[ccp4bb] COMPPA symposium registration deadline May 1!

[Oliver Clarke]

Hi all,

The deadline to register for the COMPPÅ symposium at Columbia University in New 
York (covering production, structure determination, functional analysis and 
engineering of membrane proteins, 17-19 June 2018) is coming up in less than a 
week - May 1!

Register here to attend and/or submit an abstract for a poster/short talk: 

https://www.comppaa.org/comppaa-symposium-2018

See below for a list of invited speakers with provisional titles - I think the 
meeting is shaping up very nicely, and we’d all love to see you there!

Cheers,
Oliver Clarke


Radu Aricescu: Human GABAA receptor structures and signalling mechanisms

Susan Buchanan: Structural insight into the biogenesis of beta barrel membrane 
proteins

Martin Caffrey: Mesophase Mirabilis. The Lipid Cubic Phase as a System for 
Investigating Membrane Proteins

Erhu Cao: Structures and mechanisms of the polycystic disease channel PKD2

Liz Carpenter: Structures of the glycosylation enzyme DPAGT1 help to explain 
how some congenital disorders of glycosylation arise

Bil Clemons: Computational tools to solve the membrane protein expression 
problem

Karen Fleming: Protein Folding Experiments Reveal Foundations of Stability in 
Membrane Proteins

Lucy Forrest: COMPPAAring and analyzing the structures and symmetries of 
membrane proteins using EncoMPASS

Tony Kossiakoff: Pre-Fabs: Developing “Plug and Play” fiducial marks

Werner Kühlbrandt: CryoEM of energy-converting membrane protein complexes

Kaspar Locher: Structural insight into bacterial and eukaryotic 
glycosyltransferases facilitating protein N-glycosylation

Chris Miller: A CLC-type F-/H+ antiporter in ion-swapped conformations

Dan Minor: Discovery of a Cryptic, DruggableSite in the Heart of a Polymodal 
Ion Channel

Crina Nimigean Ligand discrimination and gating in CNG channels

Poul Nissen: The structure and dynamics of P-type ATPases

Eduardo Perozo: Structural Basis of Voltage-Dependent Gating in Ion Channels 
and Enzymes

Andreas Plückthun: Evolving GPCRs for enabling structural and functional studies

Irina Serysheva: Ligand-mediated Allostery of IP3R Channel: Lessons from Cryo- 
EM

Randy Stockbridge: The unusually selective Fluc family fluoride channels

Nieng Yan: How is electrical signal generated? Structural and mechanistic 
investigations of Nav channels

Shigeyuki Yokoyama: Cell-free production of membrane proteins in soluble 
membrane fragments

Ming Zhou: Structure and mechanism of EIIC sugar transporters 

Re: [ccp4bb] Compound with flexible conformation but nM Kd

[WENHE ZHONG]

Hi Philippe,

The affinity was measured by SPR where we immobilized the protein on the chip. 
One thing I forgot to mention is that the association rate (kon) shown in SPR 
experiment for this compound is faster (>10-fold faster) compared to other 
analogues with similar koff. There is a pi-pi interaction between the scaffold 
structure and the protein (tyrosine ring). Is it possible that the hydrophobic 
substituent could facilitate the formation of this pi-pi interaction but not 
necessary to involve in the interaction? Thanks.

