[ccp4bb] Postdoctoral Position in the Murray Lab

[Dylan Murray]

The Murray Laboratory

University of California, Davis

Department of Chemistry

Postdoctoral Research Opportunity



Position Title: Postdoctoral Researcher

Location: UC Davis, One Shields Avenue, Davis, California 95616 USA



The Murray Laboratory at the University of California, Davis
, is seeking a postdoctoral associate to
join our team. Projects will include (1) investigating protein structure
and dynamics underlying the biomolecular condensation of RNA-binding
proteins and the self-assembly of cell cytoskeleton proteins; and (2)
characterizing native plant cell wall structure and the effect of
deconstruction approaches for bioproduct development. Experience in
biological NMR, cryo-electron microscopy, and/or advanced biochemical and
molecular biology methods is preferred, but not required. Training will be
provided to excellent candidates as needed. The applicant will be supported
by an NIH grant and have access to well-equipped facilities for solution
and solid-state NMR, and cryogenic and non-cryogenic electron microscopy.
Additional experimental resources are available through core facilities
across the vibrant UC Davis campus. Davis California is ideally situated
midway between the relaxing wilderness of Lake Tahoe in the Sierra Nevada
mountains and the vibrant biotechnology hub of the San Francisco Bay Area.



Recent publications from the laboratory related to the projects are:
(1) Fonda et al., *J. Am. Chem. Soc.,* 2021, 143, 6657.


(2) Sysoev et al., *Proc. Nat. Acad. Sci. USA,* 2020, 117, 23510.

(3) Gao et al., *Nat. Comm.* 2020, 11, 6081.


(4) Munson et al. *Front. Plant Sci.* 2022, 12, 766506.




The initial appointment is for one year. In accordance with policies of the
University of California, subsequent appointments are two years in length.
Salary is commensurate with the candidate’s experience and is consistent
with NIH postdoctoral pay scales. A comprehensive benefits package is also
provided.



Interested applicants should hold a Ph.D. in Biophysics, Chemistry,
Biology, Physics, or related field and submit their CV and a brief
introductory statement to Dylan Murray at: dtmur...@ucdavis.edu.

-
Dylan T. Murray, Ph.D.
Assistant Professor
Department of Chemistry
University of California, Davis
dylan.thomas.mur...@gmail.com
-



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/

Re: [ccp4bb] Tutorials for easy structure determinations

[Georg Mlynek]

Dear Yong, please have a look at this

https://www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/tutorial/index_en.html

You get even the raw data, but also all files in between till the fully 
refined structure.


It covers MR, SAD , .

I know it is CCP4 mailing list, but if you as I use both program suits 
phenix and ccp4, then phenix has built in tutorials 
https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/phenix/tutorials/mr_refine.html


Some are used in the youtube tutorial channel which I can also highly 
recommend


https://www.youtube.com/channel/UCcdI0hfHngWAZLJWynxPQWg


Br, Georg.


Am 07.04.2022 um 17:34 schrieb Yong Tang:

Dear all,

Do we have tutorials suitable for beginners to follow from Molecular 
Replacement to model building and refinement, all the way up to water 
and ligand inclusion?


I remember in the old days there were "case studies" that one could 
download and follow through in Coot/Refmac - I have trouble finding 
such links now.


Many thanks, -yong



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 







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/

[ccp4bb] Tutorials for easy structure determinations

[Yong Tang]

Dear all,

Do we have tutorials suitable for beginners to follow from Molecular
Replacement to model building and refinement, all the way up to water and
ligand inclusion?

I remember in the old days there were "case studies" that one could
download and follow through in Coot/Refmac - I have trouble finding such
links now.

Many thanks, -yong



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/

[ccp4bb] Ask the Experts | Career paths in cryo-EM | April 20, 2022

[Nylese, Tara]

Dear All,

We'd like to invite you to attend our next upcoming Ask The Experts Series 
Webinar for all levels of electron microscopists.

