XtalView Frequently Asked Questions (FAQ)


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Sections


Section 1: Downloading Xtalview

  1. Q. Following the email instructions, I tried to download XtalView from the anonymous ftp site, but I don't see anything in the /pub/ccms/xtalview directory.

    A. The instructions give the correct location. You cannot see the level below /pub/ccms/xtalview but if you enter the full and correct directory name, you will see the files.

    Rather than implement a full-blown password system we simply set the protection on the xtalview directory to x--, which means that you can download files in that directory, but you can't read it to see what else is there. It was much easier than locking down the whole SDSC ftp server, and NSF requires that we keep track of the people downloading the files.

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Section 2: Installing Xtalview

  1. Q. When I try to define or update my crystal system the program responds "Cannot open crystal file".

    A. Check the setting of your $CRYSTALDATA environment variable. This variable should be set to a directory to which you have write permissions, commonly xtal_info in your home directory. The directory should contain at a minimum a file named "crystals" and, for each crystal named in that file, a file of data for that crystal. The easiest way to get started is to go the the $XTALVIEWHOME/examples directory and copy the files "crystals", "cvccp", "sirhp", and "f432" into your xtal_info directory (or equivalent). If $CRYSTALDATA is not being set up the way you think it should be, you may be crossed up between bash and csh -- Linux normally uses bash, but there is a csh hiding in /usr/bin.

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  2. Q. After XtalView successful installation I received the following error while trying to run xfit or xtalmgr:
    XView warning: Cannot load font
    '-b&h-lucida-medium-r-*-*-*-120-*-*-*-*-*-*' (Font package)
    XView warning: Cannot load font
    '-b&h-lucida-medium-r-normal-sans-*-120-*-*-*-*-*-*' (Font package)
    XView error: Cannot open connection to window server: :0 (Server package)

    A. It looks like your computer doesn't have some fonts installed. The directory for the fonts is /usr/lib/X11/fonts. My suggestion is that you don't have 75dpi and/or 100 dpi fonts. If you will need help on managing fonts you can check the following link - http://www.uwsg.iu.edu/edcert/session3/x11/font.html

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  3. Q. When I run xtalmgr command I get the following message:
    error while loading shared libraries:
    libxview.so.3: cannot open shared object file:
    No such file or directory

    A. Did you use our install.sh script to do the installation? If so the XtalView.env and XtalView.env.sh files should set the environment variable LD_LIBRARY_PATH to include the $XTALVIEWHOME/lib/ibmpcLinux2 directory. If you haven't sourced one of the setup files above, please read the installation instructions again -- this step is important.

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Section 3: Running Xtalview

  1. Q. How do I set the contour levels of electron density maps in Xfit to lower levels (ie. 0.5, 0.66, 0.75 sigma)?

    A. The Contour window includes the electron density value for each contour level. The map is normalized so that 1 sigma is 50.

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  2. Q. Recently I started to use XtalView program. But I don't know how to convert CCP4 maps to XtalView format. Can you help me with it ?

    A. Try Chris Putnam's program "ccp2fsfour". You can find it at: http://www.scripps.edu/~cdputnam/software/ccp2fsfour.html.

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  3. Q. In XtalView's manual it is mentioned that Xfit can read mtz file with phases directly. But I never found this option.

    A. Xfit can write a CCP4 .mtz phase file using the Files/Map/Save Phases in CCP4 mtz command. This command shells out to CCP4 so it requires CCP4 to be in your command path. That is run whatever CCP4 setup command you use before you start xfit.

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  4. Q. For the "Xfit", we can see the model and electron density maps on the canvas, but, we can't drag it around to take a look at the entire molecule. We tried to drag the map while pushing the middle button of our mouse, but it didn't help.

    A. There are two things you should check on. First, focus -- that is, does the program know that the canvas should receive the mouse information? You can tell if the canvas has input focus by seeing if the title bar is highlighted. If not, left-click in the canvas to give it focus. Once the canvas has focus, if you click and hold the left mouse button the mouse pointer should change to curved arrows, indicating rotation mode. If you click and hold the middle mouse button you should see the pointer change to a large cross with arrows at each tip to indicate translation. You can also hold down both left and middle mouse buttons to get a tapering vertical arrow. If you move the mouse pointer up or down while in this mode you change the magnification, which is perhaps a better way of getting a quick overview of a molecule. You can also contour quite large volumes in Xfit, which I find very useful during early exploration.

