[ccp4bb] Postdoctoral opportunities in ultrafast electron microscopy at Columbia University in New York City

[Anthony Fitzpatrick]

Dear all,

The Fitzpatrick lab at Columbia University in New York City is seeking
postdoctoral researchers to develop an ultrafast electron microscopy suite
for biological research. A scanning ultrafast electron microscope is
operational and an F20 transmission electron microscope with K2 direct
electron detector are also in place. Salary is $70k and postdoctoral
housing is available.

Interested applicants should email anthony.fitzpatr...@columbia.edu
directly. Applications should include a cover letter, a CV, and the names
and contact information of two referees. Evaluation of applications will
commence immediately and will continue until the positions are filled.

All good wishes,

Anthony

-
Anthony Fitzpatrick, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biophysics
Mortimer B. Zuckerman Mind Brain and Behavior Institute
Columbia University
Jerome L.Green Science Center
Room L4.052
3227 Broadway
New York, NY 10027
www.fitzpatrick-lab.org/



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Re: [ccp4bb] contrast missing issue

[辛志宏]

Dear Kay,
Thank you for your responses.
Please find the window10 and Centos7 logfiles in the attachment.
Your Best,
Zhihong xin








From: Kay Diederichs 
Date: 2023-12-19 02:35:50
To:  CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] contrast missing issue>Dear Zhihong Xin,
>
>am I understanding correctly that you get very different output, using CentOS7 
>versus using Windows10, for the exact same calculation? In that case, it seems 
>surprising (to me at least) that it is only the contrast value that is 
>affected.
>There is not much to work on, from your description. It would help a lot if 
>you could attach the log files to your posting, from both the CentOS7 and the 
>Win10 runs, so that we can compare them. And please make sure that the input 
>(commands and files) to the calculations is exactly the same.
>
>Best wishes,
>Kay
>
>On Mon, 18 Dec 2023 16:54:45 +0800, 辛志宏  wrote:
>
>>Dear CCP4 development team,
>>
>>
>>I meet an issue when I use the latest version ccp4 8.0 in the Centos 7 
>>system, there is no contrast output item when I try to construct a protein 
>>model by molecular replacement with Run Molre-autoMR method, but it works in 
>>the win10 system according to the same method, the contrast value output 
>>successfully. I reinstall CCP4 in the Centos 7 system again which displayed 
>>ccp4 install successfully, but the issue is still there when I run again, are 
>>there any solution for the issue?
>>Thanks in advance. 
>>
>>
>>Your best
>>
>>
>>Zhihong Xin
>>
>>
>>Nanjing Agricultural University
>>
>>
>>
>>
>>
>>
>>
>>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 mailing 
>>list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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>
>
>
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#CCP4I VERSION CCP4Interface 8.0.016
#CCP4I SCRIPT LOG molrep
#CCP4I DATE 18 Dec 2023  20:57:26
#CCP4I USER xzhfood
#CCP4I PROJECT PROJECT
#CCP4I JOB_ID 21
#CCP4I SCRATCH /tmp/xzhfood
#CCP4I HOSTNAME localhost.localdomain
#CCP4I PID 6359

+-+
| |
| --- MOLREP ---  |
|   /Vers 11.9.02; 28.02.2022/|
| |
+-+

 ++
 ||
 | You can use program by command string with options:|
 ||
 |  molrep -f [file_sf_or_map] -m [model_crd_or_map]  |
 | -mx [fixed model]   -m2 [model_2]  |
 | -po [path_out]  -ps [path_scratch] |
 | -nmon []  -sim [<0.35>]  |
 | -pst [n/y/]  -nmr [0,1,<5>,4,11]|
 | -prf [/y/s]  -surf [/a/2]  -np [Npeak]   |
 | -dom [/y/m,g,h]   -nref [5] |
 | -s [file_sequence]  -s2 [file_seq_for_m2]  |
 | -k [file_keywords]  -doc [y/a/n]   |
 | -h -i -r   |
 ||
 | -h = only keyword and mtz label information, clean |
 | -i = interactive mode  |
 | -r = rest some special files   |
 |  nmr = 11 means to use only first model in ensemble|
 |  file_keywords = simple text file with keywords|
 |  (one line - one keyword)  |
 ||
 |  use  "molrep -h" to get short manual  |
 ||
 ++

