Re: [ccp4bb] Coot and XQuartz

[hari jayaram]

Hi Alexandra and Matt
I am using OSX Sierra 10.12.2 and Xquartz 2.7.11 and noticing severe
degradation in performance with coot and pymol. I can get the program to
load up and X11 window comes up. But if I try rotating even a small 30kd
protein , the rotation is smooth for two seconds and then the molecule
stops responding to the mouse.

I have tried this on a Macbook Pro and Macbook Air with different levels of
RAM ( 8GB and 16 GB ) and graphics card with same Xquartz and am close to
convinced there is something strange with Sierra and Xquartz ( a few months
before my Sierra upgrade -early Dec 2016 , I didnt see any issues with El
Capitaan ).

Wanted to add to your thread in case more people see this
Hari


On Thu, Dec 1, 2016 at 6:24 PM Matthew Bratkowski 
wrote:

> I recently upgraded to Sierra 10.12.1 and found that none of my
> crystallography programs (Coot, ccp4, phenix) worked.  I downloaded XQuartz
> again and that seemed to fix everything.  This is the only time that I
> upgraded my computer since probably 2013 or 2012, and the only reason that
> I did it was because I could not install Firefox on the old OS.  If you
> have the option to upgrade for free to the lastest OS, you could try doing
> that and then re-downloading XQuartz.
>
> Matt
>
> On Thu, Dec 1, 2016 at 5:09 PM, Deaconescu, Alexandra <
> alexandra_deacone...@brown.edu> wrote:
>
> Hello,
>
> I am having problems with running Coot on El Capitan 10.11.6. I have tried
> various versions of XQuartz from 2.7.7 to 2.7.9 with no success. As
> mentioned some time ago on the bb, I have also tried disabling rootless
> (System Integrity Protection) in OS X, but that also seemed to disable my
> ...keyboard.
>
> Does anyone have a solution to this, please?
>
> Thanks so much,
> Alexandra
>
>
>

Re: [ccp4bb] Off-topic question about SEC

[Christopher Colbert]

What's your monomeric molecular weight?  Increased salt concentration can 
easily drive oligomerization.

What is your evidence that it interacts with the resin?

Cheers,

Chris

--
Christopher L. Colbert, Ph.D.
Associate Professor
Department of Chemistry and Biochemistry
North Dakota State University
P.O. Box 6050 Dept. 2710
Fargo, ND 58108-6050
PH: (701) 231-7946
FAX: (701) 231-8324

From: CCP4 bulletin board > 
on behalf of Reza Khayat >
Reply-To: Reza Khayat >
Date: Wednesday, January 11, 2017 6:42 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
>
Subject: Re: [ccp4bb] Off-topic question about SEC


​All these make sense. Protein is very strange cause it goes from 60kDa 
(globular) to an apparent 360kDa. Process is reversible too.


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

From: CCP4 bulletin board > 
on behalf of Keller, Jacob 
>
Sent: Wednesday, January 11, 2017 7:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic question about SEC

Yes if it either

A) oligomerizes
B) significantly changes shape
C) aggregates reversibly

On option B: Lower NaCl could make the protein “appear” bigger by unfolding it 
a bit; hydrophobic interactions should be weaker in lower NaCl.

JPK





Artem
www.harkerbio.com
"where wild SEC columns roam free"

On Jan 11, 2017 7:22 PM, "Reza Khayat" 
> wrote:

Hi,



Sorry for the off-topic question. Can a protein in lower [NaC] run faster on a 
SEC than at higher [NaCl] (i.e. elute at an earlier volume)? The protein elutes 
well within the resolution limits of the SEC with a symmetric gaussian A280 
profile. I know that at lower [NaCl] the protein can elute later because it may 
interact with the matrix.  Thanks.



Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

[ccp4bb] Completely Off-Topic

[Keller, Jacob]

Dear Crystallographers,

Was anyone else aware that in E coli the intracellular glutamate concentration 
is ~100 mM? Also other cell types (yeast, mammalian) are 10s mM. Anything to 
say about this? I learned of this just recently, and have been amazed about it 
for more than a week. Did I miss this in Biochem 101? Does it matter?

JPK

***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email: kell...@janelia.hhmi.org
***

Re: [ccp4bb] Off-topic question about SEC

[Keller, Jacob]

Whoa! Big change! Any possible physiological relevance?

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Reza 
Khayat
Sent: Wednesday, January 11, 2017 7:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic question about SEC


​All these make sense. Protein is very strange cause it goes from 60kDa 
(globular) to an apparent 360kDa. Process is reversible too.


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

From: CCP4 bulletin board > 
on behalf of Keller, Jacob 
>
Sent: Wednesday, January 11, 2017 7:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic question about SEC

Yes if it either

A) oligomerizes
B) significantly changes shape
C) aggregates reversibly

On option B: Lower NaCl could make the protein “appear” bigger by unfolding it 
a bit; hydrophobic interactions should be weaker in lower NaCl.

JPK





Artem
www.harkerbio.com
"where wild SEC columns roam free"

On Jan 11, 2017 7:22 PM, "Reza Khayat" 
> wrote:

Hi,



Sorry for the off-topic question. Can a protein in lower [NaC] run faster on a 
SEC than at higher [NaCl] (i.e. elute at an earlier volume)? The protein elutes 
well within the resolution limits of the SEC with a symmetric gaussian A280 
profile. I know that at lower [NaCl] the protein can elute later because it may 
interact with the matrix.  Thanks.



Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

Re: [ccp4bb] Off-topic question about SEC

[Keller, Jacob]

Yes if it either

A) oligomerizes
B) significantly changes shape
C) aggregates reversibly

On option B: Lower NaCl could make the protein “appear” bigger by unfolding it 
a bit; hydrophobic interactions should be weaker in lower NaCl.

JPK





Artem
www.harkerbio.com
"where wild SEC columns roam free"

On Jan 11, 2017 7:22 PM, "Reza Khayat" 
> wrote:

Hi,



Sorry for the off-topic question. Can a protein in lower [NaC] run faster on a 
SEC than at higher [NaCl] (i.e. elute at an earlier volume)? The protein elutes 
well within the resolution limits of the SEC with a symmetric gaussian A280 
profile. I know that at lower [NaCl] the protein can elute later because it may 
interact with the matrix.  Thanks.



Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

Re: [ccp4bb] Off-topic question about SEC

[Artem Evdokimov]

Yes if it either

A) oligomerizes
B) significantly changes shape
C) aggregates reversibly

Artem
www.harkerbio.com
"where wild SEC columns roam free"

On Jan 11, 2017 7:22 PM, "Reza Khayat"  wrote:

> Hi,
>
>
> Sorry for the off-topic question. Can a protein in lower [NaC] run faster
> on a SEC than at higher [NaCl] (i.e. elute at an earlier volume)? The
> protein elutes well within the resolution limits of the SEC
> with a symmetric gaussian A280 profile. I know that at lower [NaCl] the
> protein can elute later because it may interact with the matrix.  Thanks.
>
>
> Best wishes,
> Reza
>
>
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
>
>
>

[ccp4bb] Off-topic question about SEC

[Reza Khayat]

Hi,


Sorry for the off-topic question. Can a protein in lower [NaC] run faster on a 
SEC than at higher [NaCl] (i.e. elute at an earlier volume)? The protein elutes 
well within the resolution limits of the SEC with a symmetric gaussian A280 
profile. I know that at lower [NaCl] the protein can elute later because it may 
interact with the matrix.  Thanks.


Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

Re: [ccp4bb] PDB validation of structure factors

[Pavel Afonine]

Hi Claire,

I afraid you did not provide enough information to answer your question
clearly.

What reflection file you submitted to PDB?