Career paths in cryo-EM
Wednesday, April 20, 2022 | 8 a.m. PDT | 11 a.m. EDT | 5 p.m. CEST
Career Paths in Cryo-EM 
Webinar
Attend our upcoming Ask the Experts Q session to learn about the professional 
opportunities within the field of cryo-EM.
The number of studies and solutions utilizing cryo-EM continues to grow at a 
fast pace without showing any sign of stopping. The industry must meet this 
growing demand, and access to cryo-EM technology and training earlier in an 
academic career is crucial to satisfy that workforce pipeline.
Join our experts as they discuss how both faculty members and students alike 
can gain and grow expertise for prolific careers in this high-demand field.
Register 
Now
Regards,

Tara Nylese
Market Development Manager, Americas
Life Sciences
Materials & Structural Analysis
Thermo Fisher Scientific
tara.nyl...@thermofisher.com
(845)664-8445






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/

[ccp4bb] CCP4 error in job missing

[smita yadav]

While Running CCP4 7.0. All the jobs get cleared from the main window and
project. How will I get back all the job lists?
Thanks in advance for suggestions.


SMITA



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/

[ccp4bb] Postdoctoral position in structural biology open in Bethesda, MD

[Marzena Pazgier]

A postdoctoral position is available immediately to participate in an
inter-disciplinary research program in structural immunology at the
laboratory of Dr. Pazgier (https://www.usuhs.edu/node/68252) at Uniformed
Services University of the Health Sciences (USU), Bethesda, MD

Candidates are expected to work on ongoing research projects in structural
biology with the aim to understand the molecular basis of the adaptive
immune response to HIV-1 and Sars-Cov2 and the ultimate goal to develop new
protein-based therapeutics and novel vaccine concepts. Qualifications for
the position include: a strong research interest and experience in
molecular cloning, protein expression, molecular interaction analysis,
X-ray crystallography and/or Cryo-EM and excellent
interpersonal/oral/written communication skills.



Candidates need to be highly motivated individuals who enjoy working as
part of a dynamic, collaborative and multidisciplinary team. Preference
will be given to candidates with exceptionally strong experimental skills,
a strong record of peer-reviewed publications, and a demonstrated
commitment to basic research. Qualified candidates should have a doctorate
in chemistry/biochemistry, microbiology, immunology or a closely-related
field. Candidates at any career stage are invited.



USU is in Bethesda, MD directly across the street from the NIH, and is
therefore part of an extraordinarily vibrant local biomedical research
community. Our research projects take advantage of recently established
Core facilities for Nextgen sequencing, Bioinformatics and Structural
Biology analyses. USU has a strongly collaborative environment, with weekly
Immunology data club and journal club meetings, as well as regular research
seminars featuring local and invited speakers.



Candidates should apply to Dr. Pazgier directly at marzena.pazg...@usuhs.edu



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/

Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

[Robbie Joosten]

Dear Ines,

The latest version of DSSP (https://github.com/PDB-REDO/dssp) also annotates 
the coordinate file in pdb or mmCIF. Note that mmCIF is preferred as you can do 
a more complete annotation. The latest version of mkdssp will be in CCP4 
version 8.

