[ccp4bb] postdoc position and lab manager, Halic lab, SJCRH

[Bilokapic, Silvija]

Dear all

exciting new opportunities in Halic lab:
postdoc position
https://jobrxiv.org/job/st-jude-childrens-research-hospital-27778-chromatin-silencing-in-fission-yeast/

lab manager
https://jobrxiv.org/job/st-jude-childrens-research-hospital-27778-lab-manager-in-cryo-em-chromatin-lab/


@LabHalic
To apply, send a CV and the names of at least two references to 
mario.ha...@stjude.org


Silvija Bilokapic, PhD

Structural Biology

St. Jude Children’s Research Hospital

262 Danny Thomas Place

Memphis, TN 38105-3678



Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer



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[ccp4bb] Open Position

[Carter, Charlie]

We are searching for a post-doctoral associate with expertise in analytical 
chemistry and chemical biology and interest in a project entitled 
“Translatomics of Ribosome-Free Coded Peptide Bond 
Formation”.
 This is a collaborative effort between UNC-Chapel Hill Professors Charlie 
Carter, Qi Zhang, and Abigail Knight and the position will be based in the 
Knight group. The 
project
 seeks to evaluate a ribosome-free system for high throughput experimental 
analysis of elements leading to the origin of genetic coding. Experience and 
enthusiasm for quantitative LC-MS and database generation are preferred. The 
successful candidate will participate as part of a team in all aspects of the 
experimental design and analysis and be primarily responsible for developing a 
high-throughput pipeline to quantitate synthesis of templated dipeptides using 
liquid chromatography-mass spectrometry or other means, together with designing 
and building a database for results. The position 
(https://unc.peopleadmin.com/postings/188831) is available now and will be 
filled as soon as possible. Salary will be determined by years of experience 
and based on UNC guidelines.

Please contact Dr. Abigail Knight (akni...@unc.edu) and 
copy Charlie Carter (car...@med.unc.edu) with a 
cover letter, CV, and reference letters.

Charles W. Carter, Jr
Department of Biochemistry and Biophysics CB 7260
University of North Carolina at Chapel Hill
Tel:  919 966-3263
FAX: 919 966-2852
email: car...@med.unc.edu



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Re: [ccp4bb] coot & other graphics programs draw too many bonds

[Paul Emsley]

On Thu, 2021-04-01 at 15:02 +0200, Fred Vellieux wrote:
> Hello there,
> 
> After running autodock vina on certain small molecules, the graphics 
> software I am using (e.g. Pymol, Coot) draws far too many bonds on the 
> docked small molecule. See enclosed screen capture.
> 
> Is there any way to prevent this from happening? This isn't very 
> satisfactory of you wish to produce figures for a presentation or for 
> publication.
> 

Is this a fish of the month? It looks like you are drawing a mol file
(with bond lengths equal to 1). Is that right? You need to convert it
to a 3D molecule using Acedrg or some such.

Paul.



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[ccp4bb] Improved support for extended PDBx/mmCIF structure factor files in OneDep

[Jasmine Young]

Extensions to the PDBx/mmCIF dictionary for reflection data with 
anisotropic diffraction limits, for unmerged reflection data, and for 
quality metrics of anomalous diffraction data are now supported in OneDep.


In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group 
 was convened to develop a richer 
description of experimental data and associated data quality metrics. 
Members of this Data Collection and Processing Subgroup are all actively 
engaged in development and support of diffraction data processing 
software. The Subgroup met virtually for several months discussing, 
reviewing, and finalizing a new set dictionary content extension that 
were incorporated into the PDBx/mmCIF dictionary 
 on 
February 16, 2021. A reference implementation of the new content 
extensions has been developed by Global Phasing Ltd. 



