Re: [ccp4bb] low resolution refinement

Dear CAI Qixu Refmac does an excellent job at low resolution. Many of the features available in version 5.6.x are described in a very recent Refmac paper Murshudov et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr (2011) vol. 67 (Pt 4) p

Re: [ccp4bb] low resolution refinement

Hi, External structure atomic bond distance restraints for use in refmac are generated using ProSMART. The webpage is here: http://www.ysbl.york.ac.uk/mxstat/Rob/index.html Email me if you want a pre-release version. Regards, Rob On 9 Jul 2011, at 18:00, Robbie Joosten wrote: > Hi Qixu, >

[ccp4bb] PhD position in Protein Crystallography and Biochemistry at University Kiel (Germany)

I would like to announce a PhD position in Protein crystallography and Biochemistry, on a project entitled "Structure/function studies of Toll-like receptor related proteins”. The project is associated with the centre of excellence “Inflammation at Interfaces”. The main goal of this PhD project

Re: [ccp4bb] low resolution refinement

Hi Qixu, In CCP4i the option is in the refinement parameters: Use hydrogen atoms: ["build all hydrogens"] and [] output to coordinate file What is does is build all hydrogens at the expected coordinates and constrain them in refinement (i.e. adding hydrogens does not add extra parameters

Re: [ccp4bb] low resolution refinement

Hi, Thank you for your suggestion. Could you tell me what is "riding hydrogens"? And it seems there is not "reference model" function in refmac5.6? 2011/7/9 Robbie Joosten > Dear Qixu, > > > > refamac 5.6 works well at these resolutions. You can add commands to your > refinement in CCP4i by u

Re: [ccp4bb] low resolution refinement

Hi, Thank you for your papers. I will read them carefully. 2011/7/9 Elizabeth McSweeney > Hi > > I highly recommend reading the two Brunger papers below: they will explain > the important factors to take note of when refining low-resolution > structures. I found them very useful when I was

Re: [ccp4bb] Arp/Wrap problem while model building

Dear Rojan, On 09/07/2011 09:56, Rojan Shrestha wrote: Hello, I am facing a problem in running “auto_tracing” in arp/wrap. At first I have tried using command line mode however I missed R-free value. I have added the “freelabin “ FREE=FREE ”” and have got an error “Refmac_5.5.0102: Error i

Re: [ccp4bb] how to distinguish between phase separation, spherulite, and microcrystalline?

I also got something shown in pic.3 and supposed to be some oil droplet,when I tried to break them I found that was actually a hemisphere type material attached to the coverslip like a 2D circle and sphere like shape in the hanging drop, a small hanging-drop within a large one.Ammonium sulfate w

[ccp4bb] Post-doc position in Structural Biology of RNA decay components near Paris (France)

Post-doctoral position in Structural biology of RNA decay components. Location: Orsay, near Paris (45 minutes by regular trains), France A 2,5 years post-doctoral position, funded by the ANR (Agence Nationale pour la Recherche), is available to study structural aspects of protein-protein a

Re: [ccp4bb] Potential Space Group Issue

Hi I'd run the reflection file through pointless rather than rely on cell dimensions and/or systematic absences. This is a quick and easy test to do and more reliable. As Bert suggests, the only real way to know the symmetry is after successful structure solution and refinement (but even

[ccp4bb] Fwd: [ccp4bb] Beta test versions of Mosflm & iMosflm

Dear all an addendum from Phil Evans - his aimless & pointless stuff is on our anonymous ftp site at ftp.mrc-lmb.cam.ac.uk then login with user name "anonymous" or "ftp", then cd to /pub/pre. Some web browsers (especially more modern ones) will take you straight there if you use

Re: [ccp4bb] low resolution refinement

Dear Qixu, refamac 5.6 works well at these resolutions. You can add commands to your refinement in CCP4i by using the 'Run and view command script' (or something like that) option and just typing in the extra commands. Jelly-body has worked very well for me (although I use tigheter restraint

Re: [ccp4bb] low resolution refinement

Hi I highly recommend reading the two Brunger papers below: they will explain the important factors to take note of when refining low-resolution structures.� I found them very useful when I was learning about low-resolution refinement. I would suggest using the deformable elastic network with

[ccp4bb] low resolution refinement

Dear all, Recently, I refine two low resolution structures in refmac 5.5. Their resolutions are 3A and 3.5A respectively. For 3A structure, after MR by phaser and rigidbody refinement&restraint refinement by refmac5.5, I got R factor 25% and R free 35%. And then each time, after my model build

[ccp4bb] Arp/Wrap problem while model building

Hello, I am facing a problem in running "auto_tracing" in arp/wrap. At first I have tried using command line mode however I missed R-free value. I have added the "freelabin " FREE=FREE "" and have got an error "Refmac_5.5.0102: Error in label assignments in LABIN" In another way, I use