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Installing PHYLIP 3.6 I nstalling PHYLIP 3.6 Let's assume that you have fetched the appropriate executables archives (if any) for your machine, together with the Documentation and Sources archive. These archives are not simply a single executable for general use. Instead they are a (large) number of files, squished together into one file, and thus called an 'archive'. You have to go through a step which involves getting all the files out of the archive and into a folder on your machine. We will give these instructions for four different kinds of systems, Windows, Mac OS X, Linux or Unix systems, and Mac OS 8 or 9.
Rasmol, free rasmol software downloads. Pizza.py is a collection of Python tools that perform pre- and post-processing for the LAMMPS molecular dynamics package (or other simulators).
Then we will describe how to access the documentation after installing the package. W indows When you click to download the Zip archive, most recent Windows systems will open a window which asks whether you want to open the archive with Windows Explorer, or want to Save the archive. Choose to Save it. It will be placed in the Downloads folder of your account. There are now two possibilities:. If it has been extracted, a folder called phylip-3.695 (one which does not have the image of a zipper on the folder icon) will also be there. Move that folder to where you want it to be.
Do not try to use the programs or documentation while it is still in the Downloads folder. If it has not been extracted, there will be a Zip archive folder (one which has a zipper on the folder icon). Move it to where you want it to be. This Zip archive can then be extracted by right-clicking on its icon and selecting Extract All from the menu that appears. It will create a folder called Phylip-3.695.
So if you place the archive on the Desktop, it will make that folder there. After the extraction is done, you will find the phylip-3.695 folder which has three folders within it, called doc, exe, and src.
There is also a web page phylip.html. You should read this in your browser. It contains links to the main documentation web page main.html and to the other documentation pages and programs.
Note: There has been a report that on Windows Vista (specifically the report was for Service Pack 2 on Home Edition) that if you extract the files into a folder that is somewhere under Program Files, they may not work properly. You can avoid this problem if you extract them into a folder which is somewhere in your own folders. What to do if the Avast virus-checking software complains: We have had several reports that the Avast virus-checking software will not allow PHYLIP 3.695 to be installed because it concludes that it contains a virus. It is complaining about our Java front end for program Drawgram (a file called DrawGramJava.exe).
We have had this file checked carefully by our virus-checking company, Sophos, and they find no virus there. There is the invocation of a 'shell' in that Java code that may alarm Avast, which is being overcautious. If you can extract and install the code on someone else's machine, one which has differemt virus-checking software, you then may be able to copy the folder over to your machine.
Issue with Drawgram or Drawtree not finding.dll libraries. There has been a report that using Drawgram or Drawtree's Java front-end failed because a Dynamic Link Library (.dll file) is not found. This seems to be cured by installing the latest version of Java. (Thanks to Isha Androiya).
M acintosh Mac OS X The archives for Intel iMac and PowerMac Mac OS X are in the Apple.dmg disk image format. There is one.dmg disk image distributed. It is 12 Megabytes in size, and is compressed; when uncompressed it is several times larger. It contains what looks like a normal folder called phylip-3.695, but you should not use the programs while they are in that folder.
It is important that you use a copy of the contents of the disk image elsewhere on your system. Decide where the folder phylip-3.695 is going to reside, and copy that folder to that new location. Within it is all the source code, documentation, and executables. The executables are 32-bit 'universal binaries' that will run on either the Intel iMacs or the older G3's, G4's or G5's that have PowerMac processors. (Basically the universal binaries are each simply a pair of executables set up so that the processor chooses the right one and runs it).
Enabling the programs to be run in a Terminal windows by typing their names: A set of links can be set up in the exe folder to enable you to run the programs by simply typing their name. If these are absent, which they should not be, there is one additional set of steps you need to do:. Open a Terminal window (which you will find in the Utilities folder of the Applications folder). At the prompt, change to the folder where the PHYLIP executables are kept. For example, if you have folder phylip-3.695 on your desktop, type in the command cd Desktop/phylip-3.695/exe. Copy the file linkmac from the src folder to this exe folder.
Change the permissions of the script linkmac to allow it to execute: chmod +x linkmac. Then execute the script by typing:./linkmac The result will be that the executables folder will now have a set of links, one for each program, that allow the programs to be executed simply by typing their names. Thus the programs in that folder can then be executed either by clicking on their icon, or by typing their name (in lower case) preceded by./ to indicate the current folder, such as./dnaml This setting up of these links needs to done only once, and they will be available thereafter.
Fixing the Mountain Lion permission problem: The latest Mac OS X operating system version, Mountain Lion, will not run executables of PHYLIP programs when you click in their icons. It complains that the developer name is unknown. This is a security feature. There is an easy workaround for this that needs to be done once for each program.
If this occurs, try control-clicking on the program icon instead. When you are then asked whether you want to open this program, select Open. The program will open. It also allows the program to be opened in the future by clicking on the executable icon. So it only needs to be done once for each of the programs in PHYLIP, and after that the program can be run by clicking on the icon for that program. We hope to avoid this in future versions by signing the programs with my Apple Developer identity. As far as I know, this problem does not arise if you open a program in a Terminal window by typing its name.
L inux and U nix You can easily install PHYLIP and compile it yourself on a Linux or Unix system, provided that you have a C compiler on your system. (On some Linux systems and in some recent versions of Mac OS X the C compiler is not installed by default, and you may have to make sure that it is installed). The archive for Linux or Unix systems is just the Documentation and Sources archive. You can extract the files from the archive by putting it into a folder by itself, getting into that folder, and giving the command tar -zxvf phylip-3.696.tar.gz This uncompresses the archive so that it will now be bigger and then extracts the archive. A phylip3.696 folder is created that contains within it three folders, doc, exe, and src, as well as a web page phylip.html.