Note, Phenix refinement outputs MTZ file with four blocks of arrays:

- copy of input data (Fobs or Iobs, free-R flags);

- data actually used in refinement. This may be the same as above minus,
for example, possibly a few reflection outliers that the program decided to
not use in refinement). Or, if Iobs were given, then this array will be
Fobs.

- total model structure factors Fmodel (include all scales, bulk-solvent
contribution etc);

- various Fourier map coefficients (such as 2mFo-DFc, etc).

If you submitted this file I would have no idea what data array PDB uses.

If you can send me files off list for further investigation.

Pavel

P.S.: There is a Phenix mailing list for Phenix-related questions.


On Wed, Jan 11, 2017 at 2:31 PM, Claire Smith  wrote:

> Hello,
>
> I am trying to run the PDB validation report for a structure that I have
> refined in Phenix (data was analyzed with Xtriage). However, the run
> reports a discrepancy on the completeness of data, as follows:
>
> % Data completeness  97.4 (29.08-2.10)   Depositor
>
> (in resolution range)87.5 (29.08-1.92)EDS
>
>
> Why this discrepancy?
>
>
> Thanks so much,
>
> Claire
>
>
>
>

[ccp4bb] PDB validation of structure factors

[Claire Smith]

Hello,

I am trying to run the PDB validation report for a structure that I have
refined in Phenix (data was analyzed with Xtriage). However, the run
reports a discrepancy on the completeness of data, as follows:

% Data completeness  97.4 (29.08-2.10)   Depositor

(in resolution range)87.5 (29.08-1.92)EDS


Why this discrepancy?


Thanks so much,

Claire

[ccp4bb] Postdoctoral positions available in Melbourne, Australia - protein chemistry and enzymology of DNA repair

[Andrew Deans]

Two Postdoctoral Positions are available in the Genome Stability Unit @ St 
Vincent's Institute in Melbourne, Australia.

The Genome Stability Unit studies familial cancer syndromes that cause 
predisposition to breast/ovarian cancer, leukaemias and other solid tumours. 
These families inherit a defect in the ability to maintain genome stability and 
accumulate mutations at a faster rate, thus cancer occurs earlier in life with 
a higher probability. This mechanism of genome stability is intricate and 
involves a number of signalling and DNA repair pathways. We reconstitute these 
pathways biochemically using recombinant proteins and synthetic DNA molecules. 
Together with local and international partners, we aim to understand DNA repair 
function and suitability for drug targeting. We are looking for full-time 
postdoctoral leaders of two fully-funded projects:
Project 1: Functional analysis of new breast cancer predisposition genes.

Offers the challenge of developing a new biochemical functional test for 
several breast cancer predisposition genes linked to defects in DNA repair. 
This project is funded by the National Breast Cancer Foundation, and the 
postdoc would participate in a large Australia-wide consortium into familial 
breast cancer predisposition. Experimental approaches include working with 
patient samples, producing recombinant proteins, assaying DNA repair activity 
in vivo and in vitro, and integrating findings with data collected from over 
11,000 individuals from predisposed families. Structural biology components to 
the project are available to those with experience/interest, and the Institute 
is close to the Australian Synchrotron beam line.
Project 2: Development of new chemotherapy sensitisers.

Offers the challenge of identifying new drugs for the treatment of cancer, and 
cancer predisposition disorders. In this project the postdoc would undertake 
preclinical analysis of drug hits identified as inhibitors or activators of DNA 
repair signalling. There would be a particular focus on the Fanconi Anaemia DNA 
repair pathway, for which the lab has international expertise.  Elements of the 
project include biochemical reconstitution of DNA repair processes, and 
assaying and improvement of drugs identified in lab-based screens.

