Re: [ccp4bb] Error shows in Ligand file by using PyRx

[Paul Emsley]

On 14/10/2020 13:38, Abhilasha Thakur wrote:


I have a query related to PyRx Virtual Screening Software, Some of my ligands files are not read by PyRx. I 
downloaded the SDF format and then SDF to PDB conversion by Open Bable, then uploaded the ligand library 
into the PyRx and then set as ligands by selecting individually but some ligand shows error. I tried so hard 
to identify but did not get any solution so please suggest what I can do in that case.
One picture of PyRx shows error in ligand, I have attached below. Please suggest what is the possible 
solution to solve the PyRx related issue.


Not much to go on, but the first thing that I'd check is that the ligand representation correctly describes 
the hybridization, protonation and explicit formal charge. That tertiary amine in the diazapine look suspicious.


HTH,

Paul.



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[ccp4bb] Research Technician position at EMBL Grenoble

[Jose A. marquez]

A Research Technician position is available in the High Throughput 
Crystallization Laboratory at EMBL Grenoble.


The HTX lab is one of the largest platforms for automated macromolecular 
crystallization screening in Europe and is offering services through 
Instruct and the EC-funded project iNEXT-Discovery. The Marquez Team has 
developed stream-lined pipelines for fragment screening by X-ray 
crystallography based on the CrystalDirect technology for automated 
crystal harvesting and the CRIMS software. These pipelines are applied 
to study targets of biotechnological and biomedical relevance. The 
successful candidate will contribute towards the operation of the HTX 
facility, the development of innovative methods in protein 
crystallography and will participate in research projects.


https://www.embl.fr/jobs/searchjobs/index.php?ref=GR00154&newlang=1&loc[]=4


Applications should be submitted through the
www.embl.de/jobs/ portal.

Deadline for applications is November 22nd.

For questions concerning this position please contact Jose
Marquez (marq...@embl.fr)

Best regards



Jose A. Marquez Ph.D.
Team Leader, Head of the Crystallization Facility
EMBL Grenoble Outstation
Postal address: European Molecular Biology Laboratory
71, Avenue des Martyrs
CS 90181 38042 Grenoble Cedex 9, France
Delivery address: European Molecular Biology Laboratory
71, Avenue des Martyrs
38000 Grenoble, France
Phone +33 (0)476 20 74 25
Fax. +33 (0)476 20 71 99
https://embl.fr/htxlab/
_



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[ccp4bb] Senior Scientist Structural Biology Position Available (Gent, Belgium)

[Veli-Pekka Jaakola]

Hi,

For the expansion of our drug discovery team in Ghent (Belgium) we are 
currently looking for a Senior Scientist Structural Biology. Please send your 
CV and short motivation letter to veli-pekka.jaak...@confotherapeutics.com if 
you are interested.

Confo Therapeutics, a spin-off of VIB and VUB, is a drug discovery company 
built around a disruptive technology which enables it to address 'undruggable' 
-protein coupled receptors (GPCRs). The company is building a portfolio of 
transformative medicines in various disease areas. Confo has a unique 
technology which makes use of antibody fragments or "ConfoBodies(r)" to 
stabilize GPCRs in a particular conformation of interest as a superior starting 
point for protein structure determination. Recently, Confo secured an exclusive 
license to the Megabody(tm) technology. Megabodies enable to produce high 
resolution cryo-EM structures of membrane proteins, overcoming current protein 
size limitations and potential preferential orientation issues in the study of 
GPCRs via cryo-EM.

More information about Confo's technology and strategy can be found on 
www.confotherapeutics.com.

Your responsibilities:

Biophysical, X-ray and EM experiments to produce GPCR structural biology 
results: provide experimental structural input and support to drive NCE 
projects to achieve milestone goals
Working closely with medicinal chemists and biologist to help advance the 
project and technology platforms
Supervising and coaching one or more research associates
Leading the integrated discovery activities of projects as a core member of 
project teams
Coordination and management of drug discovery projects: in a project leader 
role, you will be expected to maintain focus and provide direction to the team 
members with clear project plans and defined timelines, maintain productive 
relationships with project team members and communicate progress against goals 
in a multidisciplinary setting:  chemistry, biology, pharmacology, and modeling

Your profile:

PhD or equivalent experience in a related field, with at least 3 years of 
experience as post-doc or in a company
Extensive technical skills in purification, sample preparation for and design 
and implementation of crystallization trials as well as demonstrated experience 
in crystal optimization techniques for membrane proteins
Demonstrated experience in sample preparation and optimization for cryo-EM 
studies on membrane proteins
Demonstrated expertise in data collection and interpretation of both X-ray 
crystallography and cryo-EM co-structure data to support NCE optimization
Experience with protein biophysical characterization ((F-)SEC, spectroscopic 
methods in detergent/lipid environment) and screening (thermal shift, NMR, SPR, 
fragment-like molecule screening) is a plus
Highly collaborative, self-motivated, team-oriented individual
Ability to work in a fast-paced, highly integrated team environment where 
accuracy, accountability and timeliness are essential
You are fluent in English and can communicate research results to the team and 
cross-functional stakeholders across the company

