[ccp4bb] sunrider

Now i am looking for some person who has the same intesting in sunrider,if u like sunrider ,if u like everything about how to keep healthy,how to loose your weight,how to protect your skin,please contact me!~i am waiting for your news!~please don'ot waste your time!~

[ccp4bb] MR on low resolution soaking data.

Dear colleagues, We are now trying to soak some ligands into a protein, which is about 60kd in size and the structure has been solved before. But the molecular replacement cannot give a right solution. Below is some contrast of the data: Native 2A P212121 monomer Soaked4A F2

Re: [ccp4bb] MR on low resolution soaking data.

Dear All, Thank you for your help! There do have something needed to be checked carefully, as you suggested. Peter Zwart showed me the right way of explore_symmetry_metric, which indicated there is some relationship between the two unit cells. I hope it can explain the strange wilsonB and fa

[ccp4bb] Merohedral twining for P212121.

Dear all, Is there any possible of twining for a normal P212121 spacegroup and what is the twin law, say no equal cell dimensions? Some people said there is no twin law for such symmetry but I am not very sure. Thanks a lot. Best Yang

[ccp4bb] Programs to detwin.

Dear All, Can phenix.refine and Detwin in CCP4 handle twinning data with multiple twinning law? Or there are some other good programs can do this? If the data has some pseudo-meroheral twin operators, can it be treated as same as merohedral operates? Thanks very much! Best Yang

[ccp4bb] Off topic: PKa of protein-DNA complex.

Hi, Is there any server or program can calculate the theoretic PKa of the protein-DNA complex? Given the structure of the protein and the sequence of the DNA. Any suggestion will be appreciated! Best Yang

[ccp4bb] How to optimize protein-DNA complex conditions?

Dear All, Recently I am working on a protein-DNA complex, and from running agarose gel, there is a weak delayed band after the band of pure DNA which indicates some DNA has bind to the protein though the binding efficiency is low. Then I tried to optimize the condition to increase the bindi

Re: [ccp4bb] Micocrystals or not?

purification? Is any information can be achieved from this? Thanks a lot! Best Yang On Mon, Sep 20, 2010 at 6:28 PM, yang li wrote: > Dear All, > >After crystal screening I got something look like microcrystals but > not sure, picture taken by the robot > is attach

[ccp4bb] Mtz2various

Hi: I'd use Mtz2various to convert .mtz file to .phs format. The format of .phs file is like below: 0 0 9 29.5 0.14 220.00.00.00.00.0 0 0 12 160.5 0.97 109.0 -4.52.4 -0.91.2 0 0 15 72.6 0.87 56.0 36.5 10.5 -12.6 -7.9 0 0 1

[ccp4bb]

Hi All: Now I have two sets of data from the same crystal, and I want to calculate the phase difference of them. Anyone knows if there are programs that can calculate it from two .mtz files? Thanks Li Yang

[ccp4bb]

Hi, All, If I have a solve script named solve.com and I can use command ./solve.com to run it, now I want to write a script named test.inp and use command ./test.inp to run it, how should I write it? Thanks Li Yang

[ccp4bb] question about a script

Hi All, If I have two scripts named 1.inp, 2.inp, I can run them with command like ./1.inp, now I should modify some parameter in 2.inp according to the result of ./1.inp before run it. How can I write a program to run then together? For example, I get two numbers a and b from 1.inp, and

[ccp4bb] weighting term in refmac

Hi, There is a value of weighting term with default 0.3 in refmac5, what is the exact meaning of it? What is the best value of it for different resolution data? Does it affect the result R value much? Li Yang

[ccp4bb] compiler question

When I installed a programm, it gave such information: ./install.sh /usr/bin/ld: cannot find -lstdc++ collect2: ld returned 1 exit status make: *** [Linux] Error 1 Is it because of absence of some compilers? How can I install it? I am using the Fedora5 system. Thanks! Li Yang

[ccp4bb] refmac refinement and multiple conformations

If a pdb file contains some residues that have multiple conformations, when using refmac to refine it, will the programm take consider of these conformations? It seems that refmac would do this but I am not very sure. I downloaded a structure with some conformations from the pdb, but after refm

[ccp4bb] ccp4 pdb format

Hi: Now I need to input a heavy atom pdb file in the ccp4 interface, does ccp4 has a special format for all the programs in the package? I used heavy atom file from shelxd but it seemed not right. where can I get a model of such pdb file? Thanks!

