Re: [ccp4bb] Bond length and angle outlier fixing

Thanks all for the reply. I will follow your suggestion and will get back. Sincerely, On Thu, May 18, 2017 at 5:02 AM, Paul Adams wrote: > To add to Pavel’s comments, it is also possible to do the automated model > building in Phenix: > >

Re: [ccp4bb] Bond length and angle outlier fixing

To add to Pavel’s comments, it is also possible to do the automated model building in Phenix: http://www.phenix-online.org/documentation/reference/map_to_model.html As Pavel said: there is Phenix mailing list for Phenix-specific questions > On May 17, 2017, at 10:24 AM, Paul Emsley

Re: [ccp4bb] CYS modification and choice of PEG

If you were collecting at a long-ish wavelength (for NaI phasing, perhaps?) you might be able to see a peak there in an anomalous difference Fourier map. This would be a pretty cool discovery! JPK From: Keller, Jacob Sent: Wednesday, May 17, 2017 4:52 PM To: Antonio Ariza

Re: [ccp4bb] CYS modification and choice of PEG

Where would it get the sulphate to make sulphonate? Was there sulphate somewhere in the purification? Maybe it's a phosphate gotten off the FMN? I guess the phospho-cys bond might be a bit longer? JPK Analyst. 2014 Sep 7;139(17):4118-23. doi:

[ccp4bb] Associate Researcher Position at the University of Kansas Protein Structure Laboratory

The Protein Structure Laboratory at the University of Kansas is seeking a full-time Associate Researcher to assist with various structural biology projects. For a full description and to apply, GO TO: https://employment.ku.edu/staff/8691BR Review of applications begins 5/30/17 Regards,

Re: [ccp4bb] CYS modification and choice of PEG

On Wednesday, 17 May, 2017 20:03:42 Antonio Ariza wrote: > I haven't asked anything for a loong time, so here are a couple of > question "for the honourable members of the esteemed CCP4 bulletin board" ... > or as I'd usually say: "for y'all". ;) > > 1) I have this modified CYS in one of

Re: [ccp4bb] NAD dihedral for C2N-C3N-C7N-N7N

I’m not aware of a wide study on NAD carboxamide conformation. Lacking atomic resolution, optimizing the hydrogen bonding can be used to determine the orientation of the carboxamide, as you wrote. You may have to consider intramolecular hydrogen bonding within NAD+ as well as intermolecular

[ccp4bb] NAD dihedral for C2N-C3N-C7N-N7N

Dear all,     I came across some difficulty to refine a NAD molecule in a structure, specially its amide of the nicotinamide moiety.     A (very) brief search in deposited structures seems to point that not so ever the C2N-C3N-C7N-N7N dihedral is

Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

If your signal goes all the way to the half Nyquist frequency, oversample your map to have the pixel size equal to 1/3rd of the highest resolution. Your map will look much better in coot. Real space fitting will work much better as well. Best, Petr > On May 17, 2017, at 11:24 AM, MyeongSeon

Re: [ccp4bb] Poor density fit.

It sometimes help to use the coot tool NCS ghost control to fit the good chain over the weak. Obviously you must work at a lower contour level than for the good chain.. Of course be careful about the basics.. Is the space group right? is there twinning? Check data quality - anisotropy - tc..

Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

Hi, CCP-EM (CCP4 sister project for cryoEM) can help you here. We have a EM specific interface for several CCP4 programs as well as some others and will handle map to mtz conversions for you. You can download the suite here: http://www.ccpem.ac.uk/download.php We recently ran a workshop on

Re: [ccp4bb] Bond length and angle outlier fixing

On 17/05/2017 13:34, Vipul Panchal wrote: I am solving protein structure with 2.16A resolution. There are two chain in an asymmetric unit. While submitted to PDB validation server, i could see few ligand bond -length and -angle outlier. Coot doesn't have any module that can help me with these

Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

On 17/05/2017 17:24, MyeongSeon Lee wrote: Hi, all. I have collected cryoEM data and want to use Coot and CCP4 program to build model and to refine it. 1. What is the steps to do this? 2. How do I convert cryoEM map file to MTZ file? CCPEM provides an increasingly sophisticated tool-set

Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

Hi, 2. How do I convert cryoEM map file to MTZ file? > While technically you can do it, normally there is absolutely no need to do it. In cryo-EM the map is your data, not reflection data (structure factors!). So no need to 'massage' your data (the map) by converting it into "Fobs" and storing

[ccp4bb] Using Coot and CCP4 program for cryoEM data

Hi, all. I have collected cryoEM data and want to use Coot and CCP4 program to build model and to refine it. 1. What is the steps to do this? 2. How do I convert cryoEM map file to MTZ file? 3. Can I also use Phenix for this purpose? Thanks to all for your help in advance.

Re: [ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

Couple of wuestions: What is the procedure for updating an entry? Start a new submission, or mail revised coordinates along with an explanation of changes to deposit@rcsb? "unchanged experimental data" - does this mean the exact same structure factors, or will newly reduced data from the same

[ccp4bb] AW: [ccp4bb] Bond length and angle outlier fixing

Hi Vipul, The first thing to do is to check whether the fit of the offending residues in the electron density maps is correct. If it is not, you have to do rebuilding. If the fit is correct, I would leave them as they are. Assuming the distribution of bond lengths and angles has a bell-shape,

[ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

The wwPDB is planning to introduce in 2017 a new procedure for the management by the Depositor of Record (where the Depositor of Record is defined as the Principal Investigator for the entry) of substantial revisions to previously released PDB archival entries. At present, revised atomic

[ccp4bb] Bond length and angle outlier fixing

HI all. I am solving protein structure with 2.16A resolution. There are two chain in an asymmetric unit. While submitted to PDB validation server, i could see few ligand bond -length and -angle outlier. Coot doesn't have any module that can help me with these as per my best understanding. Kindly

[ccp4bb] 3D graphics under linux for coot, pymol and chimera

Hello, we just wanted to share our experience in finding a configuration which allows to use 3D graphics under linux using Nvidia GeForce 3D glasses. We had quite a hard time to find a configurations which works correctly.