These extensions facilitate the deposition and archiving of a broader 
range of diffraction data, as well as new quality metrics pertaining to 
these data. These extensions cover three main areas:


1. scaled and merged reflection data that have been processed to take
   account of diffraction anisotropy, by providing descriptors for that
   anisotropy, in terms of (1) a parameter-free definition of a cut-off
   surface by means of a per-reflection “signal” and a threshold value
   for that signal, and (2) the ellipsoid providing the best fit to the
   resulting cut-off surface;
2. scaled and unmerged reflection data, by providing extra item
   definitions aimed at ensuring that such data can be meaningfully
   re-analysed, and their quality assessed independently from the
   associated model, after retrieval from the archive;
3. anomalous diffraction data, by adding descriptors for numerous
   relevant, but previously missing, statistics.

The new mmCIF data extensions describing anisotropic diffraction now 
enable archiving of the results of Global Phasing’s STARANISO program. 
Developers of other software can make use of them or extend the present 
definitions to suit their applications. Example files created by 
autoPROC, BUSTER (version 20210224 
) 
and Gemmi that are compliant with the new dictionary extensions are 
provided in a GitHub repository 
.


These example files, and similarly compliant files produced by other 
data processing and/or refinement programs, are suitable for direct 
uploading to the wwPDB OneDep system. Automatic recognition of that 
compliance, implemented by means of explicit dictionary versioning using 
the new pdbx_audit_conform record, will avoid unnecessary pre-processing 
at the time of deposition. This improved OneDep support will ensure a 
lossless round trip between data processing/refinement in the lab and 
deposition at the PDB.


wwPDB strongly encourages structural biologists to always use the latest 
versions of structure determination software packages to produce data 
files for PDB deposition. wwPDB also encourages crystallographers 
wishing to deposit new structures together with their associated 
diffraction data to use the software which guarantees consistency 
between data and final model. This consistency is difficult to achieve 
when separate diffraction data files and model coordinate files are 
pieced together /a posterior/i by /ad hoc/ means.


wwPDB also encourages depositors to make their raw diffraction images 
available from one of the public repositories 
 to allow direct access to 
the original diffraction image data.





--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




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Re: [ccp4bb] coot & other graphics programs draw too many bonds

[Tomas Malinauskas]

Hi Fred,

At least Schrodinder's PyMOL 2.3.2 can open Vina's PDBQR files (with
multiple docked conformations) without any problems or additional CIFs
in my experience. Different conformations of ligands are loaded as
different states.

It if is an older version you could try to convert Vina's PDBQR to PDB:

1. Split PDBQT file (vina_split comes together with Vina):
vina_split --input file.pdbqt

2. Convert PDBQT to PDB:

cut -c-66 file_1.pdbqt > file_1.pdb
grep 'ATOM' file_1.pdb > file_1_lines_with_atoms_only.pdb

Best wishes,
Tomas

On Thu, Apr 1, 2021 at 2:02 PM Fred Vellieux
 wrote:
>
> Hello there,
>
> After running autodock vina on certain small molecules, the graphics
> software I am using (e.g. Pymol, Coot) draws far too many bonds on the
> docked small molecule. See enclosed screen capture.
>
> Is there any way to prevent this from happening? This isn't very
> satisfactory of you wish to produce figures for a presentation or for
> publication.
>
> Ta,
>
> Fred.
>
> --
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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Re: [ccp4bb] coot & other graphics programs draw too many bonds

[Johannes Cramer]

Hi Fred,

are you using the output from vina directly (I think it is called pdbrq)?
If so, you could try converting it to mol2, before loading it into pymol.

Cheers,
Johannes

Am Do., 1. Apr. 2021 um 15:59 Uhr schrieb Robbie Joosten <
robbie_joos...@hotmail.com>:

> Hi Fred,
>
> I think this is a problem of not having the right description of the
> compound. Have you tried using a restraint file for the compound in Coot so
> the bonds are properly defined? Note sure if Coot uses them, but perhaps
> also remove all the CONECT records.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Fred
> > Vellieux
> > Sent: Thursday, April 1, 2021 15:02
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] coot & other graphics programs draw too many bonds
> >
> > Hello there,
> >
> > After running autodock vina on certain small molecules, the graphics
> > software I am using (e.g. Pymol, Coot) draws far too many bonds on the
> > docked small molecule. See enclosed screen capture.
> >
> > Is there any way to prevent this from happening? This isn't very
> satisfactory
> > of you wish to produce figures for a presentation or for publication.
> >
> > Ta,
> >
> > Fred.
> >
> > --
> > MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech
> > Republic
> >
> >
> > ###
> > #
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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> available at
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> 
>
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Re: [ccp4bb] coot & other graphics programs draw too many bonds