  Input files:

 -po: /tmp/xzhfood/PROJECT_21_molrep_
 -ps: /tmp/xzhfood/PROJECT_21_molrep_


 # ---  type "keyword   

Re: [ccp4bb] solvent mask for partial ligands, addendum

[John Bacik]

 
Hi Gottfried, I was wondering what happens if you make a Polder omit map for 
the HEPES? I am also curious, if the extra positive density is for missing bulk 
solvent with ligand of occupany 0.5, do you observe the density with ligand 
present at 0.5 occupancy to be more diffuse than with no ligand present? If we 
take the example of amino acid side chains modeled with dual conformations, 
generally an abundance of extra positive density is not observed due to 
side-chains having partial occupancy and missing bulk solvent.
Regards,
John
On Thursday, December 14, 2023 at 01:55:20 PM CST, James Holton 
 wrote:  
 
 You guessed right.  Bulk solvent does not get a localized "occupancy". 
It is set to "0" anywhere near modeled atoms, even if those atoms have 
an occupancy of 0.01.  Yes, it might seem sensible to do "occupancy" for 
the bulk, but in practice it is tricky.  I tried my hand at a "fuzzy" 
bulk solvent mask, which can be read in by refmac. It tends to perform 
better than the default masks, but is rather computationally intensive 
to make. Script here:
https://github.com/bl831/fuzzymask

This is perhaps a closer approximation to what you are thinking a bulk 
solvent mask should be?

You might also want to try the Babinet inverse type of bulk solvent 
model. refmac supports this if you use "scale type bulk".

-James Holton
MAD Scientist

On 12/14/2023 2:40 AM, Palm, Gottfried wrote:
> I can only guess that the solvent at the place of the EPE is set to 0 
> (instead of 0.5)



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Re: [ccp4bb] contrast missing issue

[Kay Diederichs]

Dear Zhihong Xin,

am I understanding correctly that you get very different output, using CentOS7 
versus using Windows10, for the exact same calculation? In that case, it seems 
surprising (to me at least) that it is only the contrast value that is affected.
There is not much to work on, from your description. It would help a lot if you 
could attach the log files to your posting, from both the CentOS7 and the Win10 
runs, so that we can compare them. And please make sure that the input 
(commands and files) to the calculations is exactly the same.

Best wishes,
Kay

On Mon, 18 Dec 2023 16:54:45 +0800, 辛志宏  wrote:

>Dear CCP4 development team,
>
>
>I meet an issue when I use the latest version ccp4 8.0 in the Centos 7 system, 
>there is no contrast output item when I try to construct a protein model by 
>molecular replacement with Run Molre-autoMR method, but it works in the win10 
>system according to the same method, the contrast value output successfully. I 
>reinstall CCP4 in the Centos 7 system again which displayed ccp4 install 
>successfully, but the issue is still there when I run again, are there any 
>solution for the issue?
>Thanks in advance. 
>
>
>Your best
>
>
>Zhihong Xin
>
>
>Nanjing Agricultural University
>
>
>
>
>
>
>
>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 mailing 
>list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>https://www.jiscmail.ac.uk/policyandsecurity/



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Re: [ccp4bb] extra Fo-Fc density in two Cysteines

[Jon Cooper]

Hello, you seem to have positive difference density for the Cys sulphur/sulfur 
atom. It would be worth checking it's occupancy.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 18 Dec 2023, 17:03, Liliana Margent wrote:

