Re: [ccp4bb] How to deal with the bad omega angles?

And I should add this works just great! (given we are on the same page defining 'great'). I used this for Cryo-EM model challenge; Nigel added this functionality at that time to make this possible. Pavel On Wed, Oct 11, 2017 at 2:17 AM, Nigel Moriarty wrote: > Since you are using phenix.real_s

Re: [ccp4bb] help identifying unknown density

Dear Eleanor, I think the best way is to use Mass spectrum to identify the compound. Best regards, Jiyong 在 2017-10-10 00:07:25，Eleanor Dodson 写道： Any anomalous signal?Eleanor On 9 October 2017 at 17:05, Gang Dong wrote: Could it be a formate ion (HCO2−)? _Gang -Original Message--

Re: [ccp4bb] How to deal with the bad omega angles?

Since you are using phenix.real_space_refine, there is a rather brutal parameter peptide_link.apply_all_trans=True that will restrains all peptide links to be trans. It can help with moving all cis to trans but you should check them as best you can at 4.3A. Cheers Nigel --- Nigel W. Moriarty B

Re: [ccp4bb] RapiData 2018

w Sent via the Samsung Galaxy Note5, an AT&T 4G LTE smartphone Original message From: Ana Gonzalez Date: 10/10/17 3:59 PM (GMT-06:00) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] RapiData 2018 The 2018 RapiData Course on Data Collection and Structure Solution will take place

[ccp4bb] RapiData 2018

The 2018 RapiData Course on Data Collection and Structure Solution will take place at the Stanford Synchrotron Radiation Lightsource (SSRL) from April 22-27 2018. The aim of the course is to educate and train scientists in data collection and processing methods at synchrotron beamlines, using state

[ccp4bb] teaching PDB, electron density file formats

Dear CCP4ers I am looking preferably for some papers that describe PDB file formats, electron density refinements. A primer kind of for PDB, macromolecule world for teaching medicine students. Any suggestions gratefully recd, Veronica

Re: [ccp4bb] How to deal with the bad omega angles?

Look at http://swift.cmbi.ru.nl/servers/html/index.html under "structure validation" you will find a server that predicts which peptide planes most likely need to be flipped. This server is the implementation of: Detection of trans-cis flips and peptide-plane flips in protein structures.

[ccp4bb] RE : [ccp4bb] help identifying unknown density

(I am new to ccp4bb and it is nice to read all those insightful discussions!) Dr. Cusack, Regarding your problem, we have observed a similar phenomenon in the past with a protein expressed in E. coli and purified using Ni-NTA resin. We later discovered that the density in the structure was indee

Re: [ccp4bb] How to deal with the bad omega angles?

Hi, Tristan Croll, Thanks for your suggestion.I will consider to rebuild these first. Yang > 在 2017年10月10日，下午9:18，Tristan Croll 写道： > > Relying on refinement to fix cis peptide bonds for you is unlikely to end > well. It looks to me like you really need to spend some time investigating > and

Re: [ccp4bb] How to deal with the bad omega angles?

Relying on refinement to fix cis peptide bonds for you is unlikely to end well. It looks to me like you really need to spend some time investigating and manually rebuilding these first. On 2017-10-10 13:52, 师扬 wrote: Dear all, I am refining a model based on a 4.3A EM density map,and there are

[ccp4bb] How to deal with the bad omega angles?

Dear all, I am refining a model based on a 4.3A EM density map,and there are some cis-peptides in the beginning model. By using phenix.real_space_refine with a very low cis-peptide threshold (0), all the cis-peptide become to the twisted. The start Omega angle: cis-proline: 31.6

Re: [ccp4bb] help identifying unknown density

You may have crystallized an enzyme that uses a phosphoramidate intermediate. https://en.wikipedia.org/wiki/Phosphoramidate On Oct 9, 2017, at 10:40 AM, Stephen Cusack mailto:cus...@embl.fr>> wrote: Dear All, I am refining the crystal structure of an E. coli expressed protein at 2.65 A re