Cheers,
Robie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of
> Munoz.Ines
> Sent: Thursday, April 7, 2022 10:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Add secondary structure definition into an alphafold PDB
> 
> Harry, you are right! It was the first program that I used but as long as I 
> have
> seen it gives you the info regarding the amino acids that form those areas but
> then you have to include this info into your pdb manually.
> Best
> Inés
> 
> 
> > El 7 abr 2022, a las 10:29, Harry Powell - CCP4BB <193323b1e616-
> dmarc-requ...@jiscmail.ac.uk> escribió:
> >
> > CAUTION: This email originated from outside of the organization. Do not 
> > click
> links or open attachments unless you recognize the sender and know the
> content is safe
> >
> >
> >
> > Hi Ines
> >
> > DSSP? (In ccp4 as “mkdssp” in $CBIN)? Should work with any (valid??) PDB
> file
> >
> > “Oldie but goodie”...
> >
> > Harry
> >
> >> On 7 Apr 2022, at 09:24, Munoz.Ines  wrote:
> >>
> >> Dear all,
> >>
> >> Is there any program or server that automatically assign the secondary
> structure elements into a pdb generated by alpha fold?
> >>
> >> Many thanks
> >> Inés
> >>
> >>
> >>
> >>
> >> Inés G. Muñoz
> >> Head of Crystallography and Protein Engineering Unit
> >> Spanish National Cancer Research Centre, CNIO
> >>
> >> imu...@cnio.es
> >> Phone +34 91 732 8000 (ext. 3020)
> >>
> >> Melchor Fernández Almagro, 3
> >> 28029 Madrid, Spain
> >> www.cnio.es
> >>
> >>
> >> 
> >>
> >>
> >>
> >>
> >>
> >>
> >> Fb Amigos del CNIO |  Tw @CNIOStopCancer |  Youtube canalcnio
> >>
> >>
> >>
> >> **ADVERTENCIA LEGAL**: Este correo electrónico, y en su caso los ficheros
> adjuntos, pueden contener información protegida para el uso exclusivo de su
> destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo 
> de
> transmisión por parte de otra persona que no sea el destinatario. Si usted
> recibe por error este correo, se ruega comunicarlo al remitente y borrar el
> mensaje recibido.
> >> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a
> la protección de los datos personales de las personas físicas, la información
> personal que nos pueda facilitar a través de este correo electrónico quedará
> registrada por la Fundación CNIO con la finalidad de tramitar el objeto del
> presente correo electrónico. El tratamiento de sus datos personales se
> encuentra legitimado por ser necesario para gestionar el objeto del presente
> mensaje. Estos datos personales no serán comunicados a ningún destinatario
> salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud.
> podrá ejercer los derechos de acceso, rectificación, supresión, limitación de
> tratamiento, portabilidad y oposición en la siguiente dirección: c/Melchor
> Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con el
> Delegado de Protección de Datos en: delegado_l...@cnio.es. Para el caso de
> que Ud. precise conocer información adicional sobre el tratamiento de sus
> datos personales, puede consultar dicha información adicional en el siguiente
> enlace dentro de nuestra página web:
> https://www.cnio.es/es/privacidad/index.asp
> >>
> >> **LEGAL NOTICE**: This email and any attached files may contain protected
> information for the sole use of its intended recipient or addressee. Anyone
> other than the intended recipient or addressee is strictly prohibited from
> distributing, reproducing or transmitting the email and its contents in any 
> way.
> If you receive this email in error, please notify the sender and delete the
> message.
> >> Pursuant to the provisions of EU Regulation 2016/679 regarding the
> protection of personal data, any personal information you provide through this
> email will be registered by the CNIO Foundation in order to deal with content
> of this email. Your personal data must be processed in order to be able to 
> deal
> with the content and purpose of this message. Your personal details will not 
> be
> passed on to anyone else unless you authorise us to do so or we are required 
> to
> do so by law. You may exercise your rights regarding access, rectification,
> suppression, limitation of processing, portability and opposition by writing 
> to
> the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You
> may contact the Data Protection Delegate (Delegado de Protección de Datos)
> at: delegado_l...@cnio.es. If you require further information about the
> processing of your personal data, go to the following link on our webpage:
> https://www.cnio.es/es/privacidad/index.asp
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> 

Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

[Munoz.Ines]

Thanks Paul, I´ll give it a try
Best
Inés

> El 7 abr 2022, a las 10:33, Paul Emsley  escribió:
>
> CAUTION: This email originated from outside of the organization. Do not click 
> links or open attachments unless you recognize the sender and know the 
> content is safe
>
>
>
> On 07/04/2022 09:24, Munoz.Ines wrote:
>> Dear all,
>>
>> Is there any program or server that automatically assign the secondary
>> structure elements into a pdb generated by alpha fold?
>>
>
> If you are using Coot, you can use
>
> Calculate -> Scripting -> Python
>
> add_header_secondary_structure_info(imol)
>
>