Kind regards,
Wenhe

> On Apr 27, 2018, at 1:50 AM, DUMAS Philippe (IGBMC) 
>  wrote:
> 
> 
> Le Jeudi 26 Avril 2018 16:50 CEST, WENHE ZHONG  
> a écrit:
> 
> Just to be sure: how was the nM affinity evaluated ? By in vitro 
> measurements, or by obtaining an IC50 by tests on cells ?
> Of course, if you are mentioning an IC50, you may have a measurement of the 
> efficacy of drug entrance in the cells, not just of specific binding to your 
> protein target.
> Philippe D.
> 
>> Dear Community,
>> 
>> A little bit out of topic here. We are applying the structure-based approach 
>> to design compounds that can bind our protein target. We have synthesized a 
>> series of analogues based on the same scaffold with different substituents 
>> at one particular site. The most potent analogue (nM Kd) has a long alkyl 
>> chain substituent. We thought this hydrophobic substituent should have 
>> strong interactions with the target protein leading to nM range affinity. 
>> However, crystal structures show very weak densities for this substituent 
>> and no obvious interaction between the substituent and the target protein, 
>> suggesting that this long alkyl chain substituent is flexible without 
>> binding to the protein. This binding site is relatively negative charged 
>> according to the electrostatic potential analysis.
>> 
>> So it is a puzzle to me that how this dynamic and hydrophobic alkyl chain 
>> substituent can lead the compound to achieve nM affinity (>10-fold better 
>> than any other substituent) — in particular the binding site is not 
>> hydrophobic and no interaction is found between the substituent and the 
>> protein.
>> 
>> Anything I have miss here that can increase the binding affinity without 
>> interacting with the target?
>> 
>> Thanks.
>> 
>> Kind regards,
>> Wenhe
>> 
>> 
>> 
> 
> 
> 
> 
> 
> 

Re: [ccp4bb] What's happened over the last five years with high-throughput protein crystallization screening?

[Tom Peat]

Unfortunately it is unlikely that the costs for robotic equipment (at least the 
larger scale equipment) will come down much.
It is effectively all ‘bespoke’ equipment and will never benefit from high 
volume manufacturing (nothing like phones or cars).
How many crystallisation centres are needed around the world? Maybe 100? 
Nothing like the tens of millions of cars, phones, etc.
Cheers, tom

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Daniel M. 
Himmel, Ph. D.
Sent: Friday, 27 April 2018 8:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] What's happened over the last five years with 
high-throughput protein crystallization screening?

I skimmed your paper, and overall it looks like a good overview
of high-throughput protein crystallization.  However, I was surprised
that no mention was made of Formulatrix Rock Maker software,
which is an excellent computer-aided graphical tool for designing
crystallization screens rapidly.  This software works either as a standalone
or in conjunction with the Formulatrix Formulator (which the paper DOES 
mention),
for preparing crystallization solutions, and/or an integrated system for
storing crystal drops and automatically photographing them under a microscope.

A great deal of experience and knowhow on high-throughput
protein crystallization was accumulated by
such researchers as Wladek Minor, Steve Almo, Jeff Bonanno,
and others, with whom I had the privilege of working during the
waning years of the "Protein Structure Initiative" and "Enzyme
Function Initiative".  The controversy of these projects stemmed
from the high expense of the robotic equipment that made them
possible, but the methodologies developed and lessons learned
may be useful for high-throughput protein crystallization both
in academia and industry.  Hopefully the cost of the robotic equipment
will come down.

-Daniel


On Thu, Apr 26, 2018 at 11:43 AM, Yibin Lin 
mailto:yyb...@gmail.com>> wrote:
Dear CCP4BB Community,

I would like to comment you guy a review of the last five years of
high-throughput protein crystallization screening  that would be a
magnificent help for all scientists that struggle with macromolecular
crystallization.

Please see attachment, as well as below:


https://www.tandfonline.com/doi/full/10.1080/17460441.2018.1465924

Thanks.

Kind regards,

Frank Lin

Re: [ccp4bb] What's happened over the last five years with high-throughput protein crystallization screening?

[Yibin Lin]

Dear Daniel,

I appreciate you for your really worthwhile comments that would be useful
for other scientists in this field.

Thanks.


Frank

On Thu, Apr 26, 2018, 17:13 Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:

