From owner-chemistry@ccl.net Sun Sep 6 10:41:01 2009 From: "Joe Leonard jleonard42#,#gmail.com" To: CCL Subject: CCL: Snow Leopard? Message-Id: <-40179-090906102139-5252-6i8k+Lz3DnZp1ZWrL4Gp8Q##server.ccl.net> X-Original-From: Joe Leonard Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Sun, 6 Sep 2009 09:22:23 -0400 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Joe Leonard [jleonard42(_)gmail.com] Folks, has anybody updated to Snow Leopard yet? If so, what version of X11 comes with it? I run Leopard, and have XQuartz2.1.6. I have noticeable/annoying artifacts with X applications on my MBP, and hope there is a newer version with the newer software that might address some of this. Pointers where I might upgrade my X11 without having to type "make X11" would also be appreciated! Thanks in advance! Joe Leonard jleonard42() gmail.com -- Programming is like sex. One mistake and you have to support it for the rest of your life. From owner-chemistry@ccl.net Sun Sep 6 11:43:01 2009 From: "Chris Swain swain===mac.com" To: CCL Subject: CCL: Snow Leopard? Message-Id: <-40180-090906114133-2521-g+3iEiTj97mLdIi6YyzI3Q++server.ccl.net> X-Original-From: Chris Swain Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Sun, 06 Sep 2009 16:41:17 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain%mac.com] X11 for Mac OS X http://homepage.mac.com/swain/Sites/Macinchem/page5/files/31165a685050a2b20687a9c6da179ee0-397.html Chris On 6 Sep 2009, at 14:22, Joe Leonard jleonard42#,#gmail.com wrote: > > Sent to CCL by: Joe Leonard [jleonard42(_)gmail.com] > Folks, has anybody updated to Snow Leopard yet? If so, what version > of X11 comes with it? > > I run Leopard, and have XQuartz2.1.6. I have noticeable/annoying > artifacts with X applications on my MBP, and hope there is a newer > version with the newer software that might address some of this. > Pointers where I might upgrade my X11 without having to type "make > X11" would also be appreciated! > > Thanks in advance! > > Joe Leonard > jleonard42(a)gmail.com > -- > Programming is like sex. One mistake and you have to support it for > the rest of your life. > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/ > sub_unsub.shtml> > Job: http://www.ccl.net/jobs> > From owner-chemistry@ccl.net Sun Sep 6 13:54:01 2009 From: "Werner K werner.schroedinger^googlemail.com" To: CCL Subject: CCL: Chemical reactions and mol2 files Message-Id: <-40181-090906115314-8415-GIGYuCzkC9DeCGTO9S4Nrw]*[server.ccl.net> X-Original-From: "Werner K" Date: Sun, 6 Sep 2009 11:53:10 -0400 Sent to CCL by: "Werner K" [werner.schroedinger,,googlemail.com] Hi, I have a file in MOL2 format with around 10000 molecules. I want to perform chemical reactions on them (for instance change all -OH to -COOH) and get the results in MOL2 format with the corresponding new 3D coordinates for the new functional groups, etc. What is the best software for this purpose? Thanks W From owner-chemistry@ccl.net Sun Sep 6 14:29:00 2009 From: "Geoffrey Hutchison geoffh#,#pitt.edu" To: CCL Subject: CCL: Snow Leopard and X11 Message-Id: <-40182-090906130019-19384-SyRiFbMDgTgNYq5qCWjzkw,server.ccl.net> X-Original-From: Geoffrey Hutchison Content-transfer-encoding: 7bit Content-type: text/plain; delsp=yes; format=flowed; charset=us-ascii Date: Sun, 06 Sep 2009 12:16:00 -0400 MIME-version: 1.0 (Apple Message framework v1075.2) Sent to CCL by: Geoffrey Hutchison [geoffh|a|pitt.edu] > I run Leopard, and have XQuartz2.1.6. I have noticeable/annoying > artifacts with X applications on my MBP, and hope there is a newer > version with the newer software that might address some of this. > Pointers where I might upgrade my X11 without having to type "make > X11" would also be appreciated! What you want is here: http://xquartz.macosforge.org/ > 10.6 contains version 2.3.4 of X11. Not surprisingly, this version > lies between 2.3.3.2 and 2.4.0. It contains all the fixes that went > into Xplugin, quartz-wm, and most of the server fixes, but it is > still on the 1.4 server branch. Most of the userland libraries were > updated to what was shipped in 2.4.0 with a few exceptions. The Xquartz project is community-supported and updates do show up in Apple's software updates: > You will need to re-install this package after future OS, and > Security Updates delivered through Apple's Software Update. > Additionally, you should reinstall this package after installing > XCode. Cheers, -Geoff --- Prof. Geoffrey Hutchison Assistant Professor, Department of Chemistry University of Pittsburgh http://hutchison.chem.pitt.edu/ Office: (412) 648-0492 From owner-chemistry@ccl.net Sun Sep 6 15:36:01 2009 From: "Kalju Kahn kalju*|*chem.ucsb.edu" To: CCL Subject: CCL: Steps of docking Message-Id: <-40183-090906153406-19161-9sqZuwD+KbU4VjNwIPVWSA:server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sun, 6 Sep 2009 12:33:53 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju%a%chem.ucsb.edu] Basma, > Hi, > Thanks for the first result but I read that I have to add hydrogen then, > remove the polar one could you explain that please. You're welcome! But I am not sure what you are referring to this time. In order to calculate the electrostatic potential w/ all-atom force field such as AMBER, you need to add all hydrogen atoms; these are commonly missing in protein X-ray structures. Addition of hydrogens to tetrahedral carbons is trivial but addition of polar hydrogens is trickier: one may want to optimize the H-bonding network. Many docking programs do that during the "protein preparation" stage. In some cases you also need a structure without hydrogens. For example, in UCSF Dock, you generate the protein surface so that the binding pocket could be defined. I guess eliminating H prior to surface definition saves some computational time. Maybe you want to ask help from AutoDock mailing list at http://autodock.scripps.edu/mailing_list if this is AutoDock specific. Kalju > --- On Sun, 8/30/09, Kalju Kahn kalju() chem.ucsb.edu > wrote: > > >> From: Kalju Kahn kalju() chem.ucsb.edu > Subject: CCL: Steps of docking > To: "Ghazal, Basma " > Date: Sunday, August 30, 2009, 8:26 PM > > > > Sent to CCL by: "Kalju Kahn" [kalju]=[chem.ucsb.edu] > Basma, > > One reason would be that the experimental structure was crystallized with > a small ligand in a larger pocket, and the voids of that pocket contain > water molecules.  But you may want these voids be accessible to ligand > atoms while docking.  With standard docking methods, the water will not be > "squeezed" out during binding, as would happen with real molecules, so you > need to remove them.  Of course, other times you may want to keep some of > these waters in order to benefit from solvent-mediated interactions. > > Kalju > > >> Hi: >> Thanks for this result but I need to ask about somthing; >> Why we remove water? >> Thanks > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kalju Kahn > Department of Chemistry and Biochemistry > UC Santa Barbara, CA 93106 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106