**ADVERTENCIA LEGAL**: Este correo electrónico, y en su caso los ficheros 
adjuntos, pueden contener información protegida para el uso exclusivo de su 
destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de 
transmisión por parte de otra persona que no sea el destinatario. Si usted 
recibe por error este correo, se ruega comunicarlo al remitente y borrar el 
mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la 
protección de los datos personales de las personas físicas, la información 
personal que nos pueda facilitar a través de este correo electrónico quedará 
registrada por la Fundación CNIO con la finalidad de tramitar el objeto del 
presente correo electrónico. El tratamiento de sus datos personales se 
encuentra legitimado por ser necesario para gestionar el objeto del presente 
mensaje. Estos datos personales no serán comunicados a ningún destinatario 
salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud. 
podrá ejercer los derechos de acceso, rectificación, supresión, limitación de 
tratamiento, portabilidad y oposición en la siguiente dirección: c/Melchor 
Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con el Delegado 
de Protección de Datos en: delegado_l...@cnio.es. Para el caso de que Ud. 
precise conocer información adicional sobre el tratamiento de sus datos 
personales, puede consultar dicha información adicional en el siguiente enlace 
dentro de nuestra página web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected 
information for the sole use of its intended recipient or addressee. Anyone 
other than the intended recipient or addressee is strictly prohibited from 
distributing, reproducing or transmitting the email and its contents in any 
way. If you receive this email in error, please notify the sender and delete 
the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection 
of personal data, any personal information you provide through this email will 
be registered by the CNIO Foundation in order to deal with content of this 
email. Your personal data must be processed in order to be able to deal with 
the content and purpose of this message. Your personal details will not be 
passed on to anyone else unless you authorise us to do so or we are required to 
do so by law. You may exercise your rights regarding access, rectification, 
suppression, limitation of processing, portability and opposition by writing to 
the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may 
contact the Data Protection Delegate (Delegado de Protección de Datos) at: 
delegado_l...@cnio.es. If you require further information about the processing 
of your personal data, go to the following link on our webpage: 
https://www.cnio.es/es/privacidad/index.asp



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/

Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

[Munoz.Ines]

Harry, you are right! It was the first program that I used but as long as I 
have seen it gives you the info regarding the amino acids that form those areas 
but then you have to include this info into your pdb manually.
Best
Inés


> El 7 abr 2022, a las 10:29, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> escribió:
>
> CAUTION: This email originated from outside of the organization. Do not click 
> links or open attachments unless you recognize the sender and know the 
> content is safe
>
>
>
> Hi Ines
>
> DSSP? (In ccp4 as “mkdssp” in $CBIN)? Should work with any (valid??) PDB file
>
> “Oldie but goodie”...
>
> Harry
>
>> On 7 Apr 2022, at 09:24, Munoz.Ines  wrote:
>>
>> Dear all,
>>
>> Is there any program or server that automatically assign the secondary 
>> structure elements into a pdb generated by alpha fold?
>>
>> Many thanks
>> Inés
>>
>>
>>
>>
>> Inés G. Muñoz
>> Head of Crystallography and Protein Engineering Unit
>> Spanish National Cancer Research Centre, CNIO
>>
>> imu...@cnio.es
>> Phone +34 91 732 8000 (ext. 3020)
>>
>> Melchor Fernández Almagro, 3
>> 28029 Madrid, Spain
>> www.cnio.es
>>
>>
>> 
>>
>>
>>
>>
>>
>>
>> Fb Amigos del CNIO |  Tw @CNIOStopCancer |  Youtube canalcnio
>>
>>
>>
>> **ADVERTENCIA LEGAL**: Este correo electrónico, y en su caso los ficheros 
>> adjuntos, pueden contener información protegida para el uso exclusivo de su 
>> destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo 
>> de transmisión por parte de otra persona que no sea el destinatario. Si 
>> usted recibe por error este correo, se ruega comunicarlo al remitente y 
>> borrar el mensaje recibido.
>> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la 
>> protección de los datos personales de las personas físicas, la información 
>> personal que nos pueda facilitar a través de este correo electrónico quedará 
>> registrada por la Fundación CNIO con la finalidad de tramitar el objeto del 
>> presente correo electrónico. El tratamiento de sus datos personales se 
>> encuentra legitimado por ser necesario para gestionar el objeto del presente 
>> mensaje. Estos datos personales no serán comunicados a ningún destinatario 
>> salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud. 
>> podrá ejercer los derechos de acceso, rectificación, supresión, limitación 
>> de tratamiento, portabilidad y oposición en la siguiente dirección: 
>> c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con 
>> el Delegado de Protección de Datos en: delegado_l...@cnio.es. Para el caso 
>> de que Ud. precise conocer información adicional sobre el tratamiento de sus 
>> datos personales, puede consultar dicha información adicional en el 
>> siguiente enlace dentro de nuestra página web: 
>> https://www.cnio.es/es/privacidad/index.asp
>>
>> **LEGAL NOTICE**: This email and any attached files may contain protected 
>> information for the sole use of its intended recipient or addressee. Anyone 
>> other than the intended recipient or addressee is strictly prohibited from 
>> distributing, reproducing or transmitting the email and its contents in any 
>> way. If you receive this email in error, please notify the sender and delete 
>> the message.
>> Pursuant to the provisions of EU Regulation 2016/679 regarding the 
>> protection of personal data, any personal information you provide through 
>> this email will be registered by the CNIO Foundation in order to deal with 
>> content of this email. Your personal data must be processed in order to be 
>> able to deal with the content and purpose of this message. Your personal 
>> details will not be passed on to anyone else unless you authorise us to do 
>> so or we are required to do so by law. You may exercise your rights 
>> regarding access, rectification, suppression, limitation of processing, 
>> portability and opposition by writing to the following address: c/Melchor 
>> Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection 
>> Delegate (Delegado de Protección de Datos) at: delegado_l...@cnio.es. If you 
>> require further information about the processing of your personal data, go 
>> to the following link on our webpage: 
>> https://www.cnio.es/es/privacidad/index.asp
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> 
>
> 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/



