the Wilson B calculation assumes that all the B factors in the crystal are the same - which is also far from the true in most macromolecular crystals. A person who holds to the practice of aggressively building water molecules and loops will crea

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

I’ve made simple native Windows programs in fortran. There are proper compilers that run without the hassle of crosscompiling. Cheers, Robbie Sent from my Windows 10 phone Van: Patrick Loll Verzonden: vrijdag 14 oktober 2016 18:32 Aan: CCP4BB@JISCMAIL.AC.UK

[ccp4bb] OSX or Linux system?

Discussion on what runs/does not run under windows has moved me to asked is there a somewhat preferred platform of Linux vs. OSX. I am replacing an 8 year old Mac Pro, big silver box, as it really is slowing down comparatively speaking and 8 years is a good run for a computer and it will get re

[ccp4bb] Postdoctoral Position at Rutgers University

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Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Just for the record, the Fortran sources for all the SHELX programs are identical for Windows (32 or 64 bit), Linux (32 or 64 bit) and MacOSX (always 64 bit) except for one line that I need to comment out for Windows. I use the Intel ifort compiler for all these platforms. I pay the commercial

Re: [ccp4bb] Why Does Detwinning Not Work?

> I do not know what the current state is of developing the ML target for > refining > against twinned (I, F) data is. > Formulas are there, see "Maximum likelihood refinement for twinned structures" here: https://www.phenix-online.org/newsletter/CCN_2011_01.pdf someone just need to code it.