You should start with that web page. It contains links to the documentation web pages, including the main documentation web page main.html. To make executables, use your C compiler. It is probably as simple as going into the src directory, copying Makefile.unx and calling the copy Makefile, and then typing the command make install which will cause the programs to be compiled and the executables and font files installed in the exe directory.
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Alternatively, you can type the command make -f Makefile.unx install instead. If there are problems with the compilation, read the relevant sections of main.html and also the beginning of the Makefile. With luck this will work.
After the compilation the executables and their font files will be in folder exe. M acintosh Mac OS 8 or Mac OS 9 We don't think there are many Mac OS 8 or Mac OS 9 machines around any more - Apple long ago abandoned that operating system, and it is probably not safe to use it on the Internet as it has not been upgraded to cope with recent security threats.
We no longer distribute Mac OS 8 or 9 executables for our most recent versions of PHYLIP. Nevertheless, we do make available a Stuffit (.sit) archive of executables for PHYLIP 3.65, just in case anyone needs it. Downloading the single Stuffit archive The archives for Mac OS 8, Mac OS 9 Macintoshes are self-extracting archives. If you are fetching the files using a Web browser directly from your Mac, it will probably automatically invoke Stuffit Expander to unpack the archives into self-extracting archives. Self-extracting archives are archives with a small self-extraction program on their front, so that when they are run as programs they write a great many files into a folder.
Our default distribution is of a single large (4.9 Megabyte) Stuffit archive called phylip3.65.sit. This should automatically be unstuffed as it is downloaded.
It contains the source code, documentation, and Mac OS executables. However, at the moment we have reports of trouble running the unstuffed archives. Recent versions of Mac OS 9, and also the Classic environment under Mac OS X, seem to regard the executables files as text files, and they try to open them under SimpleText, which of course does not work. Downloading multiple smaller Stuffit archives Some people may wish instead to download these as a series of four archives. This might be necessary, for example, if you wanted to transfer them to a machine that was not connected to the Internet, and needed them each to be small enough to write onto a floppy disk.
If you choose to download these instead of the single Stuffit archive, and our system does automatically invoke Stuffit Expander, four self extracting archives will be created on your desktop, and their file names will end in.sit. If you have Stuffit Expander, you can use it to expand them.
Once the archives are downloaded and extracted, they will put folders on the desktop. One is called phylip and contains folders doc and src as well as a web page phylip.html. There are 307 files in all, as these include the documentation files, source code files, and compilation support files.
You may have to be patient while the archive is being extracted. The three archives of Macintosh Mac OS 8 and Mac OS 9 executables will create folders exe, exe.1, exe.2 and exe.3 on the desktop when they are extracted. For some reason we could not create these inside the phylip folder, but that is where these files need to be put. Do the following:.
Move the exe folder inside the phylip folder. Open the exe.1 folder, and mark all of its files (you can do this using the Select All menu option in the system Edit menu). Drag this group of marked files into the exe folder which is now inside the phylip folder. Now do the same for exe.2 (mark the files and drag them into exe). And do the same for exe.3 (mark the files and drag them into exe).
You can now discard the folders exe.1, exe.2 and exe.3 (if any). If you have four folders named phylip3.65.0.sit, exe.1.sit, exe.2.sit, and exe.3.sit on your desktop, these can be discarded too. The phylip3.65 folder can now be moved to wherever you want it to be. R eading the documentation The main folder contains a web page, phylip.html. You should start by reading it (either by clicking on it to activate your browser, or calling it to the attention of your browser in some other way such as drag-and-drop). It contains links to the documentation web pages, including the main documention page main.html, which you should read. E xecutables available from others Executables packages are also available from others.
For the moment, these are for earlier versions of PHYLIP (such as 3.61 and 3.68). They include executables for Red Hat Linux, Debian Linux, NetBSD Unix for Intel-compatible processors, and FreeBSD Unix. For links see.
RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users of RasMol and developers of open source versions of RasMol. The site itself is provided courtesy of Bernstein + Sons. Maintenance of RasMol, much of the development, and integration of modifications provided by the community is done at the ARCiB laboratory at Dowling College. Introduction: Welcome to the RasMol and Open RasMol web site. This site was established in mid-September 2000 to provide a home for developers of Open Source versions of RasMol.
In May 2002, it also became a home page for users of RasMol. RasMol is an important scientific tool for visualisation of molecules created by Roger Sayle in 1992. RasMol is used by hundreds of thousands of users world-wide to view macromolecules and to prepare publication-quality images. Science is best served when the tools we use are fully understood by those who wield those tools and by those who make used of results obtained with those tools. When a scientific tool exists as software, access to source code is an important element in achieving full understanding of that tool.
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As our field evolves and new versions of software are required, access to source allows us to adapt our tools quickly and effectively. RasMol Features: RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh, UNIX and VMS systems.
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The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server. The program reads in molecular coordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files. If connectivity information is not contained in the file this is calculated automatically.
The loaded molecule can be shown as wireframe bonds, cylinder 'Dreiding' stick bonds, alpha-carbon trace, space-filling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface representations. Atoms may also be labelled with arbitrary text strings. Alternate conformers and multiple NMR models may be specially coloured and identified in atom labels. Different parts of the molecule may be represented and coloured independently of the rest of the molecule or displayed in several representations simultaneously. The displayed molecule may be rotated, translated, zoomed and z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dial box.
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