**ADVERTENCIA LEGAL**: Este correo electrónico, y en su caso los ficheros 
adjuntos, pueden contener información protegida para el uso exclusivo 

Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

[Paul Emsley]

On 07/04/2022 09:24, Munoz.Ines wrote:

Dear all,

Is there any program or server that automatically assign the secondary 
structure elements into a pdb generated by alpha fold?




If you are using Coot, you can use

Calculate -> Scripting -> Python

add_header_secondary_structure_info(imol)



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/

Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

[Harry Powell - CCP4BB]

Also, of course, you could get the up-to-date version from - 

https://swift.cmbi.umcn.nl/gv/dssp/

Harry

> On 7 Apr 2022, at 09:29, Harry Powell - CCP4BB  
> wrote:
> 
> Hi Ines
> 
> DSSP? (In ccp4 as “mkdssp” in $CBIN)? Should work with any (valid??) PDB file
> 
> “Oldie but goodie”...
> 
> Harry
> 
>> On 7 Apr 2022, at 09:24, Munoz.Ines  wrote:
>> 
>> Dear all,
>> 
>> Is there any program or server that automatically assign the secondary 
>> structure elements into a pdb generated by alpha fold?
>> 
>> Many thanks
>> Inés
>> 
>> 
>> 
>> 
>> Inés G. Muñoz 
>> Head of Crystallography and Protein Engineering Unit
>> Spanish National Cancer Research Centre, CNIO
>> 
>> imu...@cnio.es
>> Phone +34 91 732 8000 (ext. 3020)
>> 
>> Melchor Fernández Almagro, 3
>> 28029 Madrid, Spain
>> www.cnio.es
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> Fb Amigos del CNIO |  Tw @CNIOStopCancer |  Youtube canalcnio
>> 
>> 
>> 
>> **ADVERTENCIA LEGAL**: Este correo electrónico, y en su caso los ficheros 
>> adjuntos, pueden contener información protegida para el uso exclusivo de su 
>> destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo 
>> de transmisión por parte de otra persona que no sea el destinatario. Si 
>> usted recibe por error este correo, se ruega comunicarlo al remitente y 
>> borrar el mensaje recibido.
>> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la 
>> protección de los datos personales de las personas físicas, la información 
>> personal que nos pueda facilitar a través de este correo electrónico quedará 
>> registrada por la Fundación CNIO con la finalidad de tramitar el objeto del 
>> presente correo electrónico. El tratamiento de sus datos personales se 
>> encuentra legitimado por ser necesario para gestionar el objeto del presente 
>> mensaje. Estos datos personales no serán comunicados a ningún destinatario 
>> salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud. 
>> podrá ejercer los derechos de acceso, rectificación, supresión, limitación 
>> de tratamiento, portabilidad y oposición en la siguiente dirección: 
>> c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con 
>> el Delegado de Protección de Datos en: delegado_l...@cnio.es. Para el caso 
>> de que Ud. precise conocer información adicional sobre el tratamiento de sus 
>> datos personales, puede consultar dicha información adicional en el 
>> siguiente enlace dentro de nuestra página web: 
>> https://www.cnio.es/es/privacidad/index.asp 
>> 
>> **LEGAL NOTICE**: This email and any attached files may contain protected 
>> information for the sole use of its intended recipient or addressee. Anyone 
>> other than the intended recipient or addressee is strictly prohibited from 
>> distributing, reproducing or transmitting the email and its contents in any 
>> way. If you receive this email in error, please notify the sender and delete 
>> the message.
>> Pursuant to the provisions of EU Regulation 2016/679 regarding the 
>> protection of personal data, any personal information you provide through 
>> this email will be registered by the CNIO Foundation in order to deal with 
>> content of this email. Your personal data must be processed in order to be 
>> able to deal with the content and purpose of this message. Your personal 
>> details will not be passed on to anyone else unless you authorise us to do 
>> so or we are required to do so by law. You may exercise your rights 
>> regarding access, rectification, suppression, limitation of processing, 
>> portability and opposition by writing to the following address: c/Melchor 
>> Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection 
>> Delegate (Delegado de Protección de Datos) at: delegado_l...@cnio.es. If you 
>> require further information about the processing of your personal data, go 
>> to the following link on our webpage: 
>> https://www.cnio.es/es/privacidad/index.asp
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
> 



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/

Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

[Harry Powell - CCP4BB]

Hi Ines

DSSP? (In ccp4 as “mkdssp” in $CBIN)? Should work with any (valid??) PDB file

“Oldie but goodie”...

Harry

> On 7 Apr 2022, at 09:24, Munoz.Ines  wrote:
> 
> Dear all,
> 
> Is there any program or server that automatically assign the secondary 
> structure elements into a pdb generated by alpha fold?
> 
> Many thanks
> Inés
> 
> 
> 
> 
> Inés G. Muñoz 
> Head of Crystallography and Protein Engineering Unit
> Spanish National Cancer Research Centre, CNIO
> 
> imu...@cnio.es
> Phone +34 91 732 8000 (ext. 3020)
> 
> Melchor Fernández Almagro, 3
> 28029 Madrid, Spain
> www.cnio.es
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Fb Amigos del CNIO |  Tw @CNIOStopCancer |  Youtube canalcnio
> 
> 
> 
> **ADVERTENCIA LEGAL**: Este correo electrónico, y en su caso los ficheros 
> adjuntos, pueden contener información protegida para el uso exclusivo de su 
> destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo 
> de transmisión por parte de otra persona que no sea el destinatario. Si usted 
> recibe por error este correo, se ruega comunicarlo al remitente y borrar el 
> mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la 
> protección de los datos personales de las personas físicas, la información 
> personal que nos pueda facilitar a través de este correo electrónico quedará 
> registrada por la Fundación CNIO con la finalidad de tramitar el objeto del 
> presente correo electrónico. El tratamiento de sus datos personales se 
> encuentra legitimado por ser necesario para gestionar el objeto del presente 
> mensaje. Estos datos personales no serán comunicados a ningún destinatario 
> salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud. 
> podrá ejercer los derechos de acceso, rectificación, supresión, limitación de 
> tratamiento, portabilidad y oposición en la siguiente dirección: c/Melchor 
> Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con el 
> Delegado de Protección de Datos en: delegado_l...@cnio.es. Para el caso de 
> que Ud. precise conocer información adicional sobre el tratamiento de sus 
> datos personales, puede consultar dicha información adicional en el siguiente 
> enlace dentro de nuestra página web: 
> https://www.cnio.es/es/privacidad/index.asp 
> 
> **LEGAL NOTICE**: This email and any attached files may contain protected 
> information for the sole use of its intended recipient or addressee. Anyone 
> other than the intended recipient or addressee is strictly prohibited from 
> distributing, reproducing or transmitting the email and its contents in any 
> way. If you receive this email in error, please notify the sender and delete 
> the message.
> Pursuant to the provisions of EU Regulation 2016/679 regarding the protection 
> of personal data, any personal information you provide through this email 
> will be registered by the CNIO Foundation in order to deal with content of 
> this email. Your personal data must be processed in order to be able to deal 
> with the content and purpose of this message. Your personal details will not 
> be passed on to anyone else unless you authorise us to do so or we are 
> required to do so by law. You may exercise your rights regarding access, 
> rectification, suppression, limitation of processing, portability and 
> opposition by writing to the following address: c/Melchor Fernandez Almagro 
> 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de 
> Protección de Datos) at: delegado_l...@cnio.es. If you require further 
> information about the processing of your personal data, go to the following 
> link on our webpage: https://www.cnio.es/es/privacidad/index.asp
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 



