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

Thanks for all the suggestions, and I will try them immediately! Best Yang > 在 2017年10月11日，上午8:55，Pavel Afonine 写道： > > 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

Re: [ccp4bb] ccp4 website not secure

Dear Markus, dear Michael, the certificate from ccp4 appears to be signed by QuoVadis Ltd. If I understand correctly, this is a trusted company, as of Firefox Version 32, according to the information at https://wiki.mozilla.org/CA/ Included_Certificates Maybe you need to UPdate, not DOWNdate

Re: [ccp4bb] model bias

And given that all these maps (Fo, Fc, and their differences) are made without the F000 term and so have average value zero, it is highly likely that Fc will be negative in the region of the deleted subunit (solvent is the lowest density in the model except for the chinks of vacuum between the

Re: [ccp4bb] model bias

This is hard to understand/impossible, at least in terms of simple 2fo-fc and fo-fc maps. We can think of a difference map as the difference between two maps, like fo-fc map = fo map - fc map. There is no model in the region, since you deleted it, so Fc=0, and Fo-Fc negative => Fo<0, so 2fo-fc

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Hi All, We have a postdoctoral position available and would appreciate your help in spreading the word. Postdoctoral Position in Structural and Chemical Biology of Neurodegenerative diseases. Position Description: Applicants are invited to apply for a postdoctoral fellowship position in Dr.

Re: [ccp4bb] model bias

A round of refinement with simulated annealing followed by minimization should address your concern. Pavel On Wed, Oct 11, 2017 at 4:48 PM, Karsten Dreifus wrote: > Dear all, > I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu. > Molrep (template with

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Re: [ccp4bb] ccp4 website not secure

OK, on second thought it might not be a good idea to downgrade the browser: On 10/11/2017 12:49 PM, Guillaume Gaullier wrote: Hello Edward, This website has some justification for using HTTPS everywhere: https://https.cio.gov/everything Downgrading a web browser is probably the worst advice

Re: [ccp4bb] areaimol missing symmetry mates

I got a symmetry-related molecule in the ASU (mine was about 400 A off the origin) and ran areaimol and the PDBe PISA server, and it worked on both! Got all the same contacts as my DIFFMODE COMPARE run. Thanks Paul! -Phillip From: CCP4 bulletin board

Re: [ccp4bb] ccp4 website not secure

Markus, I had that problem for a short while with slightly older versions of Firefox, but more recently (v54 - v56) it has not impacted any of the CCP4 sites. Whether it is a Firefox correction, I don’t know, but it is fine for me. Note that CCP4online is https://www.ccp4.ac.uk/ccp4online/

Re: [ccp4bb] ccp4 website not secure

Set up a certificate via letsencrypt and move to https? It is quick, easy and free. https://letsencrypt.org/ Darren On 11/10/17 18:34, Edward A. Berry wrote: Is it because of this? Its been coming for a while now: https://blog.mozilla.org/security/2015/04/30/deprecating-non-secure-http/ I

Re: [ccp4bb] ccp4 website not secure

Is it because of this? Its been coming for a while now: https://blog.mozilla.org/security/2015/04/30/deprecating-non-secure-http/ I see no reason why a website, dedicated to providing information available to everyone, should be required to use https. The web is too focused on e-commerce, where

Re: [ccp4bb] areaimol missing symmetry mates

Try moving your molecule closer to the origin, by unit cell shift or choosing a symmetry-related molecule. (In Coot, you can do this by using Extensions -> Modelling -> Symm Shift Reference Chain Here. Paul.

[ccp4bb] areaimol missing symmetry mates

Hello all, I'm having some issues with crystal contact analysis of a new structure I've solved. I initially tried to get the crystal contact areas using the PISA server on PDBe, but the results did not include several crystal contacts that I had identified myself using COOT. I tried running

[ccp4bb] model bias

Dear all, I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu. Molrep (template with 70 % seq identity) finds three NCS molecules (the template model has only 1 chain as it is in different space group). Now, REFMAC refines it to 25/30 % R/RFREE. I was just worried about model

Re: [ccp4bb] Yet another "what's my blob" thread, part II

Oops, should have mentioned that - Cryoprotectant was PEG200, 20%.

Re: [ccp4bb] teaching PDB, electron density file formats

Dear Veronica, you can look at PDB educational resourses here: http://www.rcsb.org/pdb/home/home.do#Category-learn PDB file format explained here: https://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html 2017-10-10 19:51 GMT+03:00 V F : > Dear

[ccp4bb] ccp4 website not secure

If anyone from CCP4 website has noticed that... Your connection is not secure The owner of www.ccp4.ac.uk has configured their web site improperly. To protect your information from being stolen, Firefox has not connected to this web site. (https warning message)

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