Our offer:

A competitive compensation package with extensive benefits
An entrepreneurial and stimulating working environment in a growing and 
ambitious biotech company
Excellent career development opportunity, with exposure to all aspects of R&D 
in the company, with external collaborators and partners


BR,

Veli

--
Veli-Pekka Jaakola
Head of Structural Biology
Confo Therapeutics
Technologiepark 94
9052 Zwijnaarde
Belgium
+32 471 80 01 56
www.confotherapeutics.com
veli-pekka.jaak...@confotherapeutics.com
https://www.linkedin.com/in/vpjaakol
--

Unless expressly stated otherwise, the information in this e-mail (including 
any of its attachments) is confidential. Moreover, it may be legally privileged 
and/or protected by intellectual property laws. It is intended for the 
exclusive attention of the addressee stated above and should not be used, 
copied, disclosed, distributed or retained by anyone other than the intended 
addressee.

If you have received this transmission in error, please contact the sender 
immediately and return it to the sender without retaining a copy.

Electronic communications are not secure and may be intercepted, manipulated, 
infected, delayed or misdirected, e.g. by viruses and spam filters. Confo 
Therapeutics is not liable on any legal ground for damage resulting from any 
such event.



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[ccp4bb] Element type N+1

[Sam Tang]

Dear colleagues

I am trying to refine a structure with Refmac and the work completes
without any warning. However I am a bit puzzled for one single N atom on an
Arg residue the element type becomes N+1. This doesn't happen on my another
NCS chain and the input PDB seems fine. Could anyone kindly point me to the
possible cause?

Thanks in advance!

BRS

Sam



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Re: [ccp4bb] Element type N+1

[Jon Cooper]

Hello, can you possibly show us a couple of screenshots with atom labels of the 
affected side chain and a normal one?

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

 Original Message 
On 15 Oct 2020, 15:07, Sam Tang wrote:

> Dear colleagues
>
> I am trying to refine a structure with Refmac and the work completes without 
> any warning. However I am a bit puzzled for one single N atom on an Arg 
> residue the element type becomes N+1. This doesn't happen on my another NCS 
> chain and the input PDB seems fine. Could anyone kindly point me to the 
> possible cause?
>
> Thanks in advance!
>
> BRS
>
> Sam
>
> ---
>
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Re: [ccp4bb] Element type N+1

[Eleanor Dodson]

Hmm - I have never seen anything like that - the monomer for ARG has no N+1
elements..
Garib? Rob?
Eleanor


On Thu, 15 Oct 2020 at 15:08, Sam Tang  wrote:

> Dear colleagues
>
> I am trying to refine a structure with Refmac and the work completes
> without any warning. However I am a bit puzzled for one single N atom on an
> Arg residue the element type becomes N+1. This doesn't happen on my another
> NCS chain and the input PDB seems fine. Could anyone kindly point me to the
> possible cause?
>
> Thanks in advance!
>
> BRS
>
> Sam
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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[ccp4bb] ONE DAY TO APPLY: DLS/CCP4 Data Collection and Structure Solution Workshop, 30 Nov - 11 Dec 2020

[David Waterman]

>
> Dear all,
>
> Please note there is now just one day left to apply for this year's
> DLS/CCP4 workshop (details below)!
>
> Best wishes
> -- David
>
>
> On Tue, 6 Oct 2020 at 10:03, David Waterman  wrote:
>
>> We are pleased to announce that the 7th joint Diamond-CCP4 Workshop on
>> MX data collection and structure solution is open for applications.
>>
>> Bringing together leading experts in the field of MX to teach best
>> practice in data collection and analysis, this course is aimed at PhD
>> students, postdocs and early career scientists who have a focus on
>> structural biology.
>>
>> The workshop will take place online via Zoom over the course of two
>> full weeks, as well as a preparation day in advance of the workshop.
>> It is essential that applicants commit to attending the workshop in
>> its entirety. Please note below the workshop days and timings
>> involved:
>>
>> - Preparation day: Monday 23 November 2020
>> - Week 1: Monday 30 November to Friday 4 December 2020
>> - Week 2: Monday 7 December to Friday 11 December 2020
>> Each day will begin at 08:45 and will finish at 17:15 (GMT - UK Time)
>>
>> Some prior experience of crystallography and data collection is
>> expected, and those who can bring an interesting project with them
>> (crystals and possibly previously collected datasets) will be given
>> priority.
>>
>> There is no fee to attend this online workshop, however attendance
>> will be subject to an application process and a letter of support from
>> the attendee's supervisor will be required. Both the application form
>> and supervisor's letter of support will need to be submitted by 17:00
>> (GMT) on Friday 16 October 2020.
>>
>> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2020/
>> - Apply at the Diamond website:
>>
>> https://www.diamond.ac.uk/Home/Events/2020/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2020.html
>>
>> *Disclaimer* Depending on the number of submissions we receive, we may
>> need to close applications earlier than the deadline to allow the
>> organisers time to process them. Applicants are therefore encouraged
>> to apply as soon as possible with all the required details requested,
>> including the letter of support - any incomplete applications will not
>> be processed.
>>
>> -- David (on behalf of the organisers)
>>
>



