VMD-L Mailing List

From: CPMAS Chen (cpmasmit_at_gmail.com)
Date: Thu Jun 25 2015 - 17:01:59 CDT

You are right. it needs the specification of which column in the map file
should be read by phenix.refine.

the error message is like this

Multiple equally suitable arrays of observed xray data found.

Possible choices:

  merge_unique.mtz:IMEAN,SIGIMEAN

  merge_unique.mtz:I(+),SIGI(+),I(-),SIGI(-),merged

Please use maps.input.reflection_data.labels

to specify an unambiguous substring of the target label.

Sorry: Multiple equally suitable arrays of observed xray data found.

ccp4plugin) Error opening file mapinput_2mFo-DFc_map.ccp4

ERROR: Unable to read input file. Exiting...

dxplugin) Error opening file.

ERROR: Unable to read input file. Exiting...

Charles

On Thu, Jun 25, 2015 at 5:29 PM, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
wrote:

> This indicates that something is going wrong during the map generation
> process. In your working directory there should be a "map.log" file. There
> should be some sort of error somewhere in that file. Could you send that
> file or copy the error here?
>
>
> On Thu, Jun 25, 2015 at 4:25 PM CPMAS Chen <cpmasmit_at_gmail.com> wrote:
>
>> Now, vmd started to run. but here is another error
>>
>> Command = zcat setp1.dx.Z
>>
>> Filename.Z = setp1.dx.Z
>>
>> Command = gzip -d -c setp1.dx.gz
>>
>> Filename.gz = setp1.dx.gz
>>
>> FATAL ERROR: Problem reading grid force potential file
>>
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>>
>> Reason: FATAL ERROR: Problem reading grid force potential file
>>
>>
>>
>>
>>
>> Any hints?
>>
>> Thanks!
>>
>> Charles
>> On Tue, Jun 16, 2015 at 4:11 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>>> Hi,
>>> Your cluster is missing the OpenGL-related drivers and libraries that
>>> the standard VMD builds need to be able to run. Instead of using the
>>> full-featured version of VMD, you should download and install the
>>> text-mode
>>> version of VMD which is listed on the VMD download page as:
>>> LINUX_64 Text-mode
>>>
>>> It's the 5th item down on the list of platforms. If you install that
>>> version
>>> of VMD, you should be able to run it successfully on your cluster.
>>>
>>> http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Thu, Jun 11, 2015 at 03:34:51PM -0400, CPMAS Chen wrote:
>>> > Hello:
>>> > I am following the tutorial to set up xMDFF work. when I submitted
>>> my job
>>> > to our cluster, it reported error. The message is like this:
>>> >
>>> > TCL: /opt/local/lib/vmd/vmd_LINUXAMD64: error while loading
>>> shared
>>> > libraries: libGLU.so.1: cannot open shared object file: No such
>>> file
>>> > or directory
>>> > FATAL ERROR: /opt/local/lib/vmd/vmd_LINUXAMD64: error while
>>> loading
>>> > shared libraries: libGLU.so.1: cannot open shared object file:
>>> No such
>>> > file or directory
>>> >
>>> > I have the log and namd file attached, could you guys give me some
>>> > suggestions?
>>> > 1. I am bugging the cluster administer to to see if this is
>>> setup/software
>>> > issues. but VMD/NAMD works just fine in all other jobs.
>>> > 2. I changed 'vmd' in the .namd file to '/opt/local/bin/vmd' to
>>> specify
>>> > the location of vmd executable. and it reported the above error
>>> message.
>>> > 3. I tried alias vmd="/opt/local/bin/vmd", so I can use the namd
>>> file
>>> > without anything changed. it will report error like this:
>>> >
>>> > TCL: couldn't execute "vmd": no such file or directory
>>> >
>>> > FATAL ERROR: couldn't execute "vmd": no such file or directory
>>> >
>>> > Â Â while executing
>>> >
>>> > "exec vmd -dispdev text -e xmdff_phenix.tcl -args $PSFFILE $PDBFILE
>>> > $GRIDFILE $REFS $BFS $MASK $CRYSTPDB $MASKRES $MASKC
>>> >
>>> > UTOFF > map.log"
>>> >
>>> > Thanks!
>>> > Charles
>>> > --
>>> >
>>> > ***************************************************
>>> >
>>> > Charles Chen
>>> >
>>> > Research Associate
>>> >
>>> > University of Pittsburgh School of Medicine
>>> >
>>> > Department of Anesthesiology
>>> >
>>> > ******************************************************
>>>
>>>
>>>
>>>
>>> --
>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/
>>>
>>
>>
>>
>> --
>>
>> ***************************************************
>>
>> Charles Chen
>>
>> Research Associate
>>
>> University of Pittsburgh School of Medicine
>>
>> Department of Anesthesiology
>>
>> ******************************************************
>>
>> 

-- 
***************************************************
Charles Chen
Research Associate
University of Pittsburgh School of Medicine
Department of Anesthesiology
******************************************************