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  5. Q. I have been using molecular replacement in cns to solve my structure. I am now using the model_map.inp to create an 2Fo-Fc map, however the only 2 output file type from this program are cns .map files or ezd files. I have been trying (cns, ccp4, mapman) to find a way to convert either of these file types to a phase files for xtal and cannot find a way to converting them.

    A. Instead of actually calculating the 2Fo-Fc map in CNS you can write out the structure factors. XtalView can read XPLOR format structure factors. A .phs file actually contains Fourier coefficients; XtalView calculates the map on the fly. In CCP4 you can use the GUI (ccp4i; latest version is 4.2, very nice) and go to the "Reflection Data Utilities" menu. Use Calculate Fs & Phases, which will calculate F's from a map if you ask it to do so. This produces an MTZ file, and you can use the Convert from MTZ task to write structure factors. Again, you can use the XPLOR format or the USER format. The USER format for XtalView .phs files is, for example, (3i4,f8.2,f8.2,f8.1) to write h, k, l, Fo, Fc, Phi. You can alternatively write a figure of merit instead of Fc. XtalView also reads some forms of mmCIF files, but not necessarily all.

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Section 4: Platform specific problems

  1. Q. We recently got XtalView V4.0 for our DEC alpha running under Tru64 UNIX OSF V5.1. The problem is that while xtalmgr seems to run fine, no other program will execute. Do we need to recompile the program to get it to run on our system?

    A. Unfortunately XtalView does not run under Tru64 UNIX. The XView toolkit, on which the GUI is based, has serious problems with the combination of 64 bit pointers, variable argument lists, and X11R6. It appears that hand editing of more than 100 routines will be required to fix this.

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  2. Q. I am using a SGI indigo with IRIX 6.5. When I type xfit the initial windows open for a second before the core is dumped with the follwoing error:
    System warning: No such file or directory, extras menu file
    /usr/lib/.text_extras_menu (Textsw package)
    System warning: No such file or directory, extras menu file
    /usr/lib/.text_extras_menu (Textsw package)
    Using scattering factors from
    /diskb1/mark/XtalView/data/ScatteringFactors
    User .xfitrc not found.
    Using pixmap for double-buffering.
    Screen depth = 8 for :0.0
    Color turned ON
    Loaded 122 residues into Dictionary
    Hardware stereo detected
    Linesmoothing hardware detected
    XFIT_UPDATESCRIPT set to /diskb1/mark/xfit_95997_update.script
    XView warning: Notifier error: Bad file number
    XView warning: Notifier error: Bad file number
    XView warning: Notifier error: Bad file number

    A. This error occurs in Irix 6.5 when the limit on file descriptors is greater than 246. Several crystallographic packages (like SHARP) suggest "limits unlimited". This also increases the number of file descriptors to the point where the Xview toolkit (which is archaic) breaks. Try

    limit descriptors 200
    before running XtalView and see if it works.

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  3. Q. I'm trying to get XtalView running on LINUX or IRIX systems remotely from a PC running Windows2000 and a terminal emulation program (Exceed). When I start XtalMgr the Expert Tools window pops up ok, but then the Canvas seems to hang and the Xfit control panel doesn't pop up UNTIL I kill the canvas window. Trying to launch the canvas from the Xfit panel doesn't work.

    A. It appears that if you bring up the Exceed menu (right click on Exceed in the icon tray) and click on Tools->Configuration you will get a popup that includes Protocol. Open the Protocol window and enable X Conformance Test Compatibility. This appears to get a working canvas. In the Configuration popup there is also an icon for Fonts. You may need to add the XtalView fonts to that unless you already have a set of 75dpi fonts.

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  4. Q. I installed XtalView 4.0 in Linux 7.2, but when I try to run xtalmgr or xfit the system shows:
    [root@lab207linux ibmpcLinux2]# xtalmgr
    bash: xtalmgr: command not found
    [root@lab207linux ibmpcLinux2]# ./xtalmgr
    ./xtalmgr: error while loading shared libraries:
    libxview.so.3: cannot open shared object file: No such file or directory
    The examples which open automatically after installation worked OK.

