Re: [ccp4bb] [3dem] cryoNET inaugural symposia

[Guillermo Montoya]

Dear all,

 just a kind reminder. Last day to register is September 7th.
Looking forward meeting you in CPH

best regards


G.




On 31 Jan 2018, at 17:49, Guillermo Montoya 
mailto:guillermo.mont...@cpr.ku.dk>> wrote:

Dear colleagues,

I am sending this email to call your atention about the cryoNET inaugural 
symposia (8-9 Oct 2018) in Copenhagen. CryoNET is a Nordic network in 
Cryo-electron microscopy that is funded by The Novo Nordisk Foundation in 
Denmark and the Knut and Alice Wallenberg Foundation in Sweden. CryoNET aims to 
promote collaboration and knowledge sharing across national borders and one 
main goal is to help establish state-of-the-art cryo-electron microscopy as a 
strong pillar of Nordic life science research. The 1st Annual CryoNet Symposium 
will gather Scandinavian researchers, students and technical staff to discuss 
the latest advances in Cryo-electron microscopy with some of the world leading 
reserchers in the field. For those interested in more information and 
registration please use the link below:

http://www.cpr.ku.dk/events/2018/1st-annual-cryonet-symposium/


Looking forward seeing you in Copenhagen this fall


With kind regards,

Gunnar von Heijne  Poul NIssenBernt Eric 
Uhlin Guillermo Montoya
Stockholm University  Aarhus UniversityUmeå University  
Copenhagen University





Guillermo Montoya, Prof. Dr.
Research Director, Protein Structure and Function Programme
Novo Nordisk Foundation Center for Protein Research
Faculty of Health and Medical Sciences, University of Copenhagen,
Blegdamsvej 3A, DK-2200 Copenhagen, Denmark
web: www.cpr.ku.dk
PC: Lotta Avesson lotta.aves...@cpr.ku.dk



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[ccp4bb] Fwd: Re: [ccp4bb] coiled-coil "degree"

[Jorge Iulek]

My /acknowledgements/ to all that have replied to my question.
So many interesting inputs and points to software; I will be checking in 
the next days.

I will comment upon just some of the observations.

As far as we can, we try to take as "asymmetric unit content" what is 
"expected" (or sometimes, with experimental corroboration) to be the 
functional oligomer, but of course, generally, the most probable one.


We had previously used pisa, but to compare domain-domain contacts. Now 
we will take it again in a helix-helix context. But, together with the 
other software indicated.


Yours,

Jorge


On Tue, Aug 28, 2018 at 6:03 AM, Jorge Iulek > wrote:


   Dear all,


    I am working currently on a structure that, nicely, presents
   two different orientations between its domains when one compares
   monomers of the tetramer in the asymmetric unit.

    I notice, in this nature gift, that a helix, probably central
   (in its role) for the relation (orientation) between the two
   domains,  assumes different relation to other one (helix, that
   belongs to one of the domains) such that they are (significantly)
   more or less "coiled-coiled"one to another, once the domains are in
   the "close" or "open" conformation. We have already analyzed the
   hydrogen bonds and salt bridges that are disrupted (or formed) due
   to the different (domain and helix) conformations.

    I wonder whether there is a metric (easy to evaluate) to
   characterize how much the two helix are "around each other" (id est,
   how much "coiled-coiled" they are) and, preferably, a software to
   calculate this metric.

    Thank you,


   Jorge

   State University of Ponta Grossa

   

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Re: [ccp4bb] Refmac refinement: reduced disulfides

[Ursula Neu]

Hi Joel,

I'm working on a similar structure at the moment.

If refining in refmac, you could add a line to the pdb such as:

LINKRSG ACYS A  22 SG ACYS A  96SS

and tell the program to only use links defined in the pdb file.

If refining in phenix, you could set the parameter for the disulfide
distance cutoff from 3.0 to 2.4 A so that the automatic detection only
finds the "real" disulfides.

Good luck!

Ulla



> Dear all,
>
> I am refining structures containing disulfides using refmac. Many of the
> disulfides are partly broken due to radiation damage.
>
> I tried modeling alternative conformations (i.e. one cysteine pair in a
> disulfide and the other pair as free thiols), but after refinement the
> reduced form is forced back to its original position forming a disulfide
> bridge and resulting in difference density in the fo-fc map.
>
> How do I prevent a disulfide bond from being defined for the free thiol?
>
>
>
> Best regards,
>
> Joel Heim
>
> University of Oslo
>
> 
>
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[ccp4bb] Refmac refinement: reduced disulfides

[Joël Benjamin Heim]

Dear all,

I am refining structures containing disulfides using refmac. Many of the 
disulfides are partly broken due to radiation damage.

I tried modeling alternative conformations (i.e. one cysteine pair in a 
disulfide and the other pair as free thiols), but after refinement the reduced 
form is forced back to its original position forming a disulfide bridge and 
resulting in difference density in the fo-fc map.

How do I prevent a disulfide bond from being defined for the free thiol?



Best regards,

Joel Heim

University of Oslo



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