From owner-chemistry@ccl.net Sun Nov 15 03:17:00 2009 From: "Vladimir Chupakhin chupvl]|[gmail.com" To: CCL Subject: CCL: remove salts from compounds Message-Id: <-40682-091112025452-4344-NMxiVRLpZY/HlHUeri0fdw**server.ccl.net> X-Original-From: Vladimir Chupakhin Content-Type: multipart/alternative; boundary="------------010108040403000303010907" Date: Thu, 12 Nov 2009 10:28:19 +0300 MIME-Version: 1.0 Sent to CCL by: Vladimir Chupakhin [chupvl{:}gmail.com] This is a multi-part message in MIME format. --------------010108040403000303010907 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hello, most of the salt stripping software working by removing all except the biggest one fragment. Yes, it's work in the most of the cases but there some that dosen't fit: organometalic, ferracens, etc. I was looking for software that strip "normal" salts but not removing e.g. metals from heme. I can make make my own rules but it's really time consuming for large database where number of "problem" salts is around 2%. Any ideas? Yours, Vladimir Chupakhin, Moscow State University, Moscow, Russia aa aa,+,chemaxon.hu wrote: > HI amit, > > ChemAxon Standardizer will do this. It is not free but is free (as are > all tools) for academic research. See this page > for more info and > how to download. This page > for free academic > package signup. > > Cheers > Alex > > PS - heads up on improvements on Standardizer in JChem 5.3 (due out v > soon), we are introducing checking/fixing/conversion notification > capabilities for structure files. 5.3 will be MarvinSketch only but > will be formally a part of Standardizer soon after. > > > amit dong dongamit123a/gmail.com wrote: >> Hi, >> >> Is there any free tool that can be used for removing ions/salts > >> from a large library of compounds? >> >> Thanks >> AD --------------010108040403000303010907 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello,

most of the salt stripping software working by removing all except the biggest one fragment. Yes, it's work in the most of the cases but there some that dosen't fit: organometalic, ferracens, etc. I was looking for software that strip "normal" salts but not removing e.g. metals from heme. I can make make my own rules but it's really time consuming for large database where number of "problem" salts is around 2%. Any ideas?

Yours,
Vladimir Chupakhin,
Moscow State University,
Moscow, Russia

aa aa,+,chemaxon.hu wrote:

HI amit,

ChemAxon Standardizer will do this. It is not free but is free (as are all tools) for academic research. See this page for more info and how to download. This page for free academic package signup.

Cheers
Alex

PS - heads up on improvements on Standardizer in JChem 5.3 (due out v soon), we are introducing checking/fixing/conversion notification capabilities for structure files. 5.3 will be MarvinSketch only but will be formally a part of Standardizer soon after.

amit dong dongamit123a/gmail.com wrote:

Hi,

Is there any free tool that can be used for removing ions/salts > from a large library of compounds?

Thanks

AD

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