    A. It appears that you are running bash instead of csh. In that case you need to follow the setup directions for sh -- bash is a descendant of the sh - ksh line of development instead of the csh line of development.

    Instead of

    source /usr/local/XtalView/XtalView.env
    you should use
    . /usr/local/XtalView/XtalView.env.sh
    If you are running XtalView from the root account, note that the root shell on linux defaults to bash. The shell you use in your personal account may not be the same, so you will need to set things accordingly.

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Section 5: Miscellaneous

  1. Q. How can I produce VRML output from XtalView?

    A. XtalView does not have this capability. If you only want VRML output of the molecule itself, I recommend molscript.

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  2. Q. Can you please give me a quote on the approximate cost for non-academic user license for XtalView?

    A. For that information please contact xtalview@syrrx.com -- we only do the academic distribution.

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  3. Q. I never found description of a format of the phs file. I presume it should be something like
    Hkl Po Fc Phase
    Am I correct?

    A. These comments apply to XtalView 4.1. A phase file contains either
    h k l Fo Fc phi,
    or
    h k l Fo f.o.m. phi,
    where phi is in degrees and f.o.m is the figure of merit. The Hendrickson-Lattman coefficients A,B,C,D are sometimes saved at the end of each record, in which case the file contains:
    h k l Fo f.o.m. phi A B C D

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  4. Q. CCP4 (Refemac5) generates 2fo-fc structure factors as FWT and corresponding phases PHWT and fo-fc structure factors as DELFWT with phases PHDELWT.Is it possible to enter these values in a phs file directly ?

    A. You probably don't want to construct a single .phs file to contain both 2fo-fc and fo-fc; XtalView isn't organized that way. Instead leave those in .mtz files and use the CCP4 interfaces. The CCP4i interface knows about xfit; in addition, note the following:
    CCP4 script to convert .mtz files to .phs files This is an example script to convert a CCP4 format .mtz file to a .phs file which can then be loaded as a map. This is much easier than converting CCP4 map files as the FFT for the map calculation is built into xfit. Note your labels may not be the same as these - check yours first. This is for a map using figure-of-merits. Change the FOM label to FC to make 2Fo-Fc or Fo-Fc maps. Xfit uses two map files interchangeably h,k,l,Fo,Fc,phi and h,k,l,Fo,fom,phi. If you are confused by the labels use the CCP4i interface.

    mtz2various hklin sm_phased_dm.mtz hklout sm_phased_dm.phs << eof
    labin FP=F FOM=FOMDM PHIB=PHIDM
    OUTPUT USER '(3I4,x,F7.2,3x,F7.2,3x,F7.2)'
    END
    eof

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  5. Q. How, using XtalView built-in functions, does one calculate a 2Fo-Fc map ("on the fly") by providing only some form of H K L [{I}{F}] [{SIGI}{SIGF}] (*sca or *mtz or other file) and the correctly positioned/oriented search model coordinates and crystal parameters?

    A. This answer applies to XtalView 4.1 -- (actually xfit will report 4.1; other programs may report 4.0 ...).
    Look in the XtalView/examples/ccp4 directory for scripts that will convert .mtz files into .phs or .fin files. Start xtalmgr and use the crystal editor to enter the space group and unit cell. Start xfit and give it the model (as a .pdb file) and the structure factors. Let xfit compute an Fo map, which you ignore. However, you have to have a list of structure factors for the next step.
    On the xfit control panel you will see a button marked SFCalc... -- click on it. You will get a popup window that is preloaded with the name of your model file and your structure factors. Uncheck the "Auto FFT after calculation" button, and click "Calculate All and Scale". The text panel at the bottom of the xfit control panel will report the progress of the calculation. When it completes, click on the FFT... button on the control panel. Click on the pull-down button next to "Coefficients" and pick you choice of map -- 2Fo-Fc is one of the choices. You can also check "Bulk Solvent Correction" and "Anisotropic Scaling" if you think they are appropriate. Click "Apply" and in a few seconds you will have your map.

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This file is maintained by ccms-help@sdsc.edu.

San Diego Supercomputer Center (SDSC)
University of California, San Diego (UCSD)
9500 Gilman Drive, Mail Code 0505
La Jolla, California 92093-0505
Last Modified: Tuesday, 18-Feb-2003