[ccp4bb] Searching Sequence Motif

[Cryo EM]

Hi all,

I want to search NCBI/PDB for all E.coli proteins with a specific sequence
motif.
Is there any server/software in which I can search and display all the
proteins in E.coli with this specific sequence motif?
Suggestions are highly appreciated.

Thanks!



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[ccp4bb] Coot RNA bases Mutate

[Cryo EM]

Hi everyone,

I am trying to mutate modified RNA nucleotide to standard nucleotide by
coot using "Simple Mutate" button. But it is not working despite selecting
the correct residue from the standard base list that pop up on clicking
"simple mutate button". Does anyone and an idea what could be the problem?
Or is this wrong way to do that?

I am using coot 0.9.8.3 EL (Ccp4) on my Mac.

Thanks



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[ccp4bb] Making bonds

[Cryo EM]

Hi everyone,

In one my PDBs, I see that there is a linkage break in ribonucleotides.
Specifically one of the phospodiester bond seems to be broken and thus O3'
needs to be bonded to P atom of next nucleotide. What is the easiest way to
do this in coot ? Or any other software?
I tried "make link" option in coot but it seems it just created link in PDB
and not bond?


Regards



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[ccp4bb] mRNA secondary structure prediction in 3D

[Cryo EM]

Hi all,

I have a mRNA which forms a putative secondary  structure. Is there any
Webserver which takes the primary sequence of mRNA and can give me the
predicted PDB file with the secondary structure formed?

Regards and Thanks



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[ccp4bb] MTZ to ccp4/MRC map

[Cryo EM]

Hi all,

I was wondering what would be the best way to convert a MTZ file to MRC or
CCP4 map?
I have a corresponding PDB file with me.

Thanks



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