From: CPMAS Chen (cpmasmit_at_gmail.com)
Date: Thu Jun 25 2015 - 17:29:48 CDT

It works now. Thanks, Ryan.

Charles

On Thu, Jun 25