> I skimmed your paper, and overall it looks like a good overview
> of high-throughput protein crystallization.  However, I was surprised
> that no mention was made of Formulatrix Rock Maker software,
> which is an excellent computer-aided graphical tool for designing
> crystallization screens rapidly.  This software works either as a
> standalone
> or in conjunction with the Formulatrix Formulator (which the paper DOES
> mention),
> for preparing crystallization solutions, and/or an integrated system for
> storing crystal drops and automatically photographing them under a
> microscope.
>
> A great deal of experience and knowhow on high-throughput
> protein crystallization was accumulated by
> such researchers as Wladek Minor, Steve Almo, Jeff Bonanno,
> and others, with whom I had the privilege of working during the
> waning years of the "Protein Structure Initiative" and "Enzyme
> Function Initiative".  The controversy of these projects stemmed
> from the high expense of the robotic equipment that made them
> possible, but the methodologies developed and lessons learned
> may be useful for high-throughput protein crystallization both
> in academia and industry.  Hopefully the cost of the robotic equipment
> will come down.
>
> -Daniel
>
>
> On Thu, Apr 26, 2018 at 11:43 AM, Yibin Lin  wrote:
>
>> Dear CCP4BB Community,
>>
>> I would like to comment you guy a review of the last five years of
>> high-throughput protein crystallization screening  that would be a
>> magnificent help for all scientists that struggle with macromolecular
>> crystallization.
>>
>> Please see attachment, as well as below:
>>
>>
>> https://www.tandfonline.com/doi/full/10.1080/17460441.2018.1465924
>>
>> Thanks.
>>
>> Kind regards,
>>
>> Frank Lin
>>
>
>

Re: [ccp4bb] What's happened over the last five years with high-throughput protein crystallization screening?

[Daniel M. Himmel, Ph. D.]

I skimmed your paper, and overall it looks like a good overview
of high-throughput protein crystallization.  However, I was surprised
that no mention was made of Formulatrix Rock Maker software,
which is an excellent computer-aided graphical tool for designing
crystallization screens rapidly.  This software works either as a
standalone
or in conjunction with the Formulatrix Formulator (which the paper DOES
mention),
for preparing crystallization solutions, and/or an integrated system for
storing crystal drops and automatically photographing them under a
microscope.

A great deal of experience and knowhow on high-throughput
protein crystallization was accumulated by
such researchers as Wladek Minor, Steve Almo, Jeff Bonanno,
and others, with whom I had the privilege of working during the
waning years of the "Protein Structure Initiative" and "Enzyme
Function Initiative".  The controversy of these projects stemmed
from the high expense of the robotic equipment that made them
possible, but the methodologies developed and lessons learned
may be useful for high-throughput protein crystallization both
in academia and industry.  Hopefully the cost of the robotic equipment
will come down.

-Daniel


On Thu, Apr 26, 2018 at 11:43 AM, Yibin Lin  wrote:

> Dear CCP4BB Community,
>
> I would like to comment you guy a review of the last five years of
> high-throughput protein crystallization screening  that would be a
> magnificent help for all scientists that struggle with macromolecular
> crystallization.
>
> Please see attachment, as well as below:
>
>
> https://www.tandfonline.com/doi/full/10.1080/17460441.2018.1465924
>
> Thanks.
>
> Kind regards,
>
> Frank Lin
>

Re: [ccp4bb] Compound with flexible conformation but nM Kd

[Edward A. Berry]

For proteins in membranes, or proteins purified in the presence of detergents 
and/or lipids, the active site is sometimes surrounded by a hydrophobic mileau. 
The actual concentration that the binding site sees is then dependent on 
partitioning of the ligand between the water (where its concentration for Kd is 
determined) and the hydrophobic phase. Hydrophobic substituents could then 
result in higher concentrations at the binding site, and thus lower the 
apparent Kd, while having nothing to do with binding.

On 04/26/2018 10:50 AM, WENHE ZHONG wrote:

Dear Community,

A little bit out of topic here. We are applying the structure-based approach to 
design compounds that can bind our protein target. We have synthesized a series 
of analogues based on the same scaffold with different substituents at one 
particular site. The most potent analogue (nM Kd) has a long alkyl chain 
substituent. We thought this hydrophobic substituent should have strong 
interactions with the target protein leading to nM range affinity. However, 
crystal structures show very weak densities for this substituent and no obvious 
interaction between the substituent and the target protein, suggesting that 
this long alkyl chain substituent is flexible without binding to the protein. 
This binding site is relatively negative charged according to the electrostatic 
potential analysis.

So it is a puzzle to me that how this dynamic and hydrophobic alkyl chain 
substituent can lead the compound to achieve nM affinity (>10-fold better than 
any other substituent) — in particular the binding site is not hydrophobic and no 
interaction is found between the substituent and the protein.