> Hi there, We’ve been having an issue in trying to clear regions of Fo-Fc 
> density from a few cysteines during the refinement process. We were wondering 
> if anyone had seen something similar so they could offer some insight on the 
> likely chemistry at hand, and a potential refinement solution. Attached are 
> two images of the observed extra density at two cysteines, 505 and 518. We 
> have modeled acetylated cysteine, s-hydroxycysteine, and s-mercaptocysteine 
> but it does not solve the density. The protein in question is a Protein 
> Tyrosine Phosphatase known as STEP (PTPN5), with data collected to a 
> resolution of 1.79 Å. The crystals were grown in bis-tris pH 6.65, 200mM 
> Li2SO4, ~30% PEG3350. Of note, prior to data collection the crystal was 
> conserved at room temp for long time where it dried, and was subsequently 
> rehydrated with mother liquor. Thank you so much.
>
> ---
>
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Re: [ccp4bb] extra Fo-Fc density in two Cysteines

[Wim Burmeister]

Hello, 
this looks like beta-mercaptoethanol adduct through a S-S bond. 
See 
[ https://pubmed-ncbi-nlm-nih-gov.insb.bib.cnrs.fr/12421561/ | The crystal 
structure of the Epstein-Barr virus protease shows rearrangement of the 
processed C terminus.  ] 
Buisson M, Hernandez JF, Lascoux D, Schoehn G, Forest E, Arlaud G, Seigneurin 
JM, Ruigrok RW, Burmeister WP. J Mol Biol. 2002 Nov 15;324(1):89-103. doi: 
10.1016/s0022-2836(02)01040-9. 

Wim 

De: "Liliana Margent"  
À: "CCP4BB"  
Envoyé: Lundi 18 Décembre 2023 18:03:46 
Objet: [ccp4bb] extra Fo-Fc density in two Cysteines 

Hi there, We’ve been having an issue in trying to clear regions of Fo-Fc 
density from a few cysteines during the refinement process. We were wondering 
if anyone had seen something similar so they could offer some insight on the 
likely chemistry at hand, and a potential refinement solution. Attached are two 
images of the observed extra density at two cysteines, 505 and 518. We have 
modeled acetylated cysteine, s-hydroxycysteine, and s-mercaptocysteine but it 
does not solve the density. The protein in question is a Protein Tyrosine 
Phosphatase known as STEP (PTPN5), with data collected to a resolution of 1.79 
Å. The crystals were grown in bis-tris pH 6.65, 200mM Li2SO4, ~30% PEG3350. Of 
note, prior to data collection the crystal was conserved at room temp for long 
time where it dried, and was subsequently rehydrated with mother liquor. Thank 
you so much. 



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[image/png:Screenshot 2023-12-16 at 3.36.01 PM.png] 

-- 
Wim Burmeister 
Professor 
Institut de Biologie Structurale (IBS) CIBB 
71 avenue des Martyrs / CS 20192 
38044 Grenoble Cedex 9, FRANCE 
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
Mobile: +33 (0) 7 50 49 19 91 
[ 
https://www.ibs.fr/en/research/microbiology-infection-and-immunity/viral-replication-machines-group-m-jamin/team-burmeister/
 | website ] [ 
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
 ] 

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Re: [ccp4bb] extra Fo-Fc density in two Cysteines

[Roberto Steiner]

Difficult to be sure from a single angle pic but I would suggest Cys oxidation.

There is an important 20 years old paper (see below) on Cys oxidation in a 
tyrosine phosphatase (like yours)

Best
Roberti]


Nature

  *   

  *   

  *   

. 2003 Jun 12;423(6941):773-7.
 doi: 10.1038/nature01681.
Oxidation state of the active-site cysteine in protein tyrosine phosphatase 1B
Rob L M van 
Montfort
 1, Miles 
Congreve, 
Dominic Tisi, 
Robin Carr, 
Harren Jhoti


Roberto A Steiner
www.steinerlab.org
https://twitter.com/steiner_lab

roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

Responses to emails are not expected outside of your normal working hours.








