From laaksone@finsun.csc.fi Thu Dec 23 03:19:54 1993 Received: from finsun.csc.fi for laaksone@finsun.csc.fi by www.ccl.net (8.6.4/930601.1506) id CAA26076; Thu, 23 Dec 1993 02:53:37 -0500 Received: by finsun.csc.fi id AA23706 (5.65c8+/IDA-1.4.4 for chemistry@ccl.net); Thu, 23 Dec 1993 09:53:35 +0200 Date: Thu, 23 Dec 1993 09:52:12 +0200 (EET) From: Leif Laaksonen Subject: Version 1.6 of SCARECROW To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 1993-12-23 Scarecrow Computing Proudly Presents version 1.6 of the fabulous graphics program SCARECROW. SCARECROW is a program for the display and analysis of molecular dynamics trajectories from the programs AMBER, CHARMm, Discover, GROMOS, HyperChem, MUMOD, YASP. SCARECROW is NOT a public domain program but you can use SCARECROW free of charge if you follow the lisence agreement. See the agreement form. SCARECROW runs only on SGI hardware (so far). Some of the new features: Version 1.6 This is not a major rewrite of Version 1.5 but rather a bug fix with some new additions and some new commands have been added. Some old commands have gone through some changes as well. (1) The command set window multi and set window single have been added. The single window mode is equivalent to the old display style where the structure, linear distance plot (LDP), cluster plot and the Ramachandran plots where displayed in the same window. Now it is also possible to display the different plots in separate windows. To do this the set window multi has to be defined. (2) The read command has now been changed to reflect what is read. The command is now read coordinates type. The command to read a PDB file is now read coordinates pdb file.name. It is possible to read HyperChem coordinate and trajectory files. (3) SCARECROW supports now the possibility to display or analyse only a part of the frames in the trajectory file. With the commands set trajectory limits first last step or modify trajectory limits first last step it is possible to define the trajectory frames to be included. The display or analysis will now start from frame 'first' and end at frame 'last' including every 'step' frame. The default is always every frame from first to last. (4) The quatfit program (Copyright: Ohio Supercomputer Center, David J. Heisterberg, 1990) to superimpose two structures is now included in the SCARECROW package. Use the command calculate quatfit seg1:res1:atm1 seg2:res2:atm2 to superimpose two structures. The second structure will now be imposed on the first structure using the atoms defined in the list. The number of atoms in the both lists has to be the same but different atoms can be used. (5) A primitive graphical tool has been added to do a cluster analysis of the frames in a trajectory file. The command calculate cluster seg:res:atm calculates the root mean square deviation (RMSD) matrix for the defined frames. This is done by reading frame i and j and using the quatfit algorithm to superimpose the structures according to the atoms defined in the seg:res:atm list. The calculated RMSD matrix can be saved to disk by the command write cluster data file.name or read from disk by the command read cluster data file.name. The display of the RMSD natrix is done by the command plot cluster. (6) To define a new display range for a LDP or cluster plot use the commands modify ldp range f1 f2 f3 f4 f5 f6 f7 f8 f9 or modify cluster range f1 f2 f3 f4 f5 f6 f7 f8 f9. The new range will be x > f1, f2 < x < f3, f4 < x < f5, f6 < x < f7, f8 < x f9. (7) It is possible to display in real stereo using the StereoView glasses. Use the command set stereo on to get into the stereo mode. To get off the stereo mode press the escape key. (8) To be able to rotate or translate a molecule or a part of a molecule in respect to the rest of the system one can define a subset of the system and then apply the rotation or the translation to that set. Use the command define atom selection seg:res:atm to define the atoms and then press the