[Robbie Joosten]

Hi Fred,

I think this is a problem of not having the right description of the compound. 
Have you tried using a restraint file for the compound in Coot so the bonds are 
properly defined? Note sure if Coot uses them, but perhaps also remove all the 
CONECT records.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Fred
> Vellieux
> Sent: Thursday, April 1, 2021 15:02
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] coot & other graphics programs draw too many bonds
> 
> Hello there,
> 
> After running autodock vina on certain small molecules, the graphics
> software I am using (e.g. Pymol, Coot) draws far too many bonds on the
> docked small molecule. See enclosed screen capture.
> 
> Is there any way to prevent this from happening? This isn't very satisfactory
> of you wish to produce figures for a presentation or for publication.
> 
> Ta,
> 
> Fred.
> 
> --
> MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech
> Republic
> 
> 
> ###
> #
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
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Re: [ccp4bb] AW: [ccp4bb] High Rs

[Eleanor Dodson]

Agree with Herman except re using refined model as search model. This will
almost always return the answer you started from..
Eleanor

On Thu, 1 Apr 2021 at 13:49, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> Dear Sam,
>
>
>
> The first thing that would come to my mind would be ice rings, but since
> you said you don’t have them, there must be another reason for the high Rs.
>
> Zanuda will give you back the space group you used for MR and maybe a
> higher symmetry space group, but the program cannot be used to confirm that
> the space group you assigned is correct. For that, you will have to run
> Phaser with all possible P2x2x2x permutations. I assume you have already
> done that. If not, that would be the second thing I would try. You could
> even use your rebuild model as a search model.
>
>
>
> The next thing would be to look into the ligand you used. If the ligand
> has partial occupancy and induces some conformational changes in the
> protein, your crystal may contain proteins with a mixture of conformations,
> which may also give rise to higher Rfactors.
>
>
>
> Good luck, Herman
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Sam
> Tang
> *Gesendet:* Donnerstag, 1. April 2021 14:28
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] High Rs
>
>
>
> Dear all
>
>
>
> I have a dataset processed to 2.2 A, P212121, with no major issues
> identified by Xtriage (no tNCS, no twinning, no ice ring, good
> completeness). Phaser-MR gave a good solution except some loop regions are
> shifted. There is only 1 molecule in the ASU (and seemingly no more
> molecule can be accommodated). I fitted the displaced loops, and confirmed
> the space group by Zanuda, but the R-factors stuck at 0.34/0.41 range.
> What other aspects should I look into? Twin-refinement? (I am a bit
> reluctant to do so because neither Xtriage nor Pointless report it is
> twinned) I should also point out that the crystal was grown with its ligand
> but I cannot see good density for it.
>
>
>
> BRs
>
>
>
> Sam
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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> 
>
> --
>
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[ccp4bb] coot & other graphics programs draw too many bonds

[Fred Vellieux]

Hello there,

After running autodock vina on certain small molecules, the graphics 
software I am using (e.g. Pymol, Coot) draws far too many bonds on the 
docked small molecule. See enclosed screen capture.


Is there any way to prevent this from happening? This isn't very 
satisfactory of you wish to produce figures for a presentation or for 
publication.


Ta,

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic




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[ccp4bb] AW: [ccp4bb] High Rs

[Schreuder, Herman /DE]

Dear Sam,

The first thing that would come to my mind would be ice rings, but since you 
said you don't have them, there must be another reason for the high Rs.
Zanuda will give you back the space group you used for MR and maybe a higher 
symmetry space group, but the program cannot be used to confirm that the space 
group you assigned is correct. For that, you will have to run Phaser with all 
possible P2x2x2x permutations. I assume you have already done that. If not, 
that would be the second thing I would try. You could even use your rebuild 
model as a search model.

