[ccp4bb] open pdb and mtz in qtRView1.16 interface

Dear all, As we know, when a modelbuild procedure finish(such as buccaneer), we can open the input and output pdb/mtz file directly in qtRView interface by click the Coot/ccp4mg/Display button. And now, I am revising the OASIS package and hope that the intermediate results(e.g.: circle1.pdb,

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear All, Thank you very much for your suggestions. I will refine the structure and keep you updated. Khoa

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Hi Khoa, How many rounds of refine and rebuild have you gone through on the graphics? Have you tried Lorestr in CCP4 (Automated refinement of macromolecular structures at low resolution using prior information, Oleg Kovalevskiy, Robert A. Nicholls and Garib N. Murshudov). Ben [At 2.9A

Re: [ccp4bb] Antw: Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

The R factors may be high because the structure is imperfect - almost inevitable at that resolution - but also there are often serious difficulties with scaling at this resolution . If you are using REFMAC look at the v wrt resolution plot at the end of refinement (follows R and Rfree plot v

Re: [ccp4bb] Shape similarity of ligand binding sites

Hi Steve, Have you tried CASTp server (http://sts.bioe.uic.edu/castp/). That should help you to compare the shape of the ligand-binding sites. Best wishes, Avinash

[ccp4bb] What are acceptable Rwork/Rfree for publication

Dear CCP4 members, I am refining a structure with a resolution of ~ 2.9 A and the Rwork/Rfree are are 0.34/0.37, respectively. My question is that these Rwork/Rfree are acceptable for publication. If not, how can I reduce them? Thank you. Khoa The table of statics. Space group C121

[ccp4bb] Antw: Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

If you dont use Phenix, print the figures of https://doi.org/10.1016/S0969-2126(02)00743-8 and use them beside your screen. Helps a lot if you wanna have a quick look at Rfact distributions.. >>> Paul Emsley 14.06.17 15.25 Uhr >>> On 14/06/2017 14:09, Khoa Pham

Re: [ccp4bb] Unknown Ligand Density

Difficult to guess from what is visible of the protein but is this density on a two-fold axis? Or, it could be Slimer the ghost... Cheers, Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel:

[ccp4bb] Interaction of protein's glutamine sidechain nitrogen with a bound ligand's double bond

Dear CCP4bb, I recently solved the 2.0 Å crystal structure of a small hydrophobic molecule bound to a protein. A glutamine sidechain nitrogen is positioned ~3.3-3.4 Å from a double bond in the small molecule acyl chain. Could this be a similar interaction to the X-H (where X-H is an H-bond

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

On 14/06/2017 14:09, Khoa Pham wrote: Dear CCP4 members, I am refining a structure with a resolution of ~ 2.9 A and the Rwork/Rfree are are 0.34/0.37, respectively. My question is that these Rwork/Rfree are acceptable for publication. If you have Phenix, try POLYGON. That will give you a

Re: [ccp4bb] Shape similarity of ligand binding sites

Hi Stephen, I've had some luck calculating ligand-binding cavity volume with the 3v website (http://3vee.molmovdb.org/). You might want to give it a shot. Best, Chris On Wed, Jun 14, 2017 at 12:42 PM, < stephen.c...@rc-harwell.ac.uk> wrote: > Dear ccp4bb, > > I am trying to compare the shape

Re: [ccp4bb] Interaction of protein's glutamine sidechain nitrogen with a bound ligand's double bond

Yes, it very well could be, the distance is pretty typical for this kind of weak, "non-cannonical" hydrogen bond. However, directionality is an important aspect of hydrogen bonding and its hard to say if this is a reasonable bond without a (small filesize so no one's inbox gets overloaded)

[ccp4bb] PhD fellowships, Biozentrum Basel, Switzerland

The international PhD program of the Biozentrum, University of Basel, Switzerland, is open for applications until June, 20th. We encourage highly motivated students looking for an opportunity to carry out excellent structural biology research to apply now to the Biozentrum PhD program. The

[ccp4bb] <4SSQ/LL> and resolution (in refmac logfile)

Dear all, what is the relationship between <4SSQ/LL> and resolution? In refmac logfile, there is a table: <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 FSCfree FSCwork CorrFoFcFree CorrFoFcWork$$ $$ 0.0065130 0.894171 0.872301 0.882 0.734 0.8235 0.8078

Re: [ccp4bb] Unknown Ligand Density

First thing to check - is there any anomalous scatterer peak in the density? Easy to do an anom diff map from GUI2 - choose REFMAC and add - do anom diff fourier, then follow with a diff peak search in COOT . Eleanor On 14 June 2017 at 18:04, Sanishvili, Ruslan wrote: >

Re: [ccp4bb] Unknown Ligand Density

Flying spaghetti monster. Ramen! Sorry. Could not resist. Artem www.harkerbio.com "...touched by His Noodly Appendage" On Jun 14, 2017 12:51 PM, "Nick Thomas" wrote: Dear CCP4bb, I am refining a structure and have come across strong electron density for an unknown

Re: [ccp4bb] <4SSQ/LL> and resolution (in refmac logfile)

4(sin theta/lambda)^2 = 1/d^2 > On 14 Jun 2017, at 09:30, Wei Ding wrote: > > Dear all, > what is the relationship between <4SSQ/LL> and resolution? > In refmac logfile, there is a table: > <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 FSCfree > FSCwork

Re: [ccp4bb] <4SSQ/LL> and resolution (in refmac logfile)

Got it, thank you very much. -- Wei Ding P.O.Box 603 The Institute of Physics,Chinese Academy of Sciences Beijing,China 100190 Tel: +86-10-82649083 E-mail: ding...@iphy.ac.cn At 2017-06-14 16:54:23, "Phil Evans" wrote: >4(sin theta/lambda)^2 = 1/d^2 > >> On 14

[ccp4bb] Cryo-EM symposium, 4-5 September 2017, Delft University of Technology

Dear colleagues, We are pleased to announce the International Cryo-EM Symposium that will take place from 4-5 September 2017 in Delft, the Netherlands. With the aim to share the latest developments in 3D cryo-electron microscopy (EM) with scientists and students at the Delft University of

[ccp4bb] Shape similarity of ligand binding sites

Dear ccp4bb, I am trying to compare the shape of a ligand binding site in my protein with that of some homologues and mutants and was wondering how others go about this? I specifically want to compare the shapes of the surface (similar to an sc analysis of an interface) rather than the