From yolanda.only at yahoo.com.cn Mon Mar 3 18:12:18 2008 From: yolanda.only at yahoo.com.cn (Äî Áõ) Date: Mon, 3 Mar 2008 18:12:18 -0800 (PST) Subject: [Zinc-fans] how to download the database of compounds completely Message-ID: <597972.77939.qm@web15904.mail.cnb.yahoo.com> Dear zinc-fans: I have a question that how to download the database of compounds completely. I noticed that it has a download button such as "download all these as SMILES,MOL2,SDF" in the compounds browsing web page, is that usable? Another question is that whether min-PH subset and reference subset are overlapping? I want to download the lead_like subset. And in the downloaded mol2 file, what did these compounds were sorted by? I'm a novice in zinc and sorry for so much questions. Any answer would be much appreciated. Best regards, Yolanda Guo Northeast Normal University,China. --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080303/0d5fdfa0/attachment.html From jji at cgl.ucsf.edu Wed Mar 12 16:37:54 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 12 Mar 2008 16:37:54 -0700 Subject: [Zinc-fans] how to download the database of compounds completely In-Reply-To: <597972.77939.qm@web15904.mail.cnb.yahoo.com> References: <597972.77939.qm@web15904.mail.cnb.yahoo.com> Message-ID: <47D86952.50100@cgl.ucsf.edu> Hi Yolanda > I have a question that how to download the database of compounds > completely. > I noticed that it has a download button such as "download all these as > SMILES,MOL2,SDF" in the compounds browsing web page, is that usable? It should work. If it doesn't, tell me exactly what doesn't work and I will try to fix it. > Another question is that whether min-PH subset and reference subset > are overlapping? I want to download the lead_like subset. If you are docking at or near physiological pH, you probably want the "usual" subset, which includes the reference structures (pH 7) and additional protonated forms near physiological pH ("mid" subset"). You get both with the "usual" download scripts. > And in the downloaded mol2 file, what did these compounds were sorted by? I think they are random. you can sort them any way you like. > I'm a novice in zinc and sorry for so much questions. > Any answer would be much appreciated. I hope this is of some use. Good luck! John UCSF ZINC Team From yolanda.only at yahoo.com.cn Tue Mar 18 00:17:17 2008 From: yolanda.only at yahoo.com.cn (Äî Áõ) Date: Tue, 18 Mar 2008 00:17:17 -0700 (PDT) Subject: [Zinc-fans] Some questions about the general information of the vendor Message-ID: <838519.10154.qm@web15902.mail.cnb.yahoo.com> Dear zinc-fans: I noticed that there are some informations in the vendor subset page as follows. But I'm not sure what are the meanings of the red characters. What do the numbers "0,1" represent for? "Catalog version: May 07, # in catalog: 250000 Website: dtp.nci.nih.gov, email dtpinfo at mail.nih.gov, phone no phone, fax no fax free? 1, purchasable? 1, pubchem? 0, depleted? 0 # filtered 0" Any help would be much appreciated! Thanks in advance. Best regards Yolanda Guo Northeast Normal University --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080318/e4a622d6/attachment.html From lhailema at ecn.purdue.edu Wed Mar 26 06:19:47 2008 From: lhailema at ecn.purdue.edu (Leaelaf M Hailemariam) Date: Wed, 26 Mar 2008 09:19:47 -0400 (EDT) Subject: [Zinc-fans] Help needed for Java tool to convert a molecular picture to SMILES string Message-ID: Dear Zinc forum I want to make use of the tool found in: http://zinc.docking.org/choose.shtml wherein the molecular structure is drawn in a panel and then converted to SMILES strings through the command 'save smiles'. I have developed an application that uses SMILES strings as inputs. Is there some Java code available that can be used for this purpose? regards Leaelaf From jji at cgl.ucsf.edu Wed Mar 26 12:49:31 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 26 Mar 2008 12:49:31 -0700 Subject: [Zinc-fans] Help needed for Java tool to convert a molecular picture to SMILES string In-Reply-To: References: Message-ID: <47EAA8CB.5070600@cgl.ucsf.edu> Hi Leaelaf The tool is called the Java Molecular Editor, and is available courtesy of Peter Ertl via Molinspiration.com (http://molinspiration.com for more info). John UCSF ZINC Team Leaelaf M Hailemariam wrote: > Dear Zinc forum > > I want to make use of the tool found in: http://zinc.docking.org/choose.shtml wherein the molecular structure is > drawn in a panel and then converted to SMILES strings through the command > 'save smiles'. I have developed an application that uses SMILES strings > as inputs. Is there some Java code available that can be used for this > purpose? > > regards > Leaelaf > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From yolanda.only at yahoo.com.cn Thu Mar 27 19:53:03 2008 From: yolanda.only at yahoo.com.cn (Äî Áõ) Date: Thu, 27 Mar 2008 19:53:03 -0700 (PDT) Subject: [Zinc-fans] how to sort compounds by zinc ID Message-ID: <791441.65312.qm@web15914.mail.cnb.yahoo.com> Dear zinc-fans: Sorry for asking so naive questions. I have downloaded the specs "usual" subset. And I found that compouds in the .mol2 files were sorted at random. I would like to know is there any method that can sort them by zinc ID from low-to-high. Shall I have to program by myself ? Or is there any existing method? The reason I want to do this is I think it will be compared with the properties table for convenience. Thank you for your patience. Any answer would be appreciated ! Best regards, Yolanda Guo Northeast Normal University --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080327/94db2809/attachment.html From yolanda.only at yahoo.com.cn Fri Mar 28 00:10:10 2008 From: yolanda.only at yahoo.com.cn (Äî Áõ) Date: Fri, 28 Mar 2008 00:10:10 -0700 (PDT) Subject: [Zinc-fans] What dose the subset number represent for? Message-ID: <551806.6375.qm@web15902.mail.cnb.yahoo.com> Hi all, Excuse me, I have another question. In the results browser, there is a button named created subset. When I clicked it, "Creating subset 1202.[1] 28022" displayed. But I don't know what its meaning. What does the number represent for? I have looked "user-created subset" page over , however I don't understand what does the first row named "Subset#" mean. Sorry for asking so many questions. Thanks in advance for any answer. Best regards, Yolanda Guo Northeast Normal University --------------------------------- Never miss a thing. Make Yahoo your homepage. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080328/76fa8e5c/attachment-0001.html