The next thing would be to look into the ligand you used. If the ligand has 
partial occupancy and induces some conformational changes in the protein, your 
crystal may contain proteins with a mixture of conformations, which may also 
give rise to higher Rfactors.

Good luck, Herman

Von: CCP4 bulletin board  Im Auftrag von Sam Tang
Gesendet: Donnerstag, 1. April 2021 14:28
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] High Rs

Dear all

I have a dataset processed to 2.2 A, P212121, with no major issues identified 
by Xtriage (no tNCS, no twinning, no ice ring, good completeness). Phaser-MR 
gave a good solution except some loop regions are shifted. There is only 1 
molecule in the ASU (and seemingly no more molecule can be accommodated). I 
fitted the displaced loops, and confirmed the space group by Zanuda, but the 
R-factors stuck at 0.34/0.41 range.  What other aspects should I look into? 
Twin-refinement? (I am a bit reluctant to do so because neither Xtriage nor 
Pointless report it is twinned) I should also point out that the crystal was 
grown with its ligand but I cannot see good density for it.

BRs

Sam



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Re: [ccp4bb] High Rs

[Eleanor Dodson]

Obviously something is wrong or missing but not enough info here to
diagnose..

Check data processing very carefully. Look at plots of Rmerge v batch - did
the crystal die at some point? At least in CCP4 you can restrict merging to
a range of batches..

Wilson plot shapely?

Spikes in the Second moment plot??

etc etc..
Getting the two fold screw axes for the spacegroup wrong - ie P212121 or
P21212 , etc - would give that sort of R values since 50% of the
reflections would be OK - 50% not.


Check the R search with "test all spacegroups in the Laue group" usually
fixes that.

Twinning not common for orthorhombic but in some cases possible - eh if a ~
equal b.. but twin plots usually show that.

Etc etc Eleanor

On Thu, 1 Apr 2021 at 13:28, Sam Tang  wrote:

> Dear all
>
> I have a dataset processed to 2.2 A, P212121, with no major issues
> identified by Xtriage (no tNCS, no twinning, no ice ring, good
> completeness). Phaser-MR gave a good solution except some loop regions are
> shifted. There is only 1 molecule in the ASU (and seemingly no more
> molecule can be accommodated). I fitted the displaced loops, and confirmed
> the space group by Zanuda, but the R-factors stuck at 0.34/0.41 range.
> What other aspects should I look into? Twin-refinement? (I am a bit
> reluctant to do so because neither Xtriage nor Pointless report it is
> twinned) I should also point out that the crystal was grown with its ligand
> but I cannot see good density for it.
>
> BRs
>
> Sam
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] High Rs

[Sam Tang]

Dear all

I have a dataset processed to 2.2 A, P212121, with no major issues
identified by Xtriage (no tNCS, no twinning, no ice ring, good
completeness). Phaser-MR gave a good solution except some loop regions are
shifted. There is only 1 molecule in the ASU (and seemingly no more
molecule can be accommodated). I fitted the displaced loops, and confirmed
the space group by Zanuda, but the R-factors stuck at 0.34/0.41 range.
What other aspects should I look into? Twin-refinement? (I am a bit
reluctant to do so because neither Xtriage nor Pointless report it is
twinned) I should also point out that the crystal was grown with its ligand
but I cannot see good density for it.

BRs

Sam



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Re: [ccp4bb] Why do large blobs show up in the pores of my crystal when I do refinement?

[Eleanor Dodson]

Blind almost always mean something is there. But your resolution is low.
Scaling procedures st that resolution can cause misleading features to
appear.

Q1. How good is your Wilson plot? If you used the ccp4 data scaling etc it
will have given you plots and comments. If you send s log file that would
help.

Q2. You presumably know what you crystallised. Are there any missing bits ,
ligands to put in those blobs?
Q3. Look at the bfactor analysis. Are any parts spectacularly high which
would suggest those are wrong and should be deleted then rebuilt?

