[ccp4bb] map manipulation questions
Dear All, I have a ccp4 format map file in P1 spacegroup, I would like to manipulate it in several ways: 1. enlarge the cell dimension . When I tried "CELL" keyword in MAPMAN, the density scaled up together with the cell dimension. Does anybody know how to do it without changing the density? 2. Change the space group to P2. 3. Move the density away from its original place, i.e. apply a translocation vector to it. Does anybody know the answers? Thanks in advance! Regards, Niu
[ccp4bb] Difficult MR with MBP fusion protein
Dear All, Recently we collected some data of a MBP fusion protein, at around 4A resolution. The protein itself is about half of the MBP size. However when we tried to solve it with MR, it failed. We tried to use MBP alone, homology model of target protein alone, and MBP+model. It is very strange that MBP alone can not yield any reasonable solution at all, so does searching with MBP and model together. While searching with model alone could get some better results, but when fix it to search MBP, it failed. There are 1 molecule per ASU with solvent content 55%. The spacegroup should be right and we tried to search all possible alternatives in each run, we also tried to lower it down, but did not work either. When running Phenix.phaser, there is a warning at the beginning saying eLLG suggests placing of ensembles will be very difficult. I wonder if anybody has encountered similar situation before. Any suggestions will be greatly appreciated! Regards, Niu
[ccp4bb] Refinement of data with pseudo translation symmetry
Dear All, Does any body know if the existence of pseudo translation symmetry will affect refinement ? If it does, is there any keyword or method to avoid it? Thanks! Best, Niu
Re: [ccp4bb] Fix cell dimensions
Dear Andrew, As previously I posted a MR case which has a significant 95% off origin peak, some experts suggested to reprocess the data with cutting one axis to half, from 40A to 20A. I tried HKL2000 and XDS, none of them is willing to give a solution with 20A, even I specify it in XDS script. So I wonder is there any way to force this work to be done. Thanks! Best, Niu On Mon, Nov 18, 2013 at 4:56 PM, Andrew Leslie wrote: > Dear Niu, > > It depends on which part of processing you are referring > to, i.e. the indexing step or the integration step. In MOSFLM there is no > way to enforce cell dimensions during indexing, but providing there is an > indexing solution that has cell dimensions close to the ones you want, you > can enforce a (slightly) different set of cell dimensions during the > integration step. Normally other refined parameters will ensure that you > still get a good prediction of spot positions. > > I suspect that this can be done in other programs too. > > Without knowing why you want to do this, I cannot comment on whether this > is the best procedure to follow. > > Best wishes, > > Andrew > > > > On 18 Nov 2013, at 21:48, Niu Tou wrote: > > > Dear All, > > > > Does any one know how to strictly fix the cell dimensions during data > processing? In HKL2000 there is only a keyword to define the longest > vector. In XDS there is a option to input cell parameters, but sometimes > the program would not follow the input values > > and switch back to the one it thinks best. Any suggestions will be > appreciated. Thanks! > > > > Best, > > Niu > >
[ccp4bb] Fix cell dimensions
Dear All, Does any one know how to strictly fix the cell dimensions during data processing? In HKL2000 there is only a keyword to define the longest vector. In XDS there is a option to input cell parameters, but sometimes the program would not follow the input values and switch back to the one it thinks best. Any suggestions will be appreciated. Thanks! Best, Niu
Re: [ccp4bb] Weird MR result
It may be helpful to add some information during index. HKL2000 could find four reasonable solutions: 40, 32, 101, 90, 101, 90 for P1 and P2 200, 40, 32, 90, 90, 90 for C2 and C222 It looks very strange to me since these two unit cells look differently, but during refinement the predicated spots are identical, and they produced similar quality data--at least from those output parameters. All solutions (including P21, C2221) have the 95% off origin peak and several minor ones. The 95% peak is at (0.5 0 0) on the 40 line, so if cut it into half, that dimension will be too small (20 only). HKL2000 also did not give any solution with one dimension as 20. Maybe I did not get a right index yet, I wonder any expert can tell something from these information? On Fri, Nov 15, 2013 at 6:41 AM, Melanie Vollmar < melanie.voll...@sgc.ox.ac.uk> wrote: > Dear Niu, > > I had an interesting pseudo-translation case recently where my off-origin > peak was located near the centre of the unit cell (fractions a=0.5, b=0.46, > c=0.5) of a P222 symmetry. Processing and phasing in P222 looked reasonable > and the model could be built. I had background density which I thought of > as water. I got suspicious when I identified density for a helix which was > near my build main chain but could not be joined and built or be accounted > for by looking at symmetry mates. Moreover I got stuck in refinement with > R/Rfree 25/30%. I could identify which part of the protein caused me the > trouble on crystal packing and the appearance of the off-origin peak. In my > case it was the C terminus. So I used a new construct with swapped > purification tag (N to C terminus). This altered the peptide sequence for > the C terminus and allowed the protein to pack nicely into I222. This > turned my off-origin peak into a true symmetry operator. > > I also had reasonable processing and phasing results for P2 and C2. > > So besides the strength of your off-origin peak it may be off some use to > look at the location. > > HTH > > Melanie > ---------- > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Niu Tou [ > niutou2...