Anything I have miss here that can increase the binding affinity without 
interacting with the target?

Thanks.

Kind regards,
Wenhe

Re: [ccp4bb] Compound with flexible conformation but nM Kd

[IGBMC]

Le Jeudi 26 Avril 2018 16:50 CEST, WENHE ZHONG  a 
écrit:

Just to be sure: how was the nM affinity evaluated ? By in vitro measurements, 
or by obtaining an IC50 by tests on cells ?
Of course, if you are mentioning an IC50, you may have a measurement of the 
efficacy of drug entrance in the cells, not just of specific binding to your 
protein target.
Philippe D.

> Dear Community,
>
> A little bit out of topic here. We are applying the structure-based approach 
> to design compounds that can bind our protein target. We have synthesized a 
> series of analogues based on the same scaffold with different substituents at 
> one particular site. The most potent analogue (nM Kd) has a long alkyl chain 
> substituent. We thought this hydrophobic substituent should have strong 
> interactions with the target protein leading to nM range affinity. However, 
> crystal structures show very weak densities for this substituent and no 
> obvious interaction between the substituent and the target protein, 
> suggesting that this long alkyl chain substituent is flexible without binding 
> to the protein. This binding site is relatively negative charged according to 
> the electrostatic potential analysis.
>
> So it is a puzzle to me that how this dynamic and hydrophobic alkyl chain 
> substituent can lead the compound to achieve nM affinity (>10-fold better 
> than any other substituent) — in particular the binding site is not 
> hydrophobic and no interaction is found between the substituent and the 
> protein.
>
> Anything I have miss here that can increase the binding affinity without 
> interacting with the target?
>
> Thanks.
>
> Kind regards,
> Wenhe
>
>
>

[ccp4bb] 11th CCP4/APS Crystallographic School in the US

[Qingping Xu]

Just a friendly reminder that the deadline for applying the upcoming 
CCP4 school at APS is next Wednesday (5/2/2018), please apply or finish 
your application (if you have already applied) if you wish to 
participate in the school. Please let us know if you have any 
questions/concerns.


Qingping Xu
GMCA/APS
Argonne National Laboratory

===

Dear Colleagues,

We are pleased to announce the *11th annual CCP4 crystallographic school 
*“From data collection to structure refinement and beyond” will be held 
on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National 
Laboratory (ANL), near Chicago, Illinois, USA. All details can be found 
at http://www.ccp4.ac.uk/schools/APS-2018/index.php.


*Dates*: June 18 through 25, 2018

*Location*: Advanced Photon Source, Argonne National Laboratory, Argonne 
(Near Chicago), Illinois, USA


The school comprises two parts: *data collection workshop* and 
*crystallographic computing workshop*. Data collection workshop includes 
beamline training, data collection on GM/CA@APS beamlines 23ID-D and 
23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, 
and data processing. For data collection, only the participants' 
crystals will be used. Crystallographic computation workshop will 
feature many modern crystallographic software packages taught by authors 
and other experts. The daily schedule will be organized in three 
sections – lectures, tutorials, and hands-on (interactive 
trouble-shooting of the technical difficulties the participants face in 
their projects). We have had considerable success resolving these 
problems in past years, attested by resulting publications (see 
http://www.ccp4.ac.uk/schools/APS-school/publications.php).


*Applicants*: Graduate students, postdoctoral researchers and young 
scientists at the assistant professor level, along with 
commercial/industrial researchers are encouraged to apply. Only 20 
applicants will be selected for participation. Participants of the 
workshop are strongly encouraged to bring their own problem data sets or 
crystals so the problems can be addressed during data collection and/or 
computation workshops.


*Application*: Application deadline is *Wednesday May 2nd, 2018*. The 
application form, the program, contact info and other details can be 
found at http://www.ccp4.ac.uk/schools/APS-2018/index.php


*Registration fees*: The registration for application is free but there 
is $500 participation fee for the selected academic students and $950 
for the industrial researchers. The link for the on-line payments and 
instructions will be provided once the selection process is completed. 
The students will be responsible for their transportation and lodging. 
The workshop organizers can assist in making the lodging reservations at 
the Argonne Guest House. The workshop will cover all other expenses 
(including meals).


