[ccp4bb] strange P21 cell dimensions

Dear CCP4 and XDS users, I have a P21 case with some strange ratios in the cell dimensions : a, b=a, c=1.5a, 90, 105, 90. The native patterson shows a strong peak (40% of origin) at (x,0.5,0) indicating some pseudo symmetry. Such cell dimension and peak prompted me to think that the actual space

[ccp4bb] FSEARCH question

Dear CCP4 users, I am trying to use FSEARCH to position a SAXS envelop in an attempt to solve a molecular replacement case. Could you explain what the x,y,z values in the output stand for. Do they represent the position of the center of mass of the molecule in the unit cell ? I would be grateful

Re: [ccp4bb] ROSETTA for MR model generation

Hi Kornelius, A possible solution at this resolution would be to use Arcimboldo which localizes model fragments such as small helices with Phaser and then does density modification with SHELXE. See: Nature Methods 6:651-3. "Crystallographic ab initio protein structure solution below atomic resolu

Re: [ccp4bb] No peak after self rotation function means...

Dear Marie, Look for peaks at your native Patterson map which might indicate pseudo-translation NCS that can not be detected by self-rotation. Peter. On Fri, Jul 16, 2010 at 10:04 PM, Marie Lacroix < lacroix.ma...@rocketmail.com> wrote: > Hi everybody, > > I just calculated a self rotation fun

[ccp4bb] Phased translation in MOLREP question

Dear All, I use MOLREP to fit my structure into various EM maps using phased rotation/translation. It works perfectly for some maps while for others it gets stuck in the translation search with the message : ERROR: in STRPACK: problem with memory allocation The EM maps that create this problem a

Re: [ccp4bb] SUMMARY: scala and xds data

> isomorphous intensities; or "same" cells and terrible non-isomorphism. > > phx. > > > > > > On 25/04/2010 16:05, Peter Grey wrote: > > Dear Fred and Phil, > > However there is no refinement of these parameters in XSCALE so if you need > to scale t

Re: [ccp4bb] SUMMARY: scala and xds data

Dear Fred and Phil, However there is no refinement of these parameters in XSCALE so if you need to scale together several crystals (e.g. very small crystals that show severe radiation damage after a few degrees) you end up with a sub-optimal combined dataset after XSCALE. I thought SCALA can take

Re: [ccp4bb] SUMMARY: scala and xds data

Hi Ingo, Scala might be beneficial after xds when several datasets need to be scaled together. Scala will refine cell parameters to fit best all the datasets together where as xscale uses as cell parameters those of the first dataset. If you use xscale you have to be prudent in your choice of the

[ccp4bb] Fitting high resolution structures to low resolution map

Dear All, I have a crystal (not EM) density map of a very large complex at 4.5A resolution. I have pdb files for homologs of a few of the subunits of this huge complex. I would like to fit these homologs into the density. I have tried without success so far programs that handle phased molecular re

[ccp4bb] Difference in results between v6.1.2 and v6.1.1

Dear CCP4 developers, I ran the same DM script (solvent flattening + averaging) in CCP4 6.1.2 and CCP4 6.1.1. There are differences in the results - not huge but significant. Could you please suggest a possible reason for that ? Thanks a lot, Peter.

[ccp4bb] Forcing same origin on different MR solutions

Dear crystallographers, I try to solve a MR problem in P21 with several different structures (and one EM map) as search models. I would like all solutions to have the same origin so I could compare them and see their relative positions. I think a possible solution is to bring the center of mass o

[ccp4bb] DMMULTI question

Dear CCP4 users, I am trying to improve MR phases using multi-crystal averaging in DMMULTI. First crystal has 3 fold NCS , 5A resolution and the second crystal no NCS , 4A resolution. I ask for your advice concerning two issues ; In the first cycle DMMULTI calculates solvent masks for the two cr

[ccp4bb] Histogram matching in DM - question

Hi everyone, I am trying to use density modification at rather low resolution (4-5A ) for an RNA structure. My first time ever with RNA. I usually use Histogram matching as part of the density modification scheme in DM. But this method is based on density distribution of protein maps I think. Is h

[ccp4bb] Chainsaw question

Hi all, I attempt to create a suitable model for molecular replacement using CHAINSAW. Whenever the program needs to mutate a Proline into something other than alanine I get "segmentation fault". This happens if the order of atoms in the proline residue is (N,CD,CA,CB,CG,C,O). Could you suggest

Re: [ccp4bb] maprot question

the result! ( mapslicer or coot or whatever) to > make sure you have really achieved what you are aiming for! > > Eleanor > > > > Peter Grey wrote: > >> Hi all, >> >> I am trying to cut density from EM map (in a small P1 cell) into big P1 >> cell

[ccp4bb] maprot question

Hi all, I am trying to cut density from EM map (in a small P1 cell) into big P1 cell for MR. The mask is defined by a certain cut-off level in mapmask : mapmask \ mapin em.map \ mskout em.msk << eof MASK CUT 353 MODE mapin eof I use maprot to cut the density to the bi

[ccp4bb] Problems unique to large complexes

possible ? Would you trust native Patterson to such low resolution (assuming careful measurements of these reflections) ? I'll be grateful for your thoughts and comments, Peter Grey