[ccp4bb] A question about ShelxC, D and E

[Zhichao Jiao]

Dear all:

 

When using Shelx, there are two input file formats(scalepack or mtz) to 
select. If scalepack format input file is selected, both native data and HA 
data is in need. But if mtz format input file is selected, only HA data is in 
need. Why this difference exist ? Is there a difference in the algorithm when 
using different input formats? 


Thanks, 


Jiao




Zhichao Jiao

Laboratory of Soft Matter Physics

Institute of Physics

Chinese Academy of Sciences

P.O. Box 603, Beijing 100190

Email: zhichaoj...@iphy.ac.cn

2022-01-14



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[ccp4bb] viral protein BLAST

[samer halabi]

Dear All,
Sorry to be disturbing you with my new inquiry.
I always got great and trustworthy results using FUGUE (Protein homology 
recognition using environment-specific amino acid substitution tables: 
https://mizuguchilab.org/fugue/prfsearch.html)  I use an amino acid sequence of 
a viral protein of an unknown structure and function and with FUGUE it searches 
a structural database and gives very good results. When I use the protein BLAST 
for the same amino acid sequence, I may miss or get no results, especially when 
the identity is about 25% between the viral protein and the host protein it 
mimics . I tested that with a viral protein with known structure, and protein 
BLAST was not helpful.
The only issue is that using FUGUE can be time consuming especially if I am 
searching for the possible function/structure of 100 viral proteins of one 
viral strain, not to mention that the same virus has several strains.What would 
be an efficient way to look for host protein mimics?
I would greatly appreciate any suggestion.Thank you in advance.Best 
regards,Samer



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Re: [ccp4bb] viral protein BLAST

[Krieger, James M]

PSI-BLAST (position specific iterative BLAST I think it stands for) and other 
BLAST variants may help - there are quite a few on NCBI now.

There are also some other nice tools such as HHPred at 
https://toolkit.tuebingen.mpg.de/.

Maybe HMMer could be a good option too.

I’m not sure if any of them would be fast though.

Best wishes
James

On 16 Jan 2022, at 11:38, samer halabi 
<30c2162795b2-dmarc-requ...@jiscmail.ac.uk> wrote:


Dear All,

Sorry to be disturbing you with my new inquiry.

I always got great and trustworthy results using FUGUE (Protein homology 
recognition using environment-specific amino acid substitution tables: 
https://mizuguchilab.org/fugue/prfsearch.html)
  I use an amino acid sequence of a viral protein of an unknown structure and 
function and with FUGUE it searches a structural database and gives very good 
results. When I use the protein BLAST for the same amino acid sequence, I may 
miss or get no results, especially when the identity is about 25% between the 
viral protein and the host protein it mimics . I tested that with a viral 
protein with known structure, and protein BLAST was not helpful.

The only issue is that using FUGUE can be time consuming especially if I am 
searching for the possible function/structure of 100 viral proteins of one 
viral strain, not to mention that the same virus has several strains.
What would be an efficient way to look for host protein mimics?

I would greatly appreciate any suggestion.
Thank you in advance.
Best regards,
Samer



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Re: [ccp4bb] A question about ShelxC, D and E

[Jon Cooper]

Hello, it's a while since I ran Shelx and I imagine that you are running it 
through the i2 GUI, which isn't something I've tried yet. Unless it's changed a 
lot recently, shelx itself accepts the reflection data as h, k, l, F and 
sigma(F) (HKLF 3) or h, k, l, I and sigma(I) (HKLF 4). Bit rusty on this so 
details might be wrong. The direct methods it does for finding heavy-atom sites 
or anomalous scatterers in macromolecules relies on using the differences 
between FPH and FP, or FPH+ and FPH-, hence the need for a file containing 
both. In contrast, with small molecule direct methods or macromolecular 
refinement, the F or I data (with their sigma's) alone are sufficient for the 
calculations, but probably you knew that already. Best wishes, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 16 Jan 2022, 09:28, Zhichao Jiao < zhichaoj...@iphy.ac.cn> wrote:
Dear all:

When using Shelx, there are two input file formats(scalepack or mtz) to select. 
If scalepack format input file is selected, both native data and HA data is in 
need. But if mtz format input file is selected, only HA data is in need. Why 
this difference exist ? Is there a difference in the algorithm when using 
different input formats?
Thanks,
Jiao

Zhichao Jiao
Laboratory of Soft Matter Physics
Institute of Physics
Chinese Academy of Sciences
P.O. Box 603, Beijing 100190
Email: zhichaoj...@iphy.ac.cn
2022-01-14

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[ccp4bb] University of Essex Research Fellowship

[Prischi, Filippo]

Dear all,

We welcome high-calibre candidates to join the Protein Structure and Mechanism 
of 
Disease
 (PSMD) division at the University of Essex via external Fellowships from 
funding agencies including the Royal Society, ERC, Wellcome Trust, UKRI and 
Cancer Research UK. We encourage applicants with a skillset and research 
interest in structural biology, biochemistry, molecular biology and 
computational biology. The PSMD offers substantial support for the preparation 
of your Fellowship applications and throughout their duration.
For more info and details on how to apply, please follow this link 
https://filippoprischilab.org/contact/research-fellowship-applications/

Kind Regards,
Filippo

~~
Dr Filippo Prischi
Senior Lecturer in Biochemistry
School of Life Sciences
University of Essex

T.  +44 (0)1206 873370
E.  fpris...@essex.ac.uk
► http://www.essex.ac.uk/bs/staff/profile.aspx?ID=4512



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