But 3.2 A maps are a pain
Good luck Eleanor
To test scaling

On Thu, 1 Apr 2021 at 07:29, Paul Emsley  wrote:

> On Wed, 2021-03-31 at 19:48 -0400, Jessica Besaw wrote:
> >
> > I once again am asking for your advice. ☺ I am trying to solve the
> > structure of an RBD:Fab complex.
> >
> > After molecular replacement, the density fits the model very well.
> > Looking at the overall crystal structure (by applying symmetry mates
> > in pymol), I see large pores in the crystal with only little bits of
> > density as shown in the figure below.
> >
> > After doing refinement in phenix.refine, I now get these HUGE blobs
> > of density. But, they don't really interact with any part of the
> > structure, mostly just "floating" in the center, as shown in the
> > figure below. I have attached my current refinement strategy in case
> > I am choosing a poor strategy.
> >
> > Question:
> > (1) Are these blobs likely to be a protein?
> > (2) If it is not a protein, is there an honest / scientifically-
> > approved way to deal with these density blobs. I think they are
> > keeping my R values very high.
> >
> > Potentially useful information:
> > Rwork/Rfree = 27.1  /  30.1
> > Spacegroup: P 32 2 1
> > Highest Resolution: 3.35 Angstrom
> > Completeness: 99% (99%)
> > CC1/2: 0.99 (0.35)
> >
>
> I imagine that the bulk solvent model/structure factor
> calculation/scaling is different between the first image and the
> second. Try blurring the first set of SFs by 90 A^2 or so and see if
> the blobs turn up to some extent. It does *seem* as if there is some
> connection to your model at about the 5 o'clock position of the left
> circle.
>
> This being CCP4BB, it is not inappropriate to suggest that you try
> another refinement program, one which has a different bulk solvent
> model (or a number of them from which to choose, even) to see if your
> blobs are recapitulated.
>
> So my answers to your questions are currently
> (1) I don't know, it's a close call
> (2) put atoms in them
>
> Paul.
>
> I always like "what's my blob?" questions.
>
>
>
> 
>
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Re: [ccp4bb] Why do large blobs show up in the pores of my crystal when I do refinement?

[Paul Emsley]

On Wed, 2021-03-31 at 19:48 -0400, Jessica Besaw wrote:
> 
> I once again am asking for your advice. ☺ I am trying to solve the
> structure of an RBD:Fab complex. 
> 
> After molecular replacement, the density fits the model very well.
> Looking at the overall crystal structure (by applying symmetry mates
> in pymol), I see large pores in the crystal with only little bits of
> density as shown in the figure below.
> 
> After doing refinement in phenix.refine, I now get these HUGE blobs
> of density. But, they don't really interact with any part of the
> structure, mostly just "floating" in the center, as shown in the
> figure below. I have attached my current refinement strategy in case
> I am choosing a poor strategy.
> 
> Question:
> (1) Are these blobs likely to be a protein?  
> (2) If it is not a protein, is there an honest / scientifically-
> approved way to deal with these density blobs. I think they are
> keeping my R values very high.
> 
> Potentially useful information: 
> Rwork/Rfree = 27.1  /  30.1
> Spacegroup: P 32 2 1
> Highest Resolution: 3.35 Angstrom
> Completeness: 99% (99%)
> CC1/2: 0.99 (0.35)
> 

I imagine that the bulk solvent model/structure factor
calculation/scaling is different between the first image and the
second. Try blurring the first set of SFs by 90 A^2 or so and see if
the blobs turn up to some extent. It does *seem* as if there is some
connection to your model at about the 5 o'clock position of the left
circle.

This being CCP4BB, it is not inappropriate to suggest that you try
another refinement program, one which has a different bulk solvent
model (or a number of them from which to choose, even) to see if your
blobs are recapitulated.

So my answers to your questions are currently
(1) I don't know, it's a close call
(2) put atoms in them

Paul.

I always like "what's my blob?" questions.





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