[ccp4bb] question about redundancy

Hi: I am confused by a idea for a long time, and it maybe an easy question. That is, if a cryst with p1 spacegroup, after 360 degree data collection, what the redundancy should be? I was told that it is 2, and the 2 are F(h,k,l) and F(-h,-k,-l), but I think if the reciprocal lattice rotated 360

[ccp4bb] Scale factor in ccp4

Hi: I have two set of data from the same crystal with the names 1.sca and 2.sca, they have different Intensity values due to different scale factors. Now I use Scalepack2mtz convert them to 1.mtz and 2.mtz, then use cad to merge to a cad.mtz, then convert it to cad.sca file, I find that the Int

[ccp4bb] phaser oprn error

Hi: I am using CCP4 6.0.2, it has phaser contained in this package. When I use it to do mr, error occured: * *** Phaser Module: READ DATA FROM MTZ FILE2.0 *** *

[ccp4bb] phaser in ccp46.0.2

Hi, Anyone has used phser in ccp46.0.2 which is automatically installed with ccp4? In previous ccp4 edition I installed phaser seperately and it worked well, but now it seems has some problems, it cannot read the input mtz file, I tried several data, all gave the same error information like b

[ccp4bb] How to run Java program?

Hi, I have a java program named Switch.java, I want to run it under fedora5 core, I donnot know any compiler I need to install? I installed a package named jre-1_5_0_11- linux-i586-rpm.bin, when I use command java Switch.java wrong information came out: Exception in thread "main" java.lang.NoCl

[ccp4bb] Question about cryoprotectant

Hi, l have a crystal grow at condition screen l 40: 0.1M tri-sodium citrate dihydrate pH5.6 isoproponal 20%PEG4k 20% and the crystal need a cryoprotectant, we have used the 30% glycerol but it is not good, the mosaicity of the diffraction pattern is a little high, so anyone knows which is the be

[ccp4bb] problem with HKL2000 license

Hi,All, Now I am installing HKL2000 and met a curious problem: The license cr_info was apllied before, the system is fc6 at that time. Before received the license, I reinstalled the system for some reason, now the system is fc4. the install files and anom.dat file was copied from other peopl

[ccp4bb] How to run ccp4 in php script?

Hi All, I have some scripts which need to use some programs--like cad, refmac--in ccp4, and I want to use a php script to run these scripts, with command as : $cmd =" sh aa.inp"; system($cmd); As I know, when I use php script, the account is Apache, which is a nologin account,

[ccp4bb] How to show density map in pymol?

Hi All, If I want to show the density map in pymol--like coot open mtz file--, what format should I use? It seems pymol doesnot recognise the mtz format . Thanks!

[ccp4bb] Cif file in coot

Hi All, If I have a pdb with some residues named "abc" in it, coot can read it and display it well, but I cannot do real space refine to such residues. The tips asks me to import a CIF file, I wonder what is the format of this CIF file? How can I create it and let coot recognise these residu

[ccp4bb] scalepack problem

Hi All, I met a problem while running scalepack2mtz in ccp4 interface. The program will stop with a tip said "check your data", but no error warning. This SCA file is a H3 spacegroup but maybe it is not because the spacegroup since if I use p1 had the same problem. I tried to delete some lines

[ccp4bb] problem while installing CNS1.2

Dear All, When I tried to install cns, I met such error, I asked other people, no one has seen this before, so maybe someone here had similiar problem or method to solve it: compiling: initia.f compiling: lbfgs.f compiling: lidens.f compiling: machine_f.f

Re: [ccp4bb] scalepack problem

Hi All, Thanks for your replies. I think the problem shouldnot be spacegroup because I tried several other spacegroups(just modify the sca file or specify in the script), the resluts are the same. the error is: Sort Order : 0 0 0 Spacegroup = 'p1' (number=1) Scalep

Re: [ccp4bb] scalepack problem

Hi,All, I have figured out the mistake, for some reason some -h,-k,-l reflections were missed for the spacegroup given, so the program was not happy with the format. I donnot know how it happened since not me processed the data. Then another question is how the scale porgrams do with

Re: [ccp4bb] scalepack problem

_____ > From: CCP4 bulletin board [EMAIL PROTECTED] On Behalf Of yang li [ > [EMAIL PROTECTED] > Sent: Monday, December 31, 2007 12:54 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] scalepack problem > > Hi All, > Thanks for your replies. I think the

[ccp4bb] ideal bond length and bong angel

Dear All, I've wonder for a simple problem for a long time, that is: What is the ideal bond length and angel? Every lecture or book says this is a criteria from small organic molecules, but I still donnot know exactly. Like is bond length point to the peptide bond length? Or many other bonds?