On 18 Dec 2023, at 18:03, Liliana Margent 
mailto:lmarg...@gradcenter.cuny.edu>> wrote:

You don't often get email from 
lmarg...@gradcenter.cuny.edu. Learn why 
this is important
Hi there, We’ve been having an issue in trying to clear regions of Fo-Fc 
density from a few cysteines during the refinement process. We were wondering 
if anyone had seen something similar so they could offer some insight on the 
likely chemistry at hand, and a potential refinement solution. Attached are two 
images of the observed extra density at two cysteines, 505 and 518. We have 
modeled acetylated cysteine, s-hydroxycysteine, and s-mercaptocysteine but it 
does not solve the density. The protein in question is a Protein Tyrosine 
Phosphatase known as STEP (PTPN5), with data collected to a resolution of 1.79 
Å. The crystals were grown in bis-tris pH 6.65, 200mM Li2SO4, ~30% PEG3350. Of 
note, prior to data collection the crystal was conserved at room temp for long 
time where it dried, and was subsequently rehydrated with mother liquor. Thank 
you so much.


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Re: [ccp4bb] extra Fo-Fc density in two Cysteines

[Parthasarathy Sampathkumar]

Hi Liliana,
May be it would be good to know if this adduct was formed during
crystallization or protein was modified prior to crystallization.  One
could consider performing a protease digestion, followed by LC-MS/MS to
determine the molecular weight of the adduct and then work backwards to
account for the difference in dalton.

Good Luck,
Partha

On Mon, Dec 18, 2023 at 9:14 AM Liliana Margent <
lmarg...@gradcenter.cuny.edu> wrote:

> Hi there, We’ve been having an issue in trying to clear regions of Fo-Fc
> density from a few cysteines during the refinement process. We were
> wondering if anyone had seen something similar so they could offer some
> insight on the likely chemistry at hand, and a potential refinement
> solution. Attached are two images of the observed extra density at two
> cysteines, 505 and 518. We have modeled acetylated cysteine,
> s-hydroxycysteine, and s-mercaptocysteine but it does not solve the
> density. The protein in question is a Protein Tyrosine Phosphatase known as
> STEP (PTPN5), with data collected to a resolution of 1.79 Å. The crystals
> were grown in bis-tris pH 6.65, 200mM Li2SO4, ~30% PEG3350. Of note, prior
> to data collection the crystal was conserved at room temp for long time
> where it dried, and was subsequently rehydrated with mother liquor. Thank
> you so much.
> --
>
> 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] Doctoral researcher position at University of Oulu

[Albert Galera Prat]

We have currently a Doctoral researcher position available at the Faculty of 
Biochemistry and Molecular Medicine at the University of Oulu, Finland.

Our team focuses on structure, function and selective inhibition of 
ADP-ribosyltransferases, also known as PARPs. These proteins are involved in 
signaling through ADP-ribosylation – a post-translational modification 
affecting protein stability, function, and interactions in multiple cellular 
pathways. Our goals are to study how the multidomain PARPs function and are 
regulated by addressing several key questions in their oligomerization, 
protein-protein and protein-nucleic acid interactions and use structural 
information for rational design to develop specific inhibitors.

The Faculty provides a dynamic research surrounding and cutting-edge research 
infrastructure services to academics and other users in Finland and abroad.


The position is funded for 4 years and the application deadline is 15th January 
2024. More information and application form can be found here: 
https://oulunyliopisto.varbi.com/en/what:job/jobID:681922/

If you have any question regarding this position, please contact me directly.

Best wishes,

Albert



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[ccp4bb] contrast missing issue

[辛志宏]

Dear CCP4 development team,


I meet an issue when I use the latest version ccp4 8.0 in the Centos 7 system, 
there is no contrast output item when I try to construct a protein model by 
molecular replacement with Run Molre-autoMR method, but it works in the win10 
system according to the same method, the contrast value output successfully. I 
reinstall CCP4 in the Centos 7 system again which displayed ccp4 install 
successfully, but the issue is still there when I run again, are there any 
solution for the issue?
Thanks in advance. 


Your best


Zhihong Xin


Nanjing Agricultural University







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