[ccp4bb] iMosflm bug?

Has anyone else encountered this? When I go to "processing options" in iMosflm 1.0.7, many of the parameters on the right hand side of the window are cut off, and there is no way to scroll over so that I can enter them. I've attached link to a picture of what it looks like. https://www.dropbox.c

Re: [ccp4bb] Gnuplot: how to plot with resolution values as labels on x-axis?

On 06/25/2013 12:36 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Kay, the rotation can be achieved with 'set xtics rotate by 30' I did not know about xticlabels, suggested by Abhinav - very useful! My preferred gnuplot reference: http://security.riit.tsinghua.ed

Re: [ccp4bb] ctruncate bug?

Dear Pavel, Diffuse scattering is probably the most difficult topic I have worked on. Reading Peter Moore's new book and his insights give me renewed hope we could make much more of it, as I mentioned to Tim re 'structure and dynamics'. You describe more aspects below obviously. Greetings, John P

Re: [ccp4bb] Alternating positive and negative density

Hi Tim, A side note: you are most likely not looking at 2Fo-Fc and Fo-Fc maps, > but a sigma-A weighted maps and sigma-A weighted difference maps. I > think it is worth differentiating between these terms. Fully agree. I guess just typing them as 2mFo-DFc and mFo-DFc will solve this particular

Re: [ccp4bb] Alternating positive and negative density

Based on eye-balling your map it looks to me that your grid spacing is about 0.5 A. The wavelength of your ripple is 4 grid spacings, and the ripple is right along the x axis. My guess is that you have a rogue reflection with index of h00 where h is about 2 A resolution. How you are getti

Re: [ccp4bb] str solving problem

Hi Pramod, Can you post your merging statistics in different space groups, not just log files from scaling? These are summarised nicely by Scala or Aimless. Also, have you tried indexing from different subsets of images? Perhaps there is a substantial contribution from a 'satellite' crystal in on

Re: [ccp4bb] ctruncate bug?

Refinement against images is a nice old idea. >From refinement technical point of view it's going to be challenging. Refining just two flat bulk solvent model ksol&Bsol simultaneously may be tricky, or occupancy + individual B-factor + TLS, or ask multipolar refinement folk about whole slew of magi

Re: [ccp4bb] Refinement against frames

Dear Tim, With a full interpretation of the diffuse scattering as well how about papers becoming entitled:- The structure and dynamics of enzyme X As you intimate some diffuse scattering is crystal dependent ie phonons derived. Other aspects are however not correlated over multiple unit cells but

Re: [ccp4bb] Gnuplot: how to plot with resolution values as labels on x-axis?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Kay, the rotation can be achieved with 'set xtics rotate by 30' I did not know about xticlabels, suggested by Abhinav - very useful! Best, Tim On 06/24/2013 04:54 PM, Kay Diederichs wrote: > Dear Gnuplot users, > > you all know the crystallo

Re: [ccp4bb] ctruncate bug?

Implementing refinement against images will be pretty challenging. As far as I know the problem isn't in saying what has to happen, but rather in the enormous amount of bookkeeping necessary to relate a model of a structure and a model of the entire experiment (including such details as paramet

Re: [ccp4bb] High Rwork/Rfree values

Haiying, As far as I can tell you've got a successful solution in molecular replacement via Phaser and then gone and refined it in the wrong space group. Based on what you've told us: you took your initial data in primitive orthorhombic and solved for the structure in Phaser while sampling

Re: [ccp4bb] Gnuplot: how to plot with resolution values as labels on x-axis?

Hi Kay, This may be helpful, assuming your data file has resolution in column 3. set xtics rotate by -30 plot 'file' u 1:2:xticlabels(3) Make sure you have a recent version of gnuplot. Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 On Jun 24, 2013, at 7:54 AM, Kay Diederichs wrote: Dear G

[ccp4bb] High Rwork/Rfree values

Hi, all I have encountered the high Rwork/Rfree values. Here is the story: The glycosylated native protein structure is solved in the P212121 with unit cell parameters of 72.6, 78.0, and 112.5 and the all solution statistics are perfectly fine. I am trying to crystallize and solve the structure o

[ccp4bb] Gnuplot: how to plot with resolution values as labels on x-axis?

Dear Gnuplot users, you all know the crystallographic tables which have a column of resolution values, and columns of crystallographic indicators (R, I/sigma, ... whatever). Assuming that I want to plot the indicator in column 2 as a function of resolution, I can simply say > plot 'table.dat'

[ccp4bb] High Rwork/Rfree values

Hi, all I have encountered the high Rwork/Rfree values. Here is the story: The glycosylated native protein structure is solved in the P212121 with unit cell parameters of 72.6, 78.0, and 112.5 and the all solution statistics are perfectly fine. I am trying to crystallize and solve the structure

Re: [ccp4bb] Refinement against frames

Hi Tim, I don't follow your point...frames are just data, and with more information than after integration. The data after integration is also to some extent dependent on the beamline. It should indeed give a more accurate description of the crystal contents - whether that in turn will translate

Re: [ccp4bb] Refinement against frames

Hi Tim, I agree with you. Another point to remember about this issue of pixel->F's (or I's) conversion is that small molecule crystallographers take the same route and produce structures with 1-2% R-factors, so this conversion is hardly our problem. The main culprit in the issues that have be

Re: [ccp4bb] Refinement against frames

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear John, actually I am not a friend of this idea. Processing software make an excellent job of removing the instrumental part from our data. If we start to integrate against frames, the next structural title might be something like "Crystal structur

Re: [ccp4bb] Alternating positive and negative density

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Peter, have you tried removing a few residues involved and (after a round of refinement) rebuild the area from scratch (a simple way to remove model bias)? How did you decide about the resolution cut-off of your data sets - could it be that ther

[ccp4bb] Postdoctoral Position at Univ. Mass Medical School

POSTDOCTORAL POSITION KELCH LAB UNIVERSITY OF MASSACHUSETTS, MEDICAL SCHOOL Crystallographic studies of DNA replication machines A postdoctoral position to understand the mechanism and structures of DNA replication machines is available in the lab of Professor Brian Kelch at the University of

Re: [ccp4bb] AW: [ccp4bb] query regarding RMSD calculation

Dear Ansuman - I suspect Escet is what you're after: http://webapps.embl-hamburg.de/escet/ It factors in coordinate accuracy into comparisons. Check out the references for explanation. On 24/06/2013 08:55, herman.schreu...@sanofi.com wrote: Dear Ansuman, It is not entirely clear to my wha

Re: [ccp4bb] AW: [ccp4bb] str solving problem

There is also XDSAPP, a very convenient GUI for XDS with a fairly high degree of automation. Try it out, you will like it ... http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/xdsapp/index_en.html Cheers, Manfred On 24.06.2013 10:35, herman.schreu...@sanofi.com

[ccp4bb] AW: [ccp4bb] str solving problem

Dear Pramod, To run XDS, you could try to run it via the CPP4 procedure XIA2, or via autoPROC from Global Phasing. What also may help is to retype the line: NAME_TEMPLATE_OF_DATA_FRAMES=../images/WFTig1_???.mar2300 ! MAR345 I have had cases, where there were (I believe) hidden characters in ther

[ccp4bb] AW: [ccp4bb] query regarding RMSD calculation

Dear Ansuman, It is not entirely clear to my what kind of answer you are expecting. As Tim mentioned, from the B-factor formula, one can derive an estimate of the deviations of atoms from their average positions. This should give some idea of the inherent flexibility of the protein. From my exp