Re: [ccp4bb] [phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density

Thanks for the advice Pavel! I don't want to celebrate prematurely, but I just re-ran the same refinement in both the stable and in nightly 4070, and it _seems_ to be corrected in the nightly. Will let you know if it pops up again. - Igor Petrik, PhD On Thu, Dec 3, 2020 at 9:16 AM Pavel Afonin

Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

Thanks Nigel, I will put together the input and output file from my latest refinement and send them to you and Pavel later today. - Igor Petrik, PhD On Wed, Dec 2, 2020 at 9:46 PM Folmer Fredslund wrote: > Dear Igor > > There's a phenix bulletin board for question like this, which is where yo

Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

Hi Folmer, I would choose to not do the real space refinement in phenix.refine during > the last rounds of refinement of a model, when sidechain positions are > essentially correct. > by design it is supposed to place and fit side chains as good as possible, satisfying both map fit and geometry c

Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

Dear Igor There's a phenix bulletin board for question like this, which is where you should post the question. ( I crosspost here) I would choose to not do the real space refinement in phenix.refine during the last rounds of refinement of a model, when sidechain positions are essentially correct

Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

Igor There is a Phenix BB for your Phenix related questions. You can subscribe here. http://www.phenix-online.org/mailman/listinfo/phenixbb In the meantime, please send the Phenix version and OS to myself and Pavel privately and I'm sure we can help. We may also need the inputs (privately, of co

[ccp4bb] Phenix refine distorting a sidechain despite correct density

I am refining a 1.71A X-ray structure with phenix refine. I have everything modelled in - ~150 residues in the ASU and a heme - and my R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out that two of my sidechains have distorted geometries. One is a His, and looking at it in C

Re: [ccp4bb] Phenix Refine

Hi Haytham, I'll respond on the phenix bulletin board (you can sign up at www.phenix-online.org)! All the best, Tom T >> when i refine using phenix.refine i get this error >> >> number of groups of duplicate atom labels:1 >> total number of affected atoms: 2 >> group "HETATM 3466 BR PDB F 1 .*. BR

[ccp4bb] Phenix Refine

when i refine using phenix.refine i get this error number of groups of duplicate atom labels:1 total number of affected atoms: 2 group "HETATM 3466 BR PDB F 1 .*. BR " "HETATM 3467 BR PDB F 1 .*. BR " could you please tell me what is that Haytham Wahba PhD stu UdeM

Re: [ccp4bb] Phenix refine has a problem with the added H, plz help

Dear Mohd, FYI: there is specific mailing list for PHENIX specific questions ( http://phenix-online.org/). Pavel. On Tue, Apr 26, 2011 at 10:56 AM, Salameh, Mohd A., Ph.D. < salameh.m...@mayo.edu> wrote: > Dear All, > > I normally refine my structure without the hydrogens until the final stage

[ccp4bb] Phenix refine has a problem with the added H, plz help

Dear All, I normally refine my structure without the hydrogens until the final stages. But today I'm facing a real trouble with phenix.refine!! It seems phenix.refine does not recognize the hydrogen atoms and writes out this message: "Fatal problems interpreting PDB file: number of atoms with unkno