Coming from a strong scientific background, you will be expected to have:
* creativity and scientific curiosity
* independence and ability to collaborate
* a PhD in biology, medicine or chemistry discipline (or completing in early 
2017)
* a track record of producing quality results in a laboratory setting
* at least one first author paper in a strong, peer-reviewed publication

Nice-to-have (but we can teach you if you don't):
* knowledge of DNA repair pathways and processes
* expertise in protein chemistry, cell biology, genetics or oncology (project 1)
* expertise in protein chemistry, drug screening, preclinical development 
(project 2)

Australian postdoc salaries are considerably higher than in the US or Europe 
$74,689-$93,888 (dependent upon experience).
+9.5% superannuation
+generous $15,900 tax-exempt salary packaging
Melbourne is considered one of the world's most liveable cities, and is one of 
the top six biotech hubs:
Research themes and publications http://genomestability.weebly.com
Applications (or enquiries) should be addressed to Dr Andrew Deans 
ade...@svi.edu.au (for project 1) or Dr Wayne Crismani wcrism...@svi.edu.au 
(for project 2). Applications should include a cover letter addressing 
suitability and ambition for the position, 2-3 page CV and academic referee 
contact information. Please apply by January 31, 2017.

[ccp4bb] AW: [ccp4bb] Averaging of different proteins in heteromeric complex

[Herman . Schreuder]

Dear Graham,

Best would be to create alternative residues for the two proteins. A could be 
protein 1, B protein 2. As far as refinement programs are concerned, the 
alternatives need not to be identical and both alternatives are correctly 
linked to the common chain. You may have to do some pdb-hacking with an editor 
though. A quick test with coot revealed that the "mutate residue" option 
changes both alternatives.

Since you mention that both proteins are extremely similar, I would consider 
creating a consensus sequence for them, like was done for e.g. the antibodies 
or the serine proteases. This makes description and discussion of the different 
residues in papers a lot easier. You may get some trouble with some refinement 
programs, because some programs are no longer able to handle insertions and 
deletions. However, these are allowed by the pdb definitions and I consider not 
handling them a programming oversight.

Best,
Herman  



-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Graham 
Robinson
Gesendet: Mittwoch, 11. Januar 2017 17:37
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Averaging of different proteins in heteromeric complex

Dear Crystallographers,
Thank you very much Andrew, David, and Jacob (as well as others outside of the 
BB) for very helpful input on this problem. It does in fact appear that I have 
a very nice, statistically disordered structure.
In published structures containing statistical disorder authors have placed the 
different proteins in density according to knowledge from previous structures, 
and assigned occupancy of 0.5 to the entire chain. This is not possible in my 
case: I have a large, heteromeric ring, and one of the reasons for solving the 
structure in the first place was to characterise the arrangement of the two 
different proteins in the ring. Instead, I would like to build a consensus 
model, which represents both proteins. The resolved regions of each protein are 
extremely similar in primary sequence, and so, in the positions where the amino 
acids differ, I intend to prune the side chain either to the last common atom 
or to Ala, and name the residue a generic name (DLR, for DuaL Residue for 
example). I'd be interested to know if this a reasonable approach, and whether 
others have done a similar thing before?
The N-termini of the two proteins (not resolved) differ meaning that while the 
resolved regions are very similar in sequence the chain numbering differs. Is 
there a sensible way to account for this in a consensus chain? Is it reasonable 
to adopt chain numbering of one of the two proteins?
Thank you very much,
Graham

Re: [ccp4bb] Averaging of different proteins in heteromeric complex

[Graham Robinson]

