Marvin 4.1.2 and peptides

Dear Support,





I downloaded the last version of Marvin. I stored a custom_aminoacids.dict file in my chemaxon user directory with the examples of the documentation but I don't know how to use it.





I would like to have a list of sequence with custom amino acids and convert them into sdf. If I wrote in my cmd

Code:

molconvert --peptide X(Hcy) mol -o peptide.mol

I have an error:

Code:

java.io.IOException: Unknown amino acid X?         at chemaxon.marvin.modules.PeptideReader.findAminoAcids(Unknown Source)         at chemaxon.marvin.modules.PeptideReader.convert(Unknown Source)         at chemaxon.marvin.modules.PeptideImport.readMol(Unknown Source)         at chemaxon.formats.MolImporter.readDoc(Unknown Source)         at chemaxon.formats.MolConverter.readDoc(Unknown Source)         at chemaxon.formats.MolConverter.convert0(Unknown Source)         at chemaxon.formats.MolConverter.convert(Unknown Source)         at chemaxon.formats.MolConverter.main(Unknown Source)

Moreover, I don't understand well how to convert a smarts into a peptide sequence with

Code:

echo "[H]NCC(=O)NC(C)C(=O)NCC(O)=O" | molconvert peptide:3

I obtain this error: file format not recognized.





Can you give me more explanation, please?


Thank you very much





Best regards,


Severine

Thanks for the bug report. We will fix it.

Hello, as for the first example, if you are using shell, you should escape parentheses like:





molconvert --peptide "X(Hcy)" mol





but you found a bug, it is not working for single custom AAs, but for sequences like


"X(Hcy)ASD" (there must be something next to it - I will check and fix it).





As the other question, it works fine for me, what operating system are you using?





$ echo "[H]NCC(=O)NC(C)C(=O)NCC(O)=O" | molconvert peptide:3


GlyAlaGly





You can use it in the other way, make a file like, lets call it aas.seq with SMILES as


[H]NC(C)C(=O)NC(CO)C(=O)NC(CC(O)=O)C(O)=O


[H]NC(CO)C(=O)NC(CC(O)=O)C(=O)NC(CC1=CC=CC=C1)C(O)=O


[H]NCC(=O)NC(C)C(=O)NCC(O)=O





then you can convert:





$ molconvert peptide:3 aas.seq


AlaSerAsp


SerAspPhe


GlyAlaGly

Hello,





I tried "X(Hcy)ASD" and it works. but

Code:

echo "[H]NCC(=O)NC(C)C(=O)NCC(O)=O" | molconvert peptide:3

doesn't work . My OS is Window XP SP2.





Is there a way to convert a SEQ file with 3 amino-acid sequences to a SDFile?





Severine

Code:

echo "[H]NCC(=O)NC(C)C(=O)NCC(O)=O" | molconvert peptide:3

It was a pipeline. Windows does not support this functionality incontrary of Linux and other Unix based systems.


Since Windows can not evaluate pipelines, cut it to multiple commands.

Code:

echo "[H]NCC(=O)NC(C)C(=O)NCC(O)=O" > temp.smiles molconvert.bat peptide:3 temp.simples del temp.smiles

Quote:

Is there a way to convert a SEQ file with 3 amino-acid sequences to a SDFile?

Save sequences into a file and use MolConvert to tranform it.

Code:

molconvert.bat sdf 3.seq > 3.sdf

Thank you Tamas,





the SEQ to SDF conversion works but there is something strange:





this sequence works:

Code:

AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTryTyrVal

this one does'nt work

Code:

AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTryTyrX(Hcy)Val

I obtain the error:

Quote:

java.io.IOException: Unknown amino acid U at chemaxon.marvin.modules.PeptideReader.findAminoAcids(Unknown Source) at chemaxon.marvin.modules.PeptideReader.convert(Unknown Source) at chemaxon.marvin.modules.PeptideImport.readMol(Unknown Source) at chemaxon.formats.MolImporter.readDoc(Unknown Source) at chemaxon.formats.MolConverter.readDoc(Unknown Source) at chemaxon.formats.MolConverter.convert0(Unknown Source) at chemaxon.formats.MolConverter.convert(Unknown Source) at chemaxon.formats.MolConverter.main(Unknown Source)

I thought it was because of X(Hcy) but this one works well:

Code:

TryTyrX(Hcy)Val

I tried

Code:

TryTyrX(Hcy)Val AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTryTyrX(Hcy)Val

Code:

AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTryTyrX(Hcy)Val TryTyrX(Hcy)Val AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTryTyrVal

Code:

TryTyrX(Hcy)Val AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTryTyrX(Hcy)Val AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTryTyrVal

in my file and I have the error.





I tried

Code:

TryTyrX(Hcy)Val AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTryTyrVal AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTryTyrX(Hcy)Val

and there is no problem.





Best regards,


Severine

Hello, that is apparently a bug in file format recognition. Until I fix it you can force the input file format like:





echo "AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTryTyrX(Hcy)Val" > foo.seq


molconvert mol "foo.seq{peptide:3}" -o my_peptide.mol





the molconverter options are available at:


http://www.chemaxon.com/marvin/doc/user/molconvert.html

The fix will be in the next release (coming soon) - still, better rely on the force parameter sometimes, as guessing the format can be misleading. Just an example: the string "tyralatyr" is a valid one-letter sequence with 9 aminoacids, but obviously differs from "TyrAlaTyr".





To ask an other topic: do you have problems with custom aminoacids or is the way as we handling them all right for you?