keypad key 5 while you rotate or translate the molecule with the mouse. Then only the selected part gets affected. (9) There is now a method to calculate a diffusion coefficient. It's possible to calculate the mean square displacement from the center of mass for the selected atom coordinates with the command calculate msdisplacement seg:res:atm and the "atom" mean sqare root displacement for selected atom coordinates with the command amsdisplacement seg:res:atm. The commands report also a diffusion coefficient. Most likely there is a lot more but I have lost track of the time when a particular new feature was included. Discover yourself! You can download SCARECROW from from the anonymous ftp server "nic.funet.fi". Do the following: (1) ftp nic.funet.fi (2) Use the user id "anonymous" and for the password use your user id and address (like myuserid@from.my.place). (3) Change directory to /pub/sci/chem/scarecrow and you can see the following directory. *** This is SCARECROW version 1.6 distribution. *** The files are: -rw------- 1 laaksone csc 913 Dec 17 13:00 README.FIRST This file (almost). -rw-r--r-- 1 laaksone csc 49939 Dec 17 10:54 agreement.ps PostScript version of the license agreement form. If you haven't returned me one, please do it now. -rw-r--r-- 1 laaksone csc 4972 Dec 17 10:21 agreement1.6.hqx Agreement form (Microsoft Word for Macintosh file) as a HQX file. -rw-r--r-- 1 laaksone csc 3584 Dec 17 10:33 agreementmw.doc Agreement form (Microsoft Word for Windows) as a binary file. -rw-r--r-- 1 laaksone csc 1138373 Dec 17 10:20 scarecrow1.6.hqx SCARECROW manual (Microsoft Word for Macintosh file) as a HQX file. -rw-r--r-- 1 laaksone csc 6275011 Dec 23 08:39 scarecrow1.6.tar.Z SCARECROW code and libraries. -rw-r--r-- 1 laaksone csc 1077760 Dec 17 10:22 scarecrowmw1.6.doc Scarecrow manual (Microsoft Word for Windows) as a binary file. (4) Download the files (you need) using binary mode. Please return the user agreement form if you start using SCARECROW so I know who are using the program. I will only keep SCARECROW at nic.funet.fi for a limited timed. Cheers, -Leif Laaksonen ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Telefax: 358 0 4572302 FIN-02101 Espoo | Voice Mail: 358 486257407 FINLAND | Mail: Leif.Laaksonen@csc.fi New opinions are always suspected, and usually opposed, without any other reason but because they are not already common. John Locke ------------------------------------------------------------------- From fuchs@chemdc1.tau.ac.il Thu Dec 23 05:19:49 1993 Received: from chemdc1.tau.ac.il for fuchs@chemdc1.tau.ac.il by www.ccl.net (8.6.4/930601.1506) id EAA26434; Thu, 23 Dec 1993 04:47:33 -0500 Received: by chemdc1.tau.ac.il (5.65/DEC-Ultrix/4.3) id AA23332; Thu, 23 Dec 1993 12:43:56 -0200 Date: Thu, 23 Dec 1993 12:43:56 -0200 From: fuchs@chemdc1.tau.ac.il (Benzion Fuchs) Message-Id: <9312231443.AA23332@chemdc1.tau.ac.il> To: chemistry@ccl.net, jkl@ccl.net Subject: Re: Greetings to all Dear JKL, Best Greetings of the Season and a Happy New Year to you too along with appreciative thanks for your valuable service to this community. Benzion Fuchs From raji@yu1.yu.edu Thu Dec 23 14:19:56 1993 Received: from alsys1.aecom.yu.edu for raji@yu1.yu.edu by www.ccl.net (8.6.4/930601.1506) id OAA29483; Thu, 23 Dec 1993 14:01:39 -0500 Received: from yu1.yu.edu by alsys1.aecom.yu.edu with SMTP id AA25113 (5.67a/IDA-1.4.4/AECOM-RIT for ); Thu, 23 Dec 1993 14:01:37 -0500 Received: by yu1.yu.edu (AIX 3.2/UCB 5.64/4.03) id AA43944; Thu, 23 Dec 1993 14:00:56 -0500 Date: Thu, 23 Dec 1993 14:00:56 -0500 From: raji@yu1.yu.edu (Raji Viswanathon) Message-Id: <9312231900.AA43944@yu1.yu.edu> To: budong@chem.columbia.edu, chemistry@ccl.net Subject: Re: GAMESS plotting: DENDIF for two sets and specific orbitals Hi Budong, I see that you are still unable to plot the density difference maps. I have not looked into this. I hope you receive valuable suggestions from the netters. How is the rest of your calculations coming? Bye, Raji