[ccp4bb] Postdoctoral Position in Ion Channel Physiology

Dear CCP4BB members, I am posting this on behalf of Dr. Harpreet Singh. For any informal/formal queries, please contact him directly hsi...@mednet.ucla.edu. Best. Harkewal Singh, Ph.D. ---

Re: [ccp4bb] How to compare B-factors between structures?

Perhaps I was a bit gruff, but what I was trying to do was throw out a voice of caution. In crystallography, it is very tempting to "normalize" everything by setting the mean to zero and the RMS deviation to one, but this is a "linear transformation", and linear transformations only work when the

[ccp4bb] Reminder: CCP4 summer school at APS, USA

Dear Colleagues, This is a reminder that the deadline for applications for the 6th annual CCP4 Summer School “From data collection to structure refinement and beyond” is April 5, 2013. The school will take place from June 18 through June 26, 2013 at the Advanced Photon Source (APS) near Chicago

Re: [ccp4bb] How to compare B-factors between structures?

Seriously? I believe this specific forum has become quicksand rather than a useful tool. Normalization based simply on ratios of one struct to the other should allow normalization. Correct?, or have I just simply lost my mind here? J John Fisher, M.D./PhD St. Jude Children's Research Hospital D

Re: [ccp4bb] How to compare B-factors between structures?

No, you can only add and subtract B values because that is mathematically equivalent to multiplication in reciprocal space (which is equivalent to convolution in real space): exp(-B1*s^2) * exp(-B2*s^2) = exp(-(B1+B2)*s^2) Multiplying and dividing B values is mathematically equivalent to ap

Re: [ccp4bb] How to compare B-factors between structures?

Good point; I've tested this (n=1) in the past with a high-resolution dataset (synchrotron data) and low-resolution dataset (in-house) of crystals of the same protein grown in the same drop. Same space group, same unit cell. B-factors for the low-resolution dataset were higher. After dividing ev

Re: [ccp4bb] How to compare B-factors between structures?

Yep, I agree calculate the average B per structure and divide each B by this value, then multiply it by any value that is reasonable so you can visualize color differences :-) Jürgen On Mar 4, 2013, at 2:16 PM, Jacob Keller wrote: You only entertain addition+subtraction--why not use multiplicat

Re: [ccp4bb] How to compare B-factors between structures?

You only entertain addition+subtraction--why not use multiplication/division to normalize the b-factors? JPK On Mon, Mar 4, 2013 at 2:04 PM, James Holton wrote: > Formally, the "best" way to compare B factors in two structures with > different average B is to add a constant to all the B factors

Re: [ccp4bb] How to compare B-factors between structures?

Formally, the "best" way to compare B factors in two structures with different average B is to add a constant to all the B factors in the low-B structure until the average B factor is the same in both structures. Then you can compare "apples to apples" as it were. The "extra B" being added is

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

Ed, Are the numerical results the same ? Not likely that there is a problem. But if you haven't done it already it is worth checking by running the tests provided with the suite. Aggressive optimization can be a source of bugs. Best regards Thierry -Original Message- From: CCP4 bulleti

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

On 4 March 2013 13:55, wrote: > On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote: >> Running times were, correspondingly, 32.2s, 35.1s and 18.7s. >> > Numbers are almost too impressive to believe :) It also puzzled me, but I haven't done more careful benchmarking yet. What did you get afte

Re: [ccp4bb] Off-topic PyMOL Issue

Hi Greg, Takanori Nakane's suggestion should work for you, which is our workaround for non-compliant video cards/drivers. If it doesn't or you see performance or stability problems, please try these two settings: unset use_shaders unset sphere_mode These two settings are usually only necessary f

[ccp4bb] Postdoctoral Position in Mechanism and Regulation of Transposition at EMBL Heidelberg

Dear All, We are looking for a postdoc candidate to join our lab. The ideal candidate should have some experience in crystallography and be enthusiastic to discover molecular mechanisms of complex nucleic acid - protein machines. Please see full add below. To apply please go to: www.embl.org/j

[ccp4bb] CCP4MG Version 2.7.2

Dear all, Version 2.7.2 of CCP4MG is now available for download from: http://www.ccp4.ac.uk/MG/download/ This version fixes two critical problems on Windows (failure to create movies and complete failure to work at all with many Intel graphics chips) and one critical problem on Linux (crash/

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote: > Running times were, correspondingly, 32.2s, 35.1s and 18.7s. > Numbers are almost too impressive to believe :) How does it compare with ifort (which I thought should be the fastest option on intel processors and thus unavailable (not free)

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

Indeed, the problem goes away when -static flag is omitted. Interestingly, the resulting binary dependencies do not include any ccp4-related libraries. For those interested, I was able to track the segfault down to the close() operator - so basically it fails when closing a file opened with ccpdpn

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

Adam, On Mon, 2013-03-04 at 09:56 +, Adam Ralph wrote: > One of the first routines called by CCP4 > progs is "ccp4fyp". This initialises the CCP4 environment. I think you might have missed in my original post that I get an error when I *do* source ccp4 environment. > > Does the error occur

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

Following what Marcin said, if you have a compiler other than gcc/gfortran then I would definitely recommend compiling from source. Generally they give much better performance and in addition there might be optimised maths functions. Adam > One reason to compile refmac on Linux is that

Re: [ccp4bb] Qt PISA text copy?

Apologies, I'd like to retract my post, it is indeed that only general lists of interfaces and assemblies are exported in plain text. We will try to fix this as soon as feasible. Eugene On 4 Mar 2013, at 11:13, wrote: > Dear Engin, > > QtPISA outputs the same textual information as the pre

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

One reason to compile refmac on Linux is that it can be faster. I've just run $CEXAM/unix/runnable/refmac5-simple.exam example with refmac from CCP4 6.3.0, from Garib's website and compiled with GCC 4.7.2 only with -O3 option (all are 64-bit versions). Running times were, correspondingly, 32.2s, 35

Re: [ccp4bb] Qt PISA text copy?

Dear Engin, QtPISA outputs the same textual information as the previous command-prompt routine, check "File/Export plain text". What is probably confusing is that it does not export everything in one go, but rather precisely the portion that is currently displayed in the right-hand side of the

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

Dear all I think this error has been dealt with (Ed will correct me if I am wrong). The problem was -static in compilation. For whatever reason in some gcc (gfortran) -static does not work (it compiles but has problems in running, what is the reason is not clear to me). Sometimes in later gcc -

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

Dear Ed,    The error does indeed happen in ccp4lib. One of the first routines called by CCP4 progs is "ccp4fyp". This initialises the CCP4 environment. See lib/cctbx/cctbx_sources/ccp4io/lib/src/ccp4_general.c. If you look at the code you can see that $CINCL is determined at run-time. You ar