We hope to see you at the school.

Charles, Garib and Qingping

Re: [ccp4bb] size exclusion columns

[Sebastiano Pasqualato]

Hi Markus,
just be aware that silica-based SEC columns are very sensitive to alkaline pH 
conditions, so you should not use them at pH higher that 7.5
We found that to be a limitation and thus chose polymer-based columns.
Hth,
ciao,
Sebastiano

> On 26 Apr 2018, at 18:03, Markus Heckmann  wrote:
> 
> Dear all,
> 
> We are looking for a size exclusion chromatography column
> (silica-based) for protein purification prior to a MALS-detector. We
> looked for (www.waters.com BEH-450), Sepax (Unix-C 300) and Phenomex
> (BioZen SEC-3).  Any 'column' tips or recommendations when dealing
> with large proteins (MDa)?
> 
> Many thanks
> Markus



-- 
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

[ccp4bb] size exclusion columns

[Markus Heckmann]

Dear all,

We are looking for a size exclusion chromatography column
(silica-based) for protein purification prior to a MALS-detector. We
looked for (www.waters.com BEH-450), Sepax (Unix-C 300) and Phenomex
(BioZen SEC-3).  Any 'column' tips or recommendations when dealing
with large proteins (MDa)?

Many thanks
Markus

[ccp4bb] Compound with flexible conformation but nM Kd

[WENHE ZHONG]

Dear Community,

A little bit out of topic here. We are applying the structure-based approach to 
design compounds that can bind our protein target. We have synthesized a series 
of analogues based on the same scaffold with different substituents at one 
particular site. The most potent analogue (nM Kd) has a long alkyl chain 
substituent. We thought this hydrophobic substituent should have strong 
interactions with the target protein leading to nM range affinity. However, 
crystal structures show very weak densities for this substituent and no obvious 
interaction between the substituent and the target protein, suggesting that 
this long alkyl chain substituent is flexible without binding to the protein. 
This binding site is relatively negative charged according to the electrostatic 
potential analysis. 

So it is a puzzle to me that how this dynamic and hydrophobic alkyl chain 
substituent can lead the compound to achieve nM affinity (>10-fold better than 
any other substituent) — in particular the binding site is not hydrophobic and 
no interaction is found between the substituent and the protein.

Anything I have miss here that can increase the binding affinity without 
interacting with the target?

Thanks.

Kind regards,
Wenhe

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Engin Özkan]

Just to make the point that you are not alone, I have observed the same 
issue on Mac with CCP4-installed Coot 0.8.9.1 using latest OS and 
Xquartz. This started happening with a recent update.



Interestingly, the 'Edit Chi Angles' dialogue now allows us to modify 
non-chi angles as well (not sure if this was intentional), but only for 
some residues. For example, when I click on a Leu or Cys, I am given the 
options to also modify "C <--> CA" and "CA <--> N" torsional angles, 
generally known as psi and phi. But with Asp, I get no such options to 
modify psi and phi. Interestingly, with Glu, the only angles I am 
allowed to modify in the "Edit Chi Angles" dialog are psi and phi angles.



Engin


On 4/26/18 3:19 AM, Chris Richardson wrote:


​We have an issue with the 'Edit Chi Angles' dialogue in Coot on Macs 
using the version of Coot bundled with CCP4.



For some residues - such as Glu - the dialogue only shows the C <--> 
CA angle.  If you tick the 'Add Chi Angles for Hydrogens' box, it adds 
CA <--> N.



I've just compiled Coot on the same Mac using Fink, and the dialogue 
for this version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD 
angles for the same residue.



The CCP4 version which misbehaves is 0.8.9.1; the working Fink version 
is 0.8.9.  Both are running on OS X 10.11.6.



Has anyone else experienced this?  Any suggestions as to how to fix this?


Regards,


Chris


The Institute of Cancer Research: Royal Cancer Hospital, a charitable 
Company Limited by Guarantee, Registered in England under Company No. 
534147 with its Registered Office at 123 Old Brompton Road, London SW7 
3RP.


