From chemistry-request@server.ccl.net Thu Dec 28 07:20:14 2000 Received: from mail.etang.com (mail.etang.com [202.101.42.207] (may be forged)) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA31250 for ; Thu, 28 Dec 2000 07:20:13 -0500 Received: from lizhenhua (unknown [202.109.98.131]) by mail.etang.com (Postfix) with SMTP id 4E8E11CD70461 for ; Thu, 28 Dec 2000 20:26:37 +0800 (CST) Message-ID: <003601c070c9$bd3a0ed0$de0b140a@lizhenhua> From: "tang_hairong" To: "CCL" Subject: structure of Al2O3 Date: Thu, 28 Dec 2000 20:28:47 +0800 Dear listers, Does anyone know the structure of crystal Al2O3? I need the coordinate to start a calculation. All responses will be appreciated, and I will summarize them. Happy new year! Hairong From chemistry-request@server.ccl.net Thu Dec 28 16:52:58 2000 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA01126 for ; Thu, 28 Dec 2000 16:52:58 -0500 Received: from glasgow.ks.uiuc.edu (glasgow.ks.uiuc.edu [130.126.120.45]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id PAA01109 for ; Thu, 28 Dec 2000 15:52:59 -0600 (CST) Received: (from barryi@localhost) by glasgow.ks.uiuc.edu (8.9.3+Sun/8.9.1) id PAA13705 for CHEMISTRY@ccl.net; Thu, 28 Dec 2000 15:52:58 -0600 (CST) Date: Thu, 28 Dec 2000 15:52:58 -0600 From: Barry Isralewitz To: CHEMISTRY@ccl.net Subject: Announce: ZoomSeq -- sequence browser for VMD Message-ID: <20001228155257.I13126@glasgow.ks.uiuc.edu> Mail-Followup-To: Barry Isralewitz , CHEMISTRY@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Description: message body Content-Disposition: inline User-Agent: Mutt/1.3.7i Hello, Announcing ZoomSeq 0.9a, a sequence browser for VMD. ZoomSeq is a TCL script, for the free molecular graphics program VMD, that provides a zoomable sequence browser for protein molecules. Residues are selected in the sequence window, and will appear highlighted in the molecular structure in the VMD's OpenGL window. Conversely, label a residue in the OpenGL window, and the selection appears highlighted in the ZoomSeq window. In its current state, I've found ZoomSeq especially helpful for keeping track of position in a large protein, and for highlighting large sections of a molecule all at once, while still having a "global view". I'm working on adding options to display additional columns in ZoomSeq, using various remote servers to add profiling methods (e.g. hydrophobicity) and database lookups (e.g. similarity scoring). You can access ZoomSeq at: http://www.ks.uiuc.edu/Research/vmd/script_library/categories/sequence.html The README file is inserted below. Note that pre-1.5 versions of VMD won't work with ZoomSeq, you can download the latest version of VMD (for free) at: http://www.ks.uiuc.edu/Research/vmd/ Of course, please let me know about any bugs, suggestions, questions, or interface concerns. Cheers, Barry The ZoomSeq README ===== ZoomSeq 0.9a -- a sequence browser for VMD Barry Isralewitz Dec 28, 2000 --- ZoomSeq is a TCL script for VMD that provides a zoomable sequence browser for protein molecules. Residues are selected in the sequence window, and will appear highlighted in the molecular structure in the VMD's OpenGL window. Conversely, label a residue in the OpenGL window, and the selection appears highlighted in the ZoomSeq window. -- Running ZoomSeq --------------- 1. Start vmd 2. Load a molecule. (It will be "molecule 0") 3. type source zoomseq.tcl into the "vmd console" window. 4. Wait a few seconds for setup calculation. 5. The ZoomSeq window appears. Display ------ The first column displays residue number, residue name, and chain. The second column displays B-factor. The third column displays color-coded secondary structure. (See "Coming Soon" for upcoming data types for columns.) When zoomed out ( Zoom < 1.00), residue numbers may be skipped, but the number of the last residue is always displayed. Controls -------- Sequence selection: Click anywhere in the ZoomSeq sequence listing to select a single residue. For multiple selections, click and drag the 'marquee' to surround the residues you want to highlight. Multiple marquee selections can be made, they are cancelled when a single selection is made. Sequence zoom: The Zoom Slider controls the vertical size of the residue display. The scale of '1.00' is about 8 pixels per residue. Slide the control with the left mouse button to see the sequence grow and shrink, click with the center mouse button along the slider track to jump to a zoom setting. Zoom settings less than 1.00 are useful for proteins of more than 150 residues. The right-hand vertical scroll bar lets you scroll through the sequence if the zoom setting makes the sequence longer than the ZoomSeq window. Structure selection: 1. Set mouse to 'Pick' mode (i.e. choose 'Pick Atoms' in VMD Mouse menu, or press the "1" shortcut key). 2. Click on a residue. It will appear highlighted in yellow in the structure and in the ZoomSeq window. Details/Hints ------------- ZoomSeq highlights residues with thick yellow bonds. If your current rendering would obscure these, you will not see the selection. Th defaults for all renderings (except Surf and MSMS) work fine with ZoomSeq. Every residue in molecule 0 with a "CA" atom should appear in the sequence list. ZoomSeq will work with multiple chains correctly, but may have problems with proteins with multiple segments. ZoomSeq always sets at least 1 residue highlighted. If you need to turn the ZoomSeq selection off, just change the ZoomSeq entry in the Graphics VMD menu from 'Bonds' to 'Off'. The setting will be restored with you next ZoomSeq selection. Since ZoomSeq displays secondary structure, there might be a pause at startup for secondary structure calculation. When ZoomSeq starts, it makes a new representation in the Graphics window, and alters that representation for any selections. ZoomSeq will complain if this representation isn't present to alter. If you accidentally delete ZoomSeq's representation, use 'Create New' until ZoomSeq finds a representation to change. Coming soon ---------- Handling multiple loaded molecules. Protein profiling and proteomics information for columns 4, 5, 6, etc. with most information fetched from remote bioinformatics web servers. A version should be sent shortly to the VMD mailing list (vmd-l). See http://www.ks.uiuc.edu/Research/vmd/mailing_list/ to sign up to vmd-l. Also, look for the latest version of ZoomSeq at http://www.ks.uiuc.edu/Research/vmd/script_library/categories/sequence.html ===== -- Barry Isralewitz Beckman 3121 Theoretical Biophysics Group, UIUC Office Phone: (217) 244-1612 Home Phone: (217) 337-6364 email: barryi@ks.uiuc.edu http://www.ks.uiuc.edu/~barryi From chemistry-request@server.ccl.net Thu Dec 28 21:35:15 2000 Received: from f04n07.cac.psu.edu (f04s07.cac.psu.edu [128.118.141.35]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA02010 for ; Thu, 28 Dec 2000 21:35:15 -0500 Received: from aluminum (aluminum.metsce.psu.edu [128.118.156.204]) by f04n07.cac.psu.edu (8.9.3/8.9.3) with SMTP id VAA226222 for ; Thu, 28 Dec 2000 21:35:08 -0500 Message-Id: <1.5.4.32.20001229023508.008bba00@email.psu.edu> X-Sender: txx1@email.psu.edu (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 28 Dec 2000 21:35:08 -0500 To: chemistry@ccl.net From: Tian Xie Subject: lattice crankshaft does anyone know where to find code to do crank-shaft moves on a cubic lattice? I can't find any on the net. thanks,