Re: [ccp4bb] ideal bond length and bong angel

By the way, I think my bad english embarrassed my meaning. What I want to say is which bond length is used as the standard? the C=N or Ca-N or even the side chains? Or all of them?Which angel is used to compare, the Ca-C'-N or C'-N-Ca or others. At first I suppose the bond length only calc

Re: [ccp4bb] ideal bond length and bong angel

Dear Prof Gerard: In fact I have read your Model Validation on-line, and I have to say it is youe lecture that made me to think about this problem, though I have used it as a common stand for the quality of the model without understand it for a long time. And the http://en.wikipedia.org/

[ccp4bb] apologize

A for bond length and 4 for bond angels", I just wonder about the standard of the bond length and the bond angel. I think most of you have read similar words! But maybe I didnot express clearly and made some phrasal mistakes. At last, happy new year to you all--though very late! Sincerely! Yang Li

[ccp4bb] Different chains in the dimer

Dear All, I have a protein which has the function unit as a dimer. I got two structures of it. One is the native structure, one is the mutant structure. Both structures are dimer in ASU. In the native structure the two chain look the same, but in mutant structure one chain still keep the sa

[ccp4bb] cns and refmac refinement

Dear All, I have a 3A structure, the quality of the data is not very good. Now I have refined it to Rfree=40.7 in Refmac. But it wonnot go further down. Then I used CNS to do annealing, then use refmac to do rigid body refinement. The Rfree converged to 0.34, but if I use restrain refinement

[ccp4bb] Correct the dihedral angles

Dear all, Does anybody have some good experiences or methods to adjust the outlier dihedral angles? I have a model most of which was builded manually, so though the Rfree is acceptable--0.29--manydihedral angles are not right. it is difficult to me to correct them. If there is any software to

[ccp4bb] phenix.refine and refmac

Dear All, I have post a similar question about CNS and refmac before, now in another structure I met a similar problem. I have an almost finished structure, the Rfree of which is about 0.28 by refmac. Then I used phenix to refine it, below is the result: REMARK REFINEMENT

Re: [ccp4bb] phenix.refine and refmac

lt, and that can be > auto-opened with coot, along with the coordinates. > > On Mar 4, 2008, at 7:27 AM, yang li wrote: > > > > >Since the map from phenix couldnot be opened by coot directly--or I > > donnot know how to--I used refmac to get a mtz map file. >

Re: [ccp4bb] phenix.refine and refmac

n > > addition, the presence of even a handful of strong but inaccurately > > measured/integrated low-resolution reflections in a limited test-set > > can aggravate abnormal behavior in R-free. > > > > Best wishes > > Savvas > > > > > > toQuot

[ccp4bb] Low resolution data with substrate

Hi All, We have several substrate-soaked data with resoltuion from 3.1~3.6A, after refinement with the native structure, the rfree are in the range of 0.29~0.34. We found in the expected active site there do have extra densities, but not very clear. In some chains the densities are big while in

[ccp4bb] Dashed lines in coot

Hi All, These days I found the model and the density map changed to dashed lines after typed something wrong in the keyboard, I donnot know what have been typed and couldnot change it back to the normal appearance until rerun coot. The version of my coot is 0.3.3 in fedora. Does anybody know a

[ccp4bb] Refinement of anisotropic data

Hi, I have a structure with 3 different resolutions, 2.3A, 2.4A, 2.5A, the qualities seem normal, not good but also not too bad. The B factors along a,b,c axis have notable difference, for example B(a)=80, B(b)=30, B(c)=20. We used molecular replacement to solve the structure. For the 2.3A data

Re: [ccp4bb] Refinement of anisotropic data

Hi, All, Thanks for all your replies. I checked the server as Pavel said, and found that the 2.3A data has strong anisotropy and other two has severe anisotropy. The recommend resolution cutoff in the c axis is only 3.4A. I need to read more about the manual but I think this is the problem. Ho

[ccp4bb] Generate high resolution pirctures in pymol

Hi all, Can somebody please help me to generate high resolution movie files for secondary structure of proteins? After I ray a model with high resolution in pymol and then save it as movie frames, the high resolution and ray seem lost. I have tried the command likes ray 2000,2000 and it does wo

[ccp4bb] Deal with close heavy atom sites?

Dear all, I have a 1.6A data in P21 spacegroup whith good quality, wich is assumed to contain 4 Set-Met. But the patterson map appears strange. There is a very big heavy peak in the harker section, and seems like an irregular ellipse, while there are small peaks very near(almost connect) to t