This e-mail message is confidential and for use by the addressee only. 
If the message is received by anyone other than the addressee, please 
return the message to the sender by replying to it and then delete the 
message from your computer and network.

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Charles Ballard - UKRI STFC]

Update 055 should have reverted out ASP, and update 056 (coming real soon now) 
should fix the other issues.

Charles


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
"Weiergräber, Oliver H."
Sent: 26 April 2018 15:06
To: ccp4bb 
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Indeed, update 54 from Mar 29 seems to have messed up several monomer 
definitions and/or their handling in coot (the version distributed with ccp4):
- GLU and ASP contain lines referencing GLN and ASN, respectively, preventing 
coot from finding any chi angles.
- For GLN, chi angles appear twice in the coot torsion dialog.
- Many amino acid definitions now contain main chain torsion angles, which are 
erroneously listed as chi in coot.

The coot version available from Paul Emsleys website comes with its own version 
of the monomer library, which seems to work fine.

Best
Oliver


  PD Dr. Oliver H. Weiergräber
  Institute of Complex Systems
  ICS-6: Structural Biochemistry
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson 
[176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk]
Sent: Thursday, April 26, 2018 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Oops - oh dear - GLN labels should NOT appear in a list devoted to GLU!!


Well spotted..
Eleanor



On 26 April 2018 at 10:34, Chris Richardson 
mailto:chris.richard...@icr.ac.uk>> wrote:
Many thanks for explaining where it is going awry.

Looking at GLU.cif in the monomer library that is part of the CCP4 
distribution, it contains the following lines:

 GLN  chi1 N  CA CB CG   180.000   15.000   3
 GLN  chi2 CA CB CG CD   180.000   15.000   3
 GLN  chi3 CB CG CD OE10.000   30.000   2

In the monomer library you link, it has:

 GLU  chi1 N  CA CB CG   180.000   15.000   3
 GLU  chi2 CA CB CG CD   180.000   15.000   3
 GLU  chi3 CB CG CD OE20.000   30.000   2

Which makes more sense.

Thanks again,

Chris

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Huw Jenkins mailto:h.t.jenk...@me.com>>
Sent: 26 April 2018 09:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

> On 26 Apr 2018, at 09:19, Chris Richardson 
> mailto:chris.richard...@icr.ac.uk>> wrote:
>
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
> version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
> same residue.

>From a quick look at the Fink coot.info it appears to get 
>the monomer library from here:

 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz

Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 
distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD of Glu 14 
A from the RNase tutorial model.



Huw

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten 
Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian 
M. Schmidt

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Weiergräber, Oliver H.]

Indeed, update 54 from Mar 29 seems to have messed up several monomer 
definitions and/or their handling in coot (the version distributed with ccp4):
- GLU and ASP contain lines referencing GLN and ASN, respectively, preventing 
coot from finding any chi angles.
- For GLN, chi angles appear twice in the coot torsion dialog.
- Many amino acid definitions now contain main chain torsion angles, which are 
erroneously listed as chi in coot.

The coot version available from Paul Emsleys website comes with its own version 
of the monomer library, which seems to work fine.

Best
Oliver


  PD Dr. Oliver H. Weiergräber
  Institute of Complex Systems
  ICS-6: Structural Biochemistry
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson 
[176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk]
Sent: Thursday, April 26, 2018 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Oops - oh dear - GLN labels should NOT appear in a list devoted to GLU!!


Well spotted..
Eleanor



On 26 April 2018 at 10:34, Chris Richardson 
mailto:chris.richard...@icr.ac.uk>> wrote:
Many thanks for explaining where it is going awry.

Looking at GLU.cif in the monomer library that is part of the CCP4 
distribution, it contains the following lines:

 GLN  chi1 N  CA CB CG   180.000   15.000   3
 GLN  chi2 CA CB CG CD   180.000   15.000   3
 GLN  chi3 CB CG CD OE10.000   30.000   2

In the monomer library you link, it has:

 GLU  chi1 N  CA CB CG   180.000   15.000   3
 GLU  chi2 CA CB CG CD   180.000   15.000   3
 GLU  chi3 CB CG CD OE20.000   30.000   2

Which makes more sense.

