Re: [ccp4bb] How to make covalent bond between sugar monomers?

Hi Leo, you should not need an additional cif file for coot but you might need to generate one for reciprocal space refinement. If you use REFMAC it might 'fail' in the first attempt with the message 'new ligand encountered' or something similar. It will, however, generate a single cif fi

Re: [ccp4bb] How to make covalent bond between sugar monomers?

Thank you, Paul. And do I need to provide additional cif file which describe the bond? Leo On Sep 4, 2014, at 2:23 PM, Paul Emsley wrote: > On 04/09/14 19:06, Lie Ma wrote: >> Hello all, >> >> I am trying to make a model of an oligosaccharide which contains several >> sugar monomers. I obtai

Re: [ccp4bb] Reliable criteria to tell Anomalous or not?

Also, if you process your data using XDS, it'll give you good indication for the strength of the anomalous signal. I find the XDS and Aimless indications to agree quite well.    Boaz     Boaz Shaanan, Ph.D. Dept. of Life Sciences   

Re: [ccp4bb] Extract Euler angles from fractional coordinate matrix

The orthogonal/fractional matrix is outlined here: http://www.iucr.org/__data/assets/pdf_file/0009/7011/19_06_cowtan_coordinate_frames.pdf Sorry to say I apparently ditched my old Fortran o2f and f2o programs to do that. Bear in mind, however, that orthogonal has no fixed orientation with res

Re: [ccp4bb] Reliable criteria to tell Anomalous or not?

Dear Charles, I usually look at the course of CC1/2 (anom) across the resolution bins. It should be high'ish at low resolution and a good resolution cut-off for e.g. shelxd is where it drops below 30%. The certainly by far best criteria is a traced structure (for a protein, though). With shelx c/

Re: [ccp4bb] Reliable criteria to tell Anomalous or not?

On Thu, Sep 4, 2014 at 4:05 PM, CPMAS Chen wrote: > Do you guys have some recommendation of the criteria? phenix reported > anomalous measurability, CCP4/aimless has RCRanom. Sometimes, they are not > consistent. > The "measurability" isn't always useful - it's definitely correlated with how eas

[ccp4bb] Reliable criteria to tell Anomalous or not?

Dear All CCP4 users, Recently, I have protein crystals cocrytallized with Br-containing ligand. sometimes, I feel confusion about whether the data have reliable anomalous information or not. Do you guys have some recommendation of the criteria? phenix reported anomalous measurability, CCP4/aimles

Re: [ccp4bb] Extract Euler angles from fractional coordinate matrix

I am sorry, just to clarify, the fractional coordinate matrix I referred to is a rotational matrix in the fractional coordinate system. On Thu, Sep 4, 2014 at 3:52 PM, Chen Zhao wrote: > Hi all, > > I am just curious whether there are some tools extracting the Euler angles > from a fractional c

[ccp4bb] Extract Euler angles from fractional coordinate matrix

Hi all, I am just curious whether there are some tools extracting the Euler angles from a fractional coordinate matrix. I have no luck searching it online. Alternatively, I found the analytical solution for the Euler angles from an orthogonal coordinate matrix. So in the worst case, my problem re

Re: [ccp4bb] Rmerge or Rpim for multiple datasets collected at different intensities

David, Thanks for providing your data. my CC1/2 is often about 0.6, 0.7 since I cut at I/sigmaI =2. Tim, you are right. I am conservative on this since I am still a new comer in this field. Charles On Thu, Sep 4, 2014 at 2:36 PM, Tim Gruene wrote: > Dear Charles, > > I would ignore (high reso

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Re: [ccp4bb] Rmerge or Rpim for multiple datasets collected at different intensities

Dear Charles, I would ignore (high resolution) R-values for justifying the rsolution cut-off. If you are talkig about 100s %, I have published data with Rmeas > 500% in the highest resolution shell. You are quite save cutting the resolution where I/sigI >= 2.0, by todays knowledge this is actuall

Re: [ccp4bb] How to make covalent bond between sugar monomers?

On 04/09/14 19:06, Lie Ma wrote: Hello all, I am trying to make a model of an oligosaccharide which contains several sugar monomers. I obtained the monomers from coot library and put them into the electron density. But I don't know how to make covalent bond between these monomers. If you ar

[ccp4bb] How to make covalent bond between sugar monomers?

Hello all, I am trying to make a model of an oligosaccharide which contains several sugar monomers. I obtained the monomers from coot library and put them into the electron density. But I don't know how to make covalent bond between these monomers. I tried to use PRODRG to generate a model an

Re: [ccp4bb] 3D monitors

It seems as though this topic is re-visited quite often on this discussion board. I would refer you to search the CCP4BB archives for an extensive amount of discussion on this topic over the past couple of years. A quick synopsis of an alterna

[ccp4bb] Rmerge or Rpim for multiple datasets collected at different intensities

Hi, All CCP4BB Users, I have quite some data sets(~15) collected at different beam intensities, the individual dataset can diffract to ~3.8 A @I/dI=2. If I combine them, with AIMLESS in CCP4, the resolution can be extended to ~3A@I/dI=2. But, the Rmerge or Rpim is way high, in 10s or even 100s. W

Re: [ccp4bb] 3D monitors

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[ccp4bb] 3D monitors

Dear all, I was wondering if there are 3D monitors for X-ray crystallography other than Zalman. Thanks Fares -- Dr. Fares Z. Najar Research Faculty/Adjunct Professor Department of Chemistry and Biochemistry Stephenson Life Sciences and Research Center 101 Stephenson Parkway Norman, OK 73019 E

[ccp4bb] Opportunity: transform user experience at Diamond

Hi all, recruitment plug for Diamond: The Data Acquisition (GDA) group at Diamond develop the software interfaces that many of you use a lot, if you collect your diffraction data there -- so presumably many of you have strong opinions about it, or indeed visionary ideas for what it could and s

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[ccp4bb]

Thank You all for your warm responses. The issue now has been resolved. The co-ordinate which pop up in the error box were not matching to the PDB text co-ordinates.So we have gone through the placed water molecules one by one in PBD text file and checked for the same co-ordinates. We could find t