@gmail.com] > *Sent:* 14 November 2013 23:58 > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Weird MR result > > Dear Phil, > > I used PHASER to do the task. I have double checked and both files have > the same prefix, so they are from the same output. I have also checked the > headers again, they have the same spacegroup. Actually I was trying to > search for two different molecules but only one was found. The spacegeoup > is P2 and I am quite sure it is not P21 from system absence. > > One possibility is that the space group was wrong, since there is a 95% > off origin peak. There are several choices from data processing, P1, P2, C2 > C222, all have this large off origin peak. I wonder if this 95% peak can > tell some information? > > It will not surprise me if this result is incorrect, however how could > these regular density be? > > Best, > Niu > > > On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey wrote: > >> Hello Niu, >> >> 1. We need extra information. What program did you use ? What's the >> similarity (e.g. % identity) of your model. What's your space group ? Did >> you try ALL the space groups in your point group in ALL the permutations >> (e.g. in primitive orthorhombic there are 8 possibilities). >> >> 1a. My best guess on limited info is that you've got a partial solution >> in the wrong space group with only part of the molecules at their correct >> position. >> >> 2. I recently had a very unusual case where I could solve a structure in >> EITHER P41212 or P43212 with similar statistics, but that I would see >> interpenetrating electron density for a second, partial occupancy molecule >> no matter which of these space groups I tried (and it showed this when I >> expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, >> in retrospect, but we obtained a more friendly crystal form. I hope you >> don't have something like that, but it's possible. >> >> Phil Jeffrey >> Princeton >> >> >> On 11/14/13 5:22 PM, Niu Tou wrote: >> >>> Dear All, >>> >>> I have a strange MR case which do not know how to interpret, I wonder if >>> any one had similar experiences. >>> >>> The output model does not fit into the map at all, as shown in picture >>> 1, however the map still looks good in part regions. From picture 2 we >>> can see even clear alpha helix. I guess this could not be due to some >>> random density, and I have tried to do MR with a irrelevant model >>> without producing such kind of regular secondary structure. >>> >>> This data has a long c axis, and in most parts the density are still not >>> interpretable. I do not know if this is a good starting point. Could any >>> one give some suggestions? Many thanks! >>> >>> Best, >>> Niu >>> >>> >>> >> >
Re: [ccp4bb] Weird MR result
Dear Phil, I used PHASER to do the task. I have double checked and both files have the same prefix, so they are from the same output. I have also checked the headers again, they have the same spacegroup. Actually I was trying to search for two different molecules but only one was found. The spacegeoup is P2 and I am quite sure it is not P21 from system absence. One possibility is that the space group was wrong, since there is a 95% off origin peak. There are several choices from data processing, P1, P2, C2 C222, all have this large off origin peak. I wonder if this 95% peak can tell some information? It will not surprise me if this result is incorrect, however how could these regular density be? Best, Niu On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey wrote: > Hello Niu, > > 1. We need extra information. What program did you use ? What's the > similarity (e.g. % identity) of your model. What's your space group ? Did > you try ALL the space groups in your point group in ALL the permutations > (e.g. in primitive orthorhombic there are 8 possibilities). > > 1a. My best guess on limited info is that you've got a partial solution > in the wrong space group with only part of the molecules at their correct > position. > > 2. I recently had a very unusual case where I could solve a structure in > EITHER P41212 or P43212 with similar statistics, but that I would see > interpenetrating electron density for a second, partial occupancy molecule > no matter which of these space groups I tried (and it showed this when I > expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, > in retrospect, but we obtained a more friendly crystal form. I hope you > don't have something like that, but it's possible. > > Phil Jeffrey > Princeton > > > On 11/14/13 5:22 PM, Niu Tou wrote: > >> Dear All, >> >> I have a strange MR case which do not know how to interpret, I wonder if >> any one had similar experiences. >> >> The output model does not fit into the map at all, as shown in picture >> 1, however the map still looks good in part regions. From picture 2 we >> can see even clear alpha helix. I guess this could not be due to some >> random density, and I have tried to do MR with a irrelevant model >> without producing such kind of regular secondary structure. >> >> This data has a long c axis, and in most parts the density are still not >> interpretable. I do not know if this is a good starting point. Could any >> one give some suggestions? Many thanks! >> >> Best, >> Niu >> >> >> >
[ccp4bb] How to apply "correction factors" for translational NCS in PHASER?