Thanks again,

Chris

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Huw Jenkins mailto:h.t.jenk...@me.com>>
Sent: 26 April 2018 09:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

> On 26 Apr 2018, at 09:19, Chris Richardson 
> mailto:chris.richard...@icr.ac.uk>> wrote:
>
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
> version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
> same residue.

>From a quick look at the Fink coot.info it appears to get 
>the monomer library from here:

 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz

Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 
distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD of Glu 14 
A from the RNase tutorial model.



Huw

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
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Prof. Dr. Sebastian M. Schmidt

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Eleanor Dodson]

Oops - oh dear - GLN labels should* NOT *appear in a list devoted to GLU!!


Well spotted..
Eleanor



On 26 April 2018 at 10:34, Chris Richardson 
wrote:

> Many thanks for explaining where it is going awry.
>
> Looking at GLU.cif in the monomer library that is part of the CCP4
> distribution, it contains the following lines:
>
>  GLN  chi1 N  CA CB CG   180.000   15.000   3
>  GLN  chi2 CA CB CG CD   180.000   15.000   3
>  GLN  chi3 CB CG CD OE10.000   30.000   2
>
> In the monomer library you link, it has:
>
>  GLU  chi1 N  CA CB CG   180.000   15.000   3
>  GLU  chi2 CA CB CG CD   180.000   15.000   3
>  GLU  chi3 CB CG CD OE20.000   30.000   2
>
> Which makes more sense.
>
> Thanks again,
>
> Chris
> 
> From: CCP4 bulletin board  on behalf of Huw
> Jenkins 
> Sent: 26 April 2018 09:47
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving
>
> > On 26 Apr 2018, at 09:19, Chris Richardson 
> wrote:
> >
> > I've just compiled Coot on the same Mac using Fink, and the dialogue for
> this version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles
> for the same residue.
>
> From a quick look at the Fink coot.info it appears to get the monomer
> library from here:
>
>  http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/
> refmac/Dictionary/refmac_dictionary_v5.41.tar.gz
>
> Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for
> CCP4 distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD
> of Glu 14 A from the RNase tutorial model.
>
>
>
> Huw
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee only.  If
> the message is received by anyone other than the addressee, please return
> the message to the sender by replying to it and then delete the message
> from your computer and network.
>

[ccp4bb] Postdoctoral position, Cambridge

[cwjs1]

A postdoctoral position is available to work on a Wellcome Trust funded project 
to investigate the molecular mechanisms of regulation of alternative pre-mRNA 
splicing in the group of Prof. Chris Smith 
(https://www.bioc.cam.ac.uk/research/uto/smithc 
). 
The position will be based in the University of Cambridge, Department of 
Biochemistry, Tennis Court Road, Central Cambridge. The project focuses on the 
mechanisms by which regulatory RNA binding proteins control splicing complex 
assembly at regulated splice sites, and builds upon our recent discovery of a 
master splicing regulator that acts in smooth muscle cells. It will involve a 
range of biochemical, molecular, proteomic, biophysical, structural and 
single-molecule techniques based in the PI's and collaborators labs. We need to 
recruit someone with expertise in structural biology (X-ray crystallography, 
Cryo-EM) and associated biophysical techniques to complement our established 
expertise in RNA molecular biology. Prior knowledge or experience of RNA 
splicing, RNA biology or nucleic acid-protein assemblies would be an advantage. 
The funds for this post are available for 5 years in the first instance.

Further details available at: http://www.jobs.cam.ac.uk/job/17208/ 
. 




***
Professor Chris Smith
Department of Biochemistry
Downing Site
Tennis Court Road
Cambridge CB2 1QW, UK

+44-1223-333655
cw...@cam.ac.uk 
mobile +44-7989 694083
http://www.bioc.cam.ac.uk/uto/smithc.html 


https://www.bioc.cam.ac.uk/ 
https://twitter.com/CamBiochem 
https://www.facebook.com/CamBiochem 
https://www.instagram.com/cambiochem/ 
https://www.linkedin.com/company/cambiochem/ 

***

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Chris Richardson]

Many thanks for explaining where it is going awry.