Dear Crystallographers,
Thank you very much Andrew, David, and Jacob (as well as others outside of the 
BB) for very helpful input on this problem. It does in fact appear that I have 
a very nice, statistically disordered structure.
In published structures containing statistical disorder authors have placed the 
different proteins in density according to knowledge from previous structures, 
and assigned occupancy of 0.5 to the entire chain. This is not possible in my 
case: I have a large, heteromeric ring, and one of the reasons for solving the 
structure in the first place was to characterise the arrangement of the two 
different proteins in the ring. Instead, I would like to build a consensus 
model, which represents both proteins. The resolved regions of each protein are 
extremely similar in primary sequence, and so, in the positions where the amino 
acids differ, I intend to prune the side chain either to the last common atom 
or to Ala, and name the residue a generic name (DLR, for DuaL Residue for 
example). I'd be interested to know if this a reasonable approach, and whether 
others have done a similar thing before?
The N-termini of the two proteins (not resolved) differ meaning that while the 
resolved regions are very similar in sequence the chain numbering differs. Is 
there a sensible way to account for this in a consensus chain? Is it reasonable 
to adopt chain numbering of one of the two proteins?
Thank you very much,
Graham

[ccp4bb] EMBL-EBI is recruiting a Team Leader, Cellular Structure and 3D Bioimaging

[Gerard DVD Kleywegt]

Hi all,

We are seeking to recruit a Team Leader for the Cellular Structure & 3D 
Bioimaging team at the European Bioinformatics Institute (EMBL-EBI) located at 
the Wellcome Trust Genome Campus near Cambridge in the UK. EMBL-EBI is a 
world-leader in archival and dissemination of 3D biomacromolecular and 
cellular structure data. We accept and curate depositions of structural data 
for three global archives, PDB, EMDB and EMPIAR. We also maintain a number of 
databases that support advanced search, analysis and visualisation services 
for structural biologists and the wider scientific community.


The Cellular Structure & 3D Bioimaging team at EMBL-EBI manages the EMDB and 
EMPIAR archives and thus plays a key role in the global archival and 
dissemination of 3DEM data. We are now looking to recruit a Team Leader to 
provide visionary leadership of this team. The team is relatively small at 
present (6 posts, funded by EMBL-EBI, NIH, MRC and BBSRC), but we expect it to 
grow under the new team leader, as EMBL-EBI is establishing itself as a global 
leader in image-data repositories. This is a faculty level position reporting 
to Gerard Kleywegt, Head of the Molecular and Cellular Structure cluster.


For more information, see: 
https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj=55513=15470


Feel free to bring this vacancy to the attention of any suitable candidates 
you might know.


Best wishes,

--Gerard

---
Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
Head of Molecular and  Cellular Structure
ger...@ebi.ac.uk pdbe.org emdb-empiar.org
PA: Pauline Haslam   pdbe_ad...@ebi.ac.uk

[ccp4bb] EMBO practical course:High-throughput protein production and crystallization

[Opher Gileadi]

6th-14th of July, 2017 in Harwell (near Diamond/Oxford).

Registration deadline 15th of March. 
http://meetings.embo.org/event/17-protein-production

Re: [ccp4bb] To delete main chain or not

[V F]

Dear Herman and Pavel,

>
> First a remark: the pdb is a repository and if you insist, they will accept 
> anything you send them so, yes you can deposit this.
> However, your question is off course, do I want to deposit this? One does not 
> want to end up in the twilight gallery or
> deposit a structure where other crystallographers make fun of.

Hope I can avoid this!

> If you want to keep the residues, you need help from your free Rfactor. You 
> need to refine as good as possible the

R/Rfree is about 22/26. Whether, if I remove some of the residues
(4-5), it drops by about 0.5 %.
>
> Since you mention that the disorder only occurs when a ligand is bound, it 
> might have a (biological) function, which would provide an incentive to 
> delete the poorly defined regions to illustrate this. However, if you 
> obtained your ligand complex by soaking, the disorder might be caused by the 
> fact that an interesting conformational change is blocked by the crystal 
> packing. In this case you should try to get the complex by cocrystallization 
> as well, otherwise you might have to do this when you receive the referee 
> reports of your paper.
>
> models refined against low-resolution data (diffraction or cryo-EM) should
> have zero geometry violations (such as Ramachandran plot outliers or rotamer
> outliers). This does not mean real structures do not have such violations
> (in fact they do and there plenty of examples), but low-res data can't
> justify them.

