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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 FAQ-Install
  Download
  NVIDIA Grapics Card Error
  MolCart 64 Bit
  MolCart Install
  Specifications
  Stereohard faq
  Quad Buffer
  Anaglyph Stereo
  Faq plist
  Admin Error
  Faq gl failure
  Graphics defects
  Ts crash qlock
  Stereo Fix
  Time Machine
  Font Mac
  Set Server
  Empty Hostid
  Side by side error
  Image Error
 FAQ-Graphics and Display
 FAQ ActiveICM
 FAQ-Structure
 FAQ-Dock
 Sequences and Alignments
 FAQ-Modeling
 FAQ-Cheminformatics
 FAQ MolCart
 FAQ-Script
 
Index
PrevICM User's Guide
21.1 FAQ Installation and Troubleshooting
Next

[ Download | NVIDIA Grapics Card Error | MolCart 64 Bit | MolCart Install | Specifications | Stereohard faq | Quad Buffer | Anaglyph Stereo | Faq plist | Admin Error | Faq gl failure | Graphics defects | Ts crash qlock | Stereo Fix | Time Machine | Font Mac | Set Server | Empty Hostid | Side by side error | Image Error ]

Installation FAQ:

21.1.1 How do I download and install ICM-Pro or any of the other ICM Products?


  1. Go to www.molsoft.com/support and register using your company or university e-mail address. The database will not accept e-mail addresses from gmail, yahoo, hotmail, etc...
  2. Once logged into the support center please click on the Downloads link.
  3. Choose your platform Windows, Linux, or Mac.
  4. Choose the product e.g. ICM-Pro (Full Package).
  5. Download the icm distribution and follow the instructions.
  6. A flexlm hostid is required for us to generate the license key to activate the software. Follow the links in the download instructions on how to generate this hostid (Win + Linux - use hostid utility, Mac - hostid is automatically generated when unpacked) and then e-mail it to andy@molsoft.com

21.1.2 NVIDIA error. NVIDIA: Could not open the device file /dev/nvidiactl (Permission denied).


To permanently fix this problem you need to add the following line to /etc/logindevperm file

0 0666 /dev/nvidiactl:/dev/nvidia0:/dev/nvidia1:/dev/nvidia2:/dev/nvidia3

21.1.3 MolCart installation error on 64Bit machines


If you are installing MolCart and you come across this error:


Error> Can't open shared library 'chemlib.so' (errno: 22 chemlib.so: canno
t open shared object file: No such file or dire) (/usr/molcart-1.9-1/regmol
cart:52)
Error> error while running 'ExecSql(string("CREATE FUNCTION molcart_versi.
..))' (/usr/molcart-1.9-1/regmolcart:52)
Error> error while running 'regFunction(string("molcart_version"),string("
STRING"),)' (/usr/molcart-1.9-1/regmolcart:96)

Solution-- For 64 bit platforms molcart-1.9-1-linux64.sh should be used instead of molcart-1.9-1-linux.sh

21.1.4 Where do I save my MolCart license?


Save the MolCart license in:


/var/lib/mysql/license.dat

21.1.5 What are the minimum specifications to run ICM on my computer?


The minimum specifications to run ICM are described here http://www.molsoft.com/min-specs.html

21.1.6 Stereo Hardware Questions


Hardware stereo for Windows (in-window)

Question:

I have NVIDIA Quadro4 750 (or 800/890) installed on my Windows machine but the hardware stereo does not work in ICM. What do I do ?

Answer:

The settings for your graphics card need to be changed. Perform the following steps to check and correct the problem:
1. Go to Start -> Control Panel.

2. Double click the icon labeled 'Display'.
3. Choose the 'Settings' tab.
4. Click the button labeled 'Advanced'.
5. Choose the tab labeled 'Quadro4'.
6. From the menu on the left, choose the OpenGL settings.
7. In the dialog that appears, find and enable the option labeled "Enable quadrobuffered stereo API".

8. Click the OK button to save your changes.

21.1.7 Does ICM support quad-buffer stereo?


Yes - change the stereo mode to in-a-window. To do this File/Preferences/Graphics Tab and change stereo Mode.

21.1.8 Does ICM support Anaglyph Stereo?


Yes - see the documentation here.

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21.1.9 Restoring font size and other GUI parameters on MAC : molsoft.com.plist


Situation: You are stuck with a large font size or other GUI preference and can not restore the defaults.

Solution:

  • quit ICM
  • run this Mac command in Terminal:

open ~/Library/Preferences/com.molsoft.plist

then change Molsoft.WorkspaceFontSize to 12 (or similar)

If it gives you a GUI window with access to the ICM confirugation variables, change the ones you need if the file is shown as text, just delete it: rm ~/Library/Preferences/molsoft.com.plist

  • restart ICM.

21.1.10 Error in saving configuation settings: You are not a license administrator


To solve this error:

  • Right click on the browser icon and select "Rus As Administrator".

21.1.11 ICM graphics crashes.


Some Linux installations need extra setup to permit the use of the GL graphics.