Looking at GLU.cif in the monomer library that is part of the CCP4 
distribution, it contains the following lines:

 GLN  chi1 N  CA CB CG   180.000   15.000   3
 GLN  chi2 CA CB CG CD   180.000   15.000   3
 GLN  chi3 CB CG CD OE10.000   30.000   2

In the monomer library you link, it has:

 GLU  chi1 N  CA CB CG   180.000   15.000   3
 GLU  chi2 CA CB CG CD   180.000   15.000   3
 GLU  chi3 CB CG CD OE20.000   30.000   2

Which makes more sense.

Thanks again,

Chris

From: CCP4 bulletin board  on behalf of Huw Jenkins 

Sent: 26 April 2018 09:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

> On 26 Apr 2018, at 09:19, Chris Richardson  wrote:
>
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
> version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
> same residue.

>From a quick look at the Fink coot.info it appears to get the monomer library 
>from here:

 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz

Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 
distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD of Glu 14 
A from the RNase tutorial model.



Huw

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
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[ccp4bb] MicroMAX research engineer opening at MAX IV

[Thomas Ursby]

Dear all,

A permanent position as Research Engineer for the recently funded 
microfocus and serial crystallography beamline MicroMAX is now available 
at the MAX IV Laboratory. For more information and to apply please 
follow this link:


https://lu.varbi.com/en/what:job/jobID:203507

or see the full list of vacancies at the MAX IV Laboratory website:

https://www.maxiv.lu.se/about-us/careerjobs/vacancies/

Deadline for application is May 15, 2018.

Kind regards,
Thomas Ursby

--

AX IV Laboratory logo

*Dr. Thomas Ursby
*Beamline Scientist, MicroMAX Beamline Project Manager

MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 224 84 Lund
Telephone +46 733 43 95 51
thomas.ur...@maxiv.lu.se
www.maxiv.se

[ccp4bb] 2 Postdoc positions at Fondazione Ri.MED - Palermo

[caterina alfano]

2 PostDoctoral positions are available in the Structural Biology and
Biophysics Unit @ Fondazione Ri.MED (www.fondazionerimed.eu).

The successful candidates will carry out scientific projects in the field
of structural biology and biophysics aimed at understanding the molecular
mechanisms underlying oncological and neurodegenerative pathologies with
particular emphasis on drug discovery. In particular, the research activity
will aim to provide biophysical and structural information of biological
phenomena guided by protein folding, protein aggregation and
protein-protein interactions, with the ultimate goal of discovering new
drugs.

The Ri.MED seeks two candidates with specific skills on advanced
biophysical techniques such as nuclear magnetic resonance, calorimetry,
surface plasmon resonance, high resolution atomic force microscopy and
crystallography, complemented by consolidated technical and methodological
skills in molecular biology and biochemistry.

For more info about the positions, please visit
http://www.fondazionerimed.eu/Contents/Selezioni.aspx


*DEADLINE 13th MAY 2018*

Best Regards

Caterina



Caterina Alfano, PhD

Group Leader

Structural Biology and Biophysics Unit

Fondazione Ri.MED

Via Bandiera, 11

90133, Palermo - Italy

Tel:+39 091 604 / +39 091 23893179

Email: *calf...@fondazionerimed.com*

*www.fondazionerimed.eu *

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Huw Jenkins]

> On 26 Apr 2018, at 09:19, Chris Richardson  wrote:
> 
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
> version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
> same residue.

From a quick look at the Fink coot.info it appears to get the monomer library 
from here:

 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz

Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 
distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD of Glu 14 
A from the RNase tutorial model.



Huw

[ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Chris Richardson]

?We have an issue with the 'Edit Chi Angles' dialogue in Coot on Macs using the 
version of Coot bundled with CCP4.


For some residues - such as Glu - the dialogue only shows the C <--> CA angle.  
If you tick the 'Add Chi Angles for Hydrogens' box, it adds CA <--> N.


I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
same residue.


The CCP4 version which misbehaves is 0.8.9.1; the working Fink version is 
0.8.9.  Both are running on OS X 10.11.6.


Has anyone else experienced this?  Any suggestions as to how to fix this?


Regards,


Chris

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.