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[ccp4bb] MrBUMP in CCP4I2

[Derek Logan]

Hi all,

I'm looking for some advice on MrBUMP. Is it possible to access MrBUMP via 
CCP4I2 with all the options it had in CCP4I? The options seem to have been 
drastically trimmed in CCP4I2. The reason I ask is that I have a tutorial that 
I've put a lot of work into over the years that involves the students solving 
the thaumatin structure using two different search models with higher and lower 
sequence identity, which involves specifying them individually. The advantage 
of using MrBUMP is that the students don't have to do a separate step with 
Chainsaw or Sculptor. What's more, we do one run with and one run without 
automated model building and refinement for each model to compare the final 
results. CCP4I2 doesn't seem to offer any of these options.

Of course I can run the tutorial using CCP4I but I was trying to "modernise" it 
a bit.

Any advice is welcome
Derek


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[ccp4bb] Postdoc Positions in Protein Engineering at Rice University

[George Lu]

Dear colleagues,

We have several openings for postdoctoral fellows. Please see the 
advertisement below.




The Lab for Synthetic Macromolecular Assemblies  
(PI: George J. Lu) at Rice Bioengineering has multiple openings for 
postdoctoral fellows. The research focuses on the understanding and 
engineering of a class of gas-filled protein nanostructures named gas 
vesicles, and use them to develop novel imaging and cellular control 
technologies for basic research and cell therapies. Gas vesicles were 
recently shown to enable ultrasound- and MRI-based imaging of gene 
expressions in therapeutic microbes and mammalian cells (Nature 
Materials 2018 ; Nature 
Protocols 2017 ; Nature 2018 
; Science 2019 
), and have future applications 
in remote cellular control and biomaterials. The qualified postdoc 
researchers recruited here will lead projects in understanding the 
molecular mechanism of gas vesicles, engineering novel genetic variants, 
and developing imaging and cellular control platforms that incorporate 
these agents.


Dr. Lu was previously awarded the Young Investigator of the Year 
 
from the World Molecular Imaging Society for his work on the development 
of acoustically erasable MRI reporter genes. The independent lab was 
newly established in 2020 with the support of the NIH 
Pathway-to-independence (K99/R00) 
 
and the Cancer Prevention and Research Institute of Texas (CPRIT) 
Scholar  
awards.


The ideal candidate will have strong expertise in one or several of the 
following areas: protein structural biology, computational protein 
design, directed evolution and high-throughput screening, microbial 
engineering, mammalian synthetic biology, and ultrasound imaging. The 
candidate should have strong written and oral communication skills, and 
will also be expected to aid in the supervision of junior lab members 
and in the preparation of research proposals. The application for 
postdoctoral fellowships will be encouraged, including both external and 
internal ones such as Rice University Academy of Fellows. The pay scale 
for the position follows NIH guidelines.


Rice Bioengineering is one of the top biomedical engineering departments 
with its graduate program consistently ranked among the top 10 in the 
country. The candidate will have opportunities to lead cutting-edge 
research projects and interact with outstanding scientists as 
collaborators and trainees.


//

Rice University is an Equal Opportunity Employer with commitment to 
diversity at all levels, and considers for employment qualified 
applicants without regard to race, color, religion, age, sex, sexual 
orientation, gender identity, national or ethnic origin, genetic 
information, disability, or protected veteran status.


To apply, please visit https://jobs.rice.edu/postings/24661 or email a 
cover letter and a copy of CV/resume to george...@rice.edu 
.





Best,
George

George J. Lu, PhD
Assistant Professor of Bioengineering
CPRIT Scholar in Cancer Research
Rice University
http://lulab.rice.edu






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Re: [ccp4bb] Element type N+1

[Sam Tang]

Dear all

I attach herewith the Arg concerned. I actually saw no issue in Coot when I
checked residue info. The issue was repeatable using both Refmac from Coot
and from CCP4i. I rectified the issue simply by changing "N+1" back to "N"
using a word editor, but would surely be glad to know more about the cause
of the problem.

https://drive.google.com/file/d/137Q0CybNynOlI0R-b-3-OL2eWk7f6L2a/view?usp=sharing

Best Regards

Sam


On Fri, 16 Oct 2020 at 00:51, Jon Cooper 
wrote:

> Hello, can you possibly show us a couple of screenshots with atom labels
> of the affected side chain and a normal one?
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
>
>
>
>
>  Original Message 
> On 15 Oct 2020, 15:07, Sam Tang < samtys0...@gmail.com> wrote:
>
>
> Dear colleagues
>
> I am trying to refine a structure with Refmac and the work completes
> without any warning. However I am a bit puzzled for one single N atom on an
> Arg residue the element type becomes N+1. This doesn't happen on my another
> NCS chain and the input PDB seems fine. Could anyone kindly point me to the
> possible cause?
>
> Thanks in advance!
>
> BRS
>
> Sam
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>



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