Thank you.

[ccp4bb] AW: [ccp4bb] To delete main chain or not

[Herman . Schreuder]

Hi Veronica,

First a remark: the pdb is a repository and if you insist, they will accept 
anything you send them so, yes you can deposit this.
However, your question is off course, do I want to deposit this? One does not 
want to end up in the twilight gallery or deposit a structure where other 
crystallographers make fun of.

What I would do is to keep all residues that have some density, even at low 
level. Here you could go down as low as 0.6 to 0.8 sigma. However, if no 
density is present at all at these low levels, or if the density is scattered 
and unrelated to the model, I would delete it. I would only keep a few orphaned 
residues if they are either linked to the visible part of the protein, e.g. via 
a disulfide link, or have convincing interactions (Hbonds, salt links etc.) 
with the visible part of the protein.

If you want to keep the residues, you need help from your free Rfactor. You 
need to refine as good as possible the complete structure and also the 
structure with the weak/non-existent parts deleted. If the complete model has a 
lower Rfree than the truncated model, you might convince the referees that the 
complete model is better. Otherwise I would stick to the truncated model.

Since you mention that the disorder only occurs when a ligand is bound, it 
might have a (biological) function, which would provide an incentive to delete 
the poorly defined regions to illustrate this. However, if you obtained your 
ligand complex by soaking, the disorder might be caused by the fact that an 
interesting conformational change is blocked by the crystal packing. In this 
case you should try to get the complex by cocrystallization as well, otherwise 
you might have to do this when you receive the referee reports of your paper.

Best,
Herman




-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von V F
Gesendet: Mittwoch, 11. Januar 2017 12:25
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] To delete main chain or not

Hi all,
Since some emails were not REPLY ALL, I have answered them here:

The structure solved with MR; high sequence identity. Disorder occurs only when 
ligand is bound.  Model is almost 90 % complete except the disordered region. 
Please let me know if I can deposit structure as it is. I took example 1fcc 
(also low resolution). Seems many residues are outside Ramachandran plot (even 
Residue 266 has no density at all).
Does it mean I can deposit this?

> Yes, it is okay to exclude few residues or even short stretches of 
> loops/helices/strands if there is no reliable/convincing electron density for 
> them even at low map contours because if there is no convincing density you 
> cannot reliably model the local structure.

>
> However, if you refine with tight NCS, which you probably should do at this 
> resolution unless there are significant differences in the 4 molecules, you 
> can also choose to keep residues for which there is no reliable density in 
> one of the molecules, provided those residues are well resolved in the other 
> molecules and refine well (density, B-factors). Also use TLS refinement.

>
> Irrespective of which of the 2 options you choose, make sure to add a remark 
> in the PDB header about the option chosen, so that others know what was done 
> and if you write it up in a manuscript, describe it there as well.


> What is your R/Rfree currently? And what is the CC(1/2) of your data 
> at 2.8

> If you haven’t done so already, I’d delete suspect, refine and see if 
> difference density comes back for it.
The density looks similar to it.

> Perhaps the domain is disordered and really needs to be deleted.
> Other possibilities are that it is in an unexpected orientation or 
> conformation.
> You may need several iterations of deleting, rebuilding and adapting.
>

>   Were the input phases experimental or from a molecular replacement model, 
> and if the latter how complete was the model?
>
>

Re: [ccp4bb] To delete main chain or not

[Pavel Afonine]

Hi,

The structure solved with MR; high sequence identity. Disorder occurs
> only when ligand is bound.  Model is almost 90 % complete except the
> disordered region. Please let me know if I can deposit structure as it
> is. I took example 1fcc (also low resolution). Seems many residues are
> outside Ramachandran plot (even Residue 266 has no density at all).
> Does it mean I can deposit this?


models refined against low-resolution data (diffraction or cryo-EM) should
have zero geometry violations (such as Ramachandran plot outliers or
rotamer outliers). This does not mean real structures do not have such
violations (in fact they do and there plenty of examples), but low-res data
can't justify them.

