Re: [ccp4bb] secondary structure prediction

[zheng zhou]

Thanks for many advices. I was not clear in the previous email. I know
the close homologous protein (20% identity, total 500aa), but the
fragment hits (30~40aa, identity 40~50%) are from other proteins in
PDB. I am trying to see whether the fragments from non-homologous
proteins may help the secondary structure prediction.

Best,
Z

On Wed, Dec 6, 2017 at 10:14 PM, zheng zhou  wrote:
> Dear CCP4 community,
>
> Sorry for the off-topic question. I am trying to design constructs for
> structure studies. It only has a homolog structure in PDB with
> sequence identity ~20%. When I blast against PDB sequence, there are
> quite a few motif hits (30~40aa, identity 40~50%). Any prediction
> tools utilize this information?
>
> Thanks for your advice in advance.
>
> Best,
>
> Zheng

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Bernhard Rupp]

You can find these numbers in the header of the output model coordinate file.

 

BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiao Lei
Sent: Wednesday, December 6, 2017 2:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to find the Rfree and R in the highest resolution bin in 
Refmac 5?

 

Dear All,
 
I am asking how to find the Rfree and R in the highest resolution bin in Refmac 
5 output?

I used Refmac5 in refinement of protein structure at 3A resolution.
Output of Refmac5 gives Rfee and R as:

  InitialFinal

   R factor0.2900   0.2052

 R free0.3015   0.2639


I'd also like to see the Rfree and R in the highest resolution bin. I checked 
log file in Refmac5 and found M(4SSQ/LL) resolution range table with columns of 
Rf_free and WR_free, I searched in internet and still could not understand the 
Rf_free and WR_free label meaning.  I'd like to find something like Rfree XXX 
(XXX);  R XXX (XXX)  (the highest resolution bin value in the parenthesis). 

 

thanks ahead.

 

 

[ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Xiao Lei]

Dear All,

I am asking how to find the Rfree and R in the highest resolution bin in
Refmac 5 output?

I used Refmac5 in refinement of protein structure at 3A resolution.
Output of Refmac5 gives Rfee and R as:

  InitialFinal

   R factor0.2900   0.2052

 R free0.3015   0.2639


I'd also like to see the Rfree and R in the highest resolution bin. I
checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
with columns of Rf_free and WR_free, I searched in internet and still could
not understand the Rf_free and WR_free label meaning.  I'd like to find
something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
value in the parenthesis).

thanks ahead.

Re: [ccp4bb] secondary structure prediction

[Missoury Sophia]

Modeller 


Sophia Missoury 



- Mail original -

De: "Smith Liu"  
À: CCP4BB@JISCMAIL.AC.UK 
Envoyé: Mercredi 6 Décembre 2017 16:04:12 
Objet: Re: [ccp4bb] secondary structure prediction 

Rosetta 





Smith Liu 


邮箱：smith_liu...@163.com 


签名由 网易邮箱大师 定制 




在 2017年12月06日 22:14 ， zheng zhou 写道： 
Dear CCP4 community, 

Sorry for the off-topic question. I am trying to design constructs for 
structure studies. It only has a homolog structure in PDB with 
sequence identity ~20%. When I blast against PDB sequence, there are 
quite a few motif hits (30~40aa, identity 40~50%). Any prediction 
tools utilize this information? 

Thanks for your advice in advance. 

Best, 

Zheng 

Re: [ccp4bb] secondary structure prediction

[Gert Vriend]

I would try your local bioinformatician (or a remote one if there isn't
any one local).

With the sequence in the mail, I could have given it a shot...

Gert


On 12/6/2017 3:14 PM, zheng zhou wrote:

Dear CCP4 community,

Sorry for the off-topic question. I am trying to design constructs for
structure studies. It only has a homolog structure in PDB with
sequence identity ~20%. When I blast against PDB sequence, there are
quite a few motif hits (30~40aa, identity 40~50%). Any prediction
tools utilize this information?

Thanks for your advice in advance.

Best,

Zheng


Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het 
handelsregister onder nummer 41055629.
The Radboud university medical center is listed in the Commercial Register of 
the Chamber of Commerce under file number 41055629.

Re: [ccp4bb] secondary structure prediction

[Anastassis Perrakis]

Dear Zheng,

You might want to try the tools at:

https://ccd.rhpc.nki.nl

Tassos

On Dec 6, 2017, at 15:14, zheng zhou 
> wrote:

Dear CCP4 community,

Sorry for the off-topic question. I am trying to design constructs for
structure studies. It only has a homolog structure in PDB with
sequence identity ~20%. When I blast against PDB sequence, there are
quite a few motif hits (30~40aa, identity 40~50%). Any prediction
tools utilize this information?

Thanks for your advice in advance.

Best,

Zheng

Re: [ccp4bb] secondary structure prediction

[Smith Liu]

Rosetta




| |
Smith Liu
|
|
邮箱：smith_liu...@163.com
|

签名由 网易邮箱大师 定制




在2017年12月06日 22:14，zheng zhou 写道：
Dear CCP4 community,

Sorry for the off-topic question. I am trying to design constructs for
structure studies. It only has a homolog structure in PDB with
sequence identity ~20%. When I blast against PDB sequence, there are
quite a few motif hits (30~40aa, identity 40~50%). Any prediction
tools utilize this information?

Thanks for your advice in advance.

Best,

Zheng

[ccp4bb] secondary structure prediction

[zheng zhou]

Dear CCP4 community,

Sorry for the off-topic question. I am trying to design constructs for
structure studies. It only has a homolog structure in PDB with
sequence identity ~20%. When I blast against PDB sequence, there are
quite a few motif hits (30~40aa, identity 40~50%). Any prediction
tools utilize this information?

Thanks for your advice in advance.

Best,

Zheng

[ccp4bb] Postdoc position at Pasteur Institute, Paris

[Nicolas Reyes]

Dear all,

Please, find below an ad for a Postdoctoral position in the Reyes'
laboratory at Pasteur Institute in Paris to work on human transporters.

Best regards,

Nico



A Postdoctoral position is available in the Laboratory of Nico Reyes at the
Pasteur Institute in Paris for initial 2-3 years with the possibility of
extensions. Our work focuses on physiological and pathological mechanisms
of Human Membrane Transporters using structural and biophysical techniques
(for a recent publication see: http://www.nature.com/articles/nature22064).
We are an international team with excellent biochemistry and biophysics
resources, and have access to state-of-the-art X-ray and EM facilities for
sample preparation and data collection, among others.



We are looking for a highly motivated candidate with a Ph.D
in Structural Biology, Biophysics or related disciplines with a good
publication record and willing to work on challenging projects to
unravel molecular mechanisms of human membrane proteins. Hands on
experience and knowledge in protein expression and purification, as well as
X-ray crystallography and/or Cryo-EM are essential for the position.



To apply, please send an email to nre...@pasteur.fr with subject "postdoc
application”, and a single pdf file including: your CV (2-page max. Please,
include graduation date and list of publications), research interest and
experience (1 page max.), the reference of the most exciting research
article you have read in the last 2 years, and the name and contact
information of 2-3 references.