From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Thu Jun 25 2015 - 17:14:58 CDT

In that case, you can edit the maps.params file in that directory to
indicate which set of labels you want to use. Under the heading
"reflection_data {" there should be a "labels = None" field. Change that
"None" to either IMEAN,SIGIMEAN or I(+),SIGI(+),I(-),SIGI(-),merged

On Thu, Jun 25, 2015 at 5:02 PM CPMAS Chen <cpmasmit_at_gmail.com> wrote:

> 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
>
> ******************************************************
>
>