User: srdjanmasirevic2

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Posts by srdjanmasirevic2

<prev • 14 results • page 1 of 2 • next >
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Comment: C: How can I find full formula of the ligand in PDB files?
... For example for `ligand` `ID` `FGA` that I extracted from protein `PDB` with `ID` `2MTZ.pdb` the formula is `FORMUL 2 FGA 6(C5 H9 N O4)` and when I searched the same compound in `PDBeChem` database for same compound under `Formula` it is written `C5 H9 N O4`. Which one is correct and how do I ...
written 9 months ago by srdjanmasirevic210
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How can I find full formula of the ligand in PDB files?
... Hello I have many pdb files and I am trying to find full formula of an ligand in each pdb file without considering brackets? So, I know that under `FORMUL` I can find a formula with considering brackets. If the formula is `10(C5 N10 O5 H1)` I need this version `C50 N100 O50 H10`. Or in other way ...
pdb written 9 months ago by srdjanmasirevic210 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: How to extract and calculate all protein atom to ligand atom distances from pdb
... Actually from my script I manage to change two lines: 1. Just deleted `next;` line after `$part ++;` 2. Delete `==1` in line `} elsif ($part ==1){` its is calculating fine, but I am just not sure how to assign to this script that if the distance is more then 5 then to delete those lines, and i ...
written 9 months ago by srdjanmasirevic210
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Comment: C: How to extract and calculate all protein atom to ligand atom distances from pdb
... I wanted to check the distances between all protein atoms (`ATOM`) and ligand atoms (`HETATM`). Something like `ATOM1 X HETATM1; ATOM2 X HETATM1 X ATOM3 X HETATM1` and so on.. I tried to put coordinated from the protein atoms `ATOM` into the one array and same for ligand atoms and then to calculate ...
written 9 months ago by srdjanmasirevic210
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Comment: C: How to extract and calculate all protein atom to ligand atom distances from pdb
... I have made some progress, but I cant figure it out why script doesnt work. I have wrote two loops and pushed values of coordinates into seperate arrays and ttried to print distances but it doesnt work. Can You please take a look cause I am trying to change it numerous times. This is the script : ...
written 9 months ago by srdjanmasirevic210 • updated 9 months ago by Michael Dondrup44k
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Answer: A: How to extract and calculate all protein atom to ligand atom distances from pdb
... Im using perl because whole project I started to do in perl and want to finish it in the same manner. I have some basics of Python and Perl but I have never used R; overall to be honest my programming sucks :P Perl seems to be fine for data proccessing but it is also a bit confusing in some aspects. ...
written 9 months ago by srdjanmasirevic210
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Comment: C: How to extract and calculate all protein atom to ligand atom distances from pdb
... So basically I am trying to calculate `ATOM(1)` with all `HETATM(1,2,3,4)` and the same for each atom of the protein. if I end up with result that is <= to five then I should keep this file. Overall from all files I am trying to keep only those in which the distance between ligand and some protei ...
written 9 months ago by srdjanmasirevic210
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Comment: C: How to extract and calculate all protein atom to ligand atom distances from pdb
... It's some kind of personal homework, not for school but form me to make some dataset. So what I have done so far is wrote a script in perl that from the whole pdb dataset I kept only those pdb files that have ligand in its binding pocket (I included some cut off for number of heavy atoms to exclude ...
written 9 months ago by srdjanmasirevic210
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How to extract and calculate all protein atom to ligand atom distances from pdb files in PERL
... Hello, I am trying to find the way how to calculate all atom distances from pdb file ? CAn anybody help me. I have a txt files that look like this : ATOM 1279 C ALA 81 -1.925 -11.270 1.404 ATOM 1280 O ALA 81 -0.279 9.355 15.557 ATOM 1281 OXT ...
perl written 9 months ago by srdjanmasirevic210 • updated 9 months ago by fishgolden200
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Answer: A: Chemical formula of a ligand in PDB file
... Oh, I've found it. It's under the line that starts with FORMUL. I somehow missed this line, if somebody will need it in the future. ...
written 9 months ago by srdjanmasirevic210

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Scholar 9 months ago, created an answer that has been accepted. For A: Chemical formula of a ligand in PDB file

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