Pavel

[ccp4bb] Reminder: Call for access to Synchrotron Beamline Facilities, 2017 - EMBL Hamburg, Germany

[Sarah Marshall-Bensch]

*REMINDER: Call for access to Synchrotron Beamline Facilities, 2017 - 
EMBL Hamburg, Germany*


We would like to reminder you about the call for synchrotron beam time 
applications in biological small-angle X-ray scattering (SAXS) and 
macromolecular crystallography (MX) for the period April - December 
2017. The following EMBL beamlines at PETRA III (DESY, Hamburg) are 
available: P12 (SAXS), P13 (MX), and P14 (MX).


Single proposals and BAG proposals are now being accepted for both 
methods, MX and SAXS. Groups applying for beamtime to work on several 
projects are strongly encouraged to submit a BAG (Block Allocation 
Group) proposal. The deadline for submission of proposals is *Monday 
January 23rd, 2017*, after which the proposals will be evaluated by an 
external Project Evaluation Committee. The users will be informed about 
the results of their application by March 13th, 2017.


A detailed description of the three beamlines and links to the 
electronic proposal forms can be found at:


SAXS: http://www.embl-hamburg.de/services/saxs/index.html
MX: http://www.embl-hamburg.de/services/mx/index.html

Submit a proposal via the EMBL Hamburg user portal 



Access to the EMBL Hamburg facilities also includes assistance with 
crystallisation, sample preparation and, in combination with an EMBL 
beamline visit, with sample characterisation and optimisation. Usage of 
the beamlines and biophysical facilities for translational research can 
in part be supported by the iNEXT project 
(http://www.inext-eu.org/access/), a Horizon 2020 programme of the 
European Union.


For further general information, please contact the EMBL Hamburg user 
office:

Tel.: +49 40-89902-111 / 183
Email: useroffice (at) embl-hamburg.de

For specific information:
saxs (at) embl-hamburg.de (small-angle X-ray scattering)
mx (at) embl-hamburg.de (macromolecular crystallography)
spc (at) embl-hamburg.de (sample preparation and characterization

Re: [ccp4bb] To delete main chain or not

[V F]

Hi all,
Since some emails were not REPLY ALL, I have answered them here:

The structure solved with MR; high sequence identity. Disorder occurs
only when ligand is bound.  Model is almost 90 % complete except the
disordered region. Please let me know if I can deposit structure as it
is. I took example 1fcc (also low resolution). Seems many residues are
outside Ramachandran plot (even Residue 266 has no density at all).
Does it mean I can deposit this?

> Yes, it is okay to exclude few residues or even short stretches of 
> loops/helices/strands if there is no reliable/convincing electron density for 
> them even at low map contours because if there is no convincing density you 
> cannot reliably model the local structure.

>
> However, if you refine with tight NCS, which you probably should do at this 
> resolution unless there are significant differences in the 4 molecules, you 
> can also choose to keep residues for which there is no reliable density in 
> one of the molecules, provided those residues are well resolved in the other 
> molecules and refine well (density, B-factors). Also use TLS refinement.

>
> Irrespective of which of the 2 options you choose, make sure to add a remark 
> in the PDB header about the option chosen, so that others know what was done 
> and if you write it up in a manuscript, describe it there as well.


> What is your R/Rfree currently? And what is the CC(1/2) of your data at 2.8

> If you haven’t done so already, I’d delete suspect, refine and see if 
> difference density comes back for it.
The density looks similar to it.

> Perhaps the domain is disordered and really needs to be deleted.
> Other possibilities are that it is in an unexpected orientation or 
> conformation.
> You may need several iterations of deleting, rebuilding and adapting.
>

>   Were the input phases experimental or from a molecular replacement model, 
> and if the latter how complete was the model?
>
>