Description of the problem

ICM starts, GUI is launched and works OK, however ICM crashes after the first attempt to display any 3D object in the GL window. System issues an error message stating:

"Error: Could not open /dev/nvidiactl because the permissions are too restrictive. Please see the FREQUENTLY ASKED QUESTIONS section of /usr/share/doc/NVIDIA_GLX-1.0/README for steps to correct."

Solution

(tested only for the Suse Linux): do not follow the instructions contained in the /usr/share/doc/NVIDIA_GLX-1.0/README document. Instead do the following:

  1. find /etc/logindevperm file
  2. edit the file by changing/uncommenting the line containing '/dev/nvidiactl...' to this: 0 0666 /dev/nvidiactl:/dev/nvidia0:/dev/nvidia1:/dev/nvidia2:/dev/nvidia3
  3. logout and login again

21.1.12 Defective graphics on a laptop or Windows computer with a low end graphics card.


This problem can manifest itself in multiple ways, but always with the FOG depth-cueing effect on. Usually graphics behaves strangely, for example:

  • the selection crosses have the color of the background, or
  • the skin representation appears to be damaged, or
  • 3D Labels and site annotations disappear with when FOG is on
The solution is to reduce the level and the OpenGL acceleration from the maximal one to some intermediate.

Some inexpensive graphics cards (e.g. Intel 82915G/GV910GL Express Chipset Family) have a problem with high level of hardware acceleration. 3D labels or site labels disappear when you press a FOG button. We found that the problem is due to the hardware acceleration. By switching to the lower levels of hardware acceleration one can avoid the problem.

Solution: switch the FOG effect off, or change the settings of OpenGL acceleration.

  • Right-click on the screen, get the main pop-up menu
  • Go to Properties (the last item)
  • Go to the Settings tab
  • Click on the Advanced button
  • Choose the Troubleshoot tab
  • Reset Hardware acceleration to the 3rd level or lower

21.1.13 ICM crashes, or hangs if you are trying to start the Chemical Editor, or a Query window


Platform under which this problem had been detected: Linux

ICM may hang of crash when you are trying to start an new window with a Chemical editor, or a Query. One possible reason is that for some reason the molsoft preference file in the ~/.qt directory is locked. In this case there is the .lock file which need to be deleted.

Recovery under Unix/Linux.Delete the file called .molsoftrc.lock in the .qt directory


rm .qt/.molsoftrc.lock

21.1.14 Problem with stereo?


ICM is working fine but for some reason your stereo is not working.

Check if "Stereo Mode" preference is set to "in-a-window" in ICM.

To do this :

  • IMPORTANT make sure there is no graphics session started.
  • Go to File/Preferences menu.
  • select the Graphics tab
  • Set the "Stereo Mode" combo box to "in-a-window"
  • Then press "Apply " button to write preferences and* restart ICM.

21.1.15 How do I remove the messages regarding time machine upon start up in Mac?


Upon ICM startup on a Mac you might see this message:

This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.

This message is related to QT and does not affect the performance of ICM in any way so the message can be ignored.

21.1.16 How to restore font sizes and other GUI defaults on a Mac?


See http://www.molsoft.com/man/example-scripts.html#faq-mac-gui-preferences

21.1.17 Set ICM to remember the server name on startup in Windows


In Windows sometimes the license server name is not remembered and you have to enter the server name each time you open ICM. To fix this:

  • Right click on the ICM-Pro icon and choose "Run as Administrator".
  • Enter the server name.

21.1.18 lmhostid returns and empty hostid


Question: I run lmhostid and it returns empty string or just zeros.

e.g.



The FLEXlm host ID of this machine is ""

or


The FLEXlm host ID of this machine is "000000000000"

Answer:This happens if system has non-standard name for the network card which does not start with 'eth'. Flexlm wants at least one network adapter to be named eth0 or eth1 etc..

Fixing the problem:

To check the list of all available network card type:


 /sbin/ifconfig -a

If nothing starts with 'eth' then you need to edit file below:


sudo vi /etc/udev/rules.d/70-persistent-net.rules

Then you need to change NAME= field in at least one line. (comment the original line). For example to change wlan0 -> eth0 modify the file like below:



# SUBSYSTEM=="net", ACTION=="add", DRIVERS=="?*", ATTR{address}=="20:16:d8:13:10:2e", ATTR{dev_id}=="0x0", ATTR{type}=="1", KERNEL=="wlan*", NAME="wlan0"
SUBSYSTEM=="net", ACTION=="add", DRIVERS=="?*", ATTR{address}=="20:16:d8:13:10:2e", ATTR{dev_id}=="0x0", ATTR{type}=="1", KERNEL=="wlan*", NAME="eth0"

Reboot the system and check 'lmhostid' again. It should be non-empty.

21.1.19 Side-by-Side Configuration Error.


This error can be fixed by:

21.1.20 Write image outputs multiple copies of original image.


With some graphics drivers the high resolution image may be distorted or multiple representations of the image in one frame.

The are two ways to write the high res image (internally the different openGL API is used)

  • File/ Write Image - High resolution PNG (uses 'write png' command)
  • File/ Write Image - High resolution (uses 'write image' command)

If one way causes the problem then we recommend to try the other way. If both does not work, the only way is to try to decrease resolution.


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