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/

[ccp4bb] Add secondary structure definition into an alphafold PDB

[Munoz.Ines]

Dear all,

Is there any program or server that automatically assign the secondary 
structure elements into a pdb generated by alpha fold?

Many thanks
Inés




Inés G. Muñoz
Head of Crystallography and Protein Engineering Unit
Spanish National Cancer Research Centre, CNIO

imu...@cnio.es
Phone +34 91 732 8000 (ext. 3020)

Melchor Fernández Almagro, 3
28029 Madrid, Spain
www.cnio.es


[cid:image002.jpg@01D3CCFF.80156950]





[Hazte Amigo del CNIO. Más investigación, menos cáncer] 


Fb Amigos del CNIO |  Tw 
@CNIOStopCancer |  Youtube 
canalcnio


**ADVERTENCIA LEGAL**: Este correo electrónico, y en su caso los ficheros 
adjuntos, pueden contener información protegida para el uso exclusivo de su 
destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de 
transmisión por parte de otra persona que no sea el destinatario. Si usted 
recibe por error este correo, se ruega comunicarlo al remitente y borrar el 
mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la 
protección de los datos personales de las personas físicas, la información 
personal que nos pueda facilitar a través de este correo electrónico quedará 
registrada por la Fundación CNIO con la finalidad de tramitar el objeto del 
presente correo electrónico. El tratamiento de sus datos personales se 
encuentra legitimado por ser necesario para gestionar el objeto del presente 
mensaje. Estos datos personales no serán comunicados a ningún destinatario 
salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud. 
podrá ejercer los derechos de acceso, rectificación, supresión, limitación de 
tratamiento, portabilidad y oposición en la siguiente dirección: c/Melchor 
Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con el Delegado 
de Protección de Datos en: delegado_l...@cnio.es. Para el caso de que Ud. 
precise conocer información adicional sobre el tratamiento de sus datos 
personales, puede consultar dicha información adicional en el siguiente enlace 
dentro de nuestra página web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected 
information for the sole use of its intended recipient or addressee. Anyone 
other than the intended recipient or addressee is strictly prohibited from 
distributing, reproducing or transmitting the email and its contents in any 
way. If you receive this email in error, please notify the sender and delete 
the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection 
of personal data, any personal information you provide through this email will 
be registered by the CNIO Foundation in order to deal with content of this 
email. Your personal data must be processed in order to be able to deal with 
the content and purpose of this message. Your personal details will not be 
passed on to anyone else unless you authorise us to do so or we are required to 
do so by law. You may exercise your rights regarding access, rectification, 
suppression, limitation of processing, portability and opposition by writing to 
the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may 
contact the Data Protection Delegate (Delegado de Protección de Datos) at: 
delegado_l...@cnio.es. If you require further information about the processing 
of your personal data, go to the following link on our webpage: 
https://www.cnio.es/es/privacidad/index.asp



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/