Dear All, I have a MR case which may contain two different molecules, ideally 1:1 ratio. Solvent content analysis indicates most likely to be 4~6 hetero molecules. The data shows at least 5 strong translational NCS vectors. When I tried to run PHASER, it always said "correction factors NOT applied", but I have chosen to count it in the interface. Is there anyway I could use these NCS information, either by checking some options in the GUI of modifying the script? Many thanks! Best, Niu
[ccp4bb] Negative IOBS in XDS
Dear Colleagues, When I processed one data set with XDS, the index step said there is no sufficient (<50%) spots indexed, however after I tried various parameters to get the same cell unit and space group, I chose to ignore this message and wen on to integration. During the integration I had to modify the following keywords to finish as instructed by the manual: REFLECTING_RANGE REFLECTING_RANGE_E.S.D. BEAM_DIVERGENCE= BEAM_DIVERGENCE_E.S.D. Finally I got a scaled file, but there are many negative numbers in the column 4 IOBS, and the SIGMA seems very high, for example: 0 0-6 1.751E+03 9.025E+02 1547.9 1935.5 55.0 0.32158 95 33 -85.79 0 0-6 -1.795E+00 5.171E+02 1547.9 1117.2 22.7 0.32158 100 -2 93.56 0 0 6 1.426E+03 7.902E+02 1550.9 1117.2 58.7 0.32158 100 38 85.86 0 0 6 8.512E+02 5.216E+02 1550.9 1935.5 19.0 0.32158 95 23 -93.63 0 0-7 -4.436E+01 4.495E+02 1547.5 2011.5 54.7 0.37469 100 -11 -85.79 Does this mean the process is wrong? Anything I can do in this case? Best, Niu
[ccp4bb] Resolution limit of index in XDS
Dear All, Is there any command can set the resolution limit for index step in XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to be a definition of resolution range after index step as it says: INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT Thanks! Niu
Re: [ccp4bb] Diffraction data with big rotation angle
Hi Tim, I only tried HKL2000, and index with different resolution and different number of images. I am not quite familiar with XDS or d*trek. One thing I am not sure is if this large oscillation angle will cause problem in indexing? If this is true, any method to overcome it? The situation I met was when I chose different settings to do index, HKL2000 would give different cell dimensions while most of them were not small enough for a peptide crystal. The unit cell should be pretty small since even collecting data with 5 degree oscillation angle, the spots in one image were still fewer than a normal protein crystal case, so there is no spots overlap. Best, Yang On Thu, Mar 14, 2013 at 5:20 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Niu, > > could you let us know more about what you have already tried? > > - - use more images, maybe all images for indexing > - - try a different program: xds instead of mosflm instead of hkl200 > instead of d*trek instead of xds depending what you have tried. > - - try to find the unit cell dimensions manually from adxv > - - try cell_now with the SPOTS.XDS > > in XDS I would check the output of IDXREF.LP to figure out if indexing > seems possible, i.e. if the input parameters seem stable or if they > are just floating around > > and many more - it depends on the data set, really! > > Best, > Tim > > On 03/13/2013 09:12 PM, Niu Tou wrote: > > Dear colleagues, > > > > We have some diffraction data from small peptide crystals, the > > shape of diffraction spots looks normal, and resolution is beyond > > 2A. The data were collected with 5 degree rotation per image. Later > > on we found it is hard to do index. Does anybody know some skills > > to figure this problem? > > > > Best wishes, Niu > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFRQZZFUxlJ7aRr7hoRAmr3AKD28Mml3XY2LIWkDknKrkJFToLDvwCgu1DI > LDaPuAMfGlEIEObuWcckM7Y= > =yuwC > -END PGP SIGNATURE- >
[ccp4bb] Diffraction data with big rotation angle
Dear colleagues, We have some diffraction data from small peptide crystals, the shape of diffraction spots looks normal, and resolution is beyond 2A. The data were collected with 5 degree rotation per image. Later on we found it is hard to do index. Does anybody know some skills to figure this problem? Best wishes, Niu
[ccp4bb] HKL2000 24IDE beam center.
Hi colleagues, We have collected several datasets at APS with detector 24IDE, while processing date, the beam center is obviously not in position. But no matter what values we set in "Site Configuration" or "def.site", it remains about (156, 165). Based on the image, the estimated correct center should be around (156, 157). Does anyone know how to solve this problem? Thanks Niu
[ccp4bb] Maprot question.
Dear Colleagues, Does anybody know if the definition of rotation parameters in Maprot are different from that of Coot? I used Coot to superimpose a model A to model B, to get a new model A* and rotation parameters (Euler angles and translations), howerver when I used these parameters to move the original map with Maprot, the new map did not fit with model A*. I tried the 3x3 matrix and translations, it did not work either. I wonder if there is any different from these two prgrams? Thanks! Niu
[ccp4bb] Program for map rotation
Dear colleagues, Is there any program can rotate a density map (generated by FFT, could be read in Coot and Pymol) given the matrix? I have tried Extension->Maps-> Transform map by LSQ model fit, it looks doesnot work. While the program Edit/Rotate map & Mask in CCP4 gave an error message: mapmask: mapextend - input map does not contain a whole ASU. Thanks! Niu
[ccp4bb] Series termination effect calculation.
Dear Colleagues,
I am trying to repeat a series termination effect calculation displayed as
figure 2 in a publihsed paper
(http://www.ncbi.nlm.nih.gov/pubmed/12215645). Formula
(1) was used to implement this calculation. Since f(s) is not defined in
detail in this paper, I used formula and parameters listed in another
paper (http://scripts.iucr.org/cgi-bin/paper?a05896) to calculate it.
However, the result I got is not consistent with figure 2 of the first
paper. I am not sure if the formulas I used are right or not. Or if there
is any problem in the MatLab code, which I list below:
###
clear all;clc;format compact;format long;
% matrix of a, b, c coefficients:
% rows: Fe, S, Fe1, Mo
% columns: A1; B1; A2; B2; A3; B3; A4; B4; C
fM = ...
[11.9185 4.87394 7.04848 0.34023 3.34326 15.9330 2.27228 79.0339 1.40818;...
7.18742 1.43280 5.88671 0.02865 5.15858 22.1101 1.64403 55.4651
-3.87732;...
11.9185 4.87394 7.04848 0.34023 3.34326 15.9330 2.27228 79.0339 1.40818;...
19.3885 0.97877 11.8308 10.0885 3.75919 31.9738 1.46772 117.932 5.55047];
%%% store radius data:
% distance from: origin
% columns: Fe, S, Fe, Mo
R_el = [2.0 3.3 3.5 3.5];
RHO_t = zeros(4,400);
for numel = 1:4
EL = numel;
RHO = zeros(1,400);
dmax = zeros(1,400);
for iter = 1:400
dmax(iter) = iter/100; % in angstroms
% numerical integration
int_fun = @(s) 4*pi*(s.^2).* ...
(fM(EL,1).*exp(-fM(EL,2).*(s.^2)*0.25) + ...
fM(EL,3).*exp(-fM(EL,4).*(s.^2)*0.25) + ...
fM(EL,5).*exp(-fM(EL,6).*(s.^2)*0.25) + ...
fM(EL,7).*exp(-fM(EL,8).*(s.^2)*0.25) + fM(EL,9)).* ...
sin(2*pi*s*R_el(EL))./(2*pi*s*R_el(EL));
RHO(iter) = quad(int_fun,0,1/dmax(iter));
clc;display(iter);display(numel);
end
RHO_t(numel,:) = RHO;
end
RHO_t(1,:)= 6*RHO_t(1,:);
RHO_t(2,:)= 9*RHO_t(2,:);
figure;
axis([0.5 3.5 -10 10]); hold on;
plot(dmax,RHO_t(1,:),...
dmax,RHO_t(2,:),...
dmax,RHO_t(3,:),...
dmax,RHO_t(4,:),...
dmax,sum(RHO_t,1));
title('Electron Density Profile');
legend('Fe','S','Fe1','Mo','Sum');
xlabel('d_m_a_x'); ylabel('Rho(r)');
set(gca,'XDir','reverse');
##
Any suggestions will be appreciated. Thanks!
Niu
[ccp4bb] IUCr checkCIF server.
Dear Collegues, Does anybody know how to use the server http://checkcif.iucr.org/? I have downloaded structure factor and structure model cif files of a structure from PDB. However it looks this server only accept one single file, it does not work if these two files are uploaded separately. My question is: do I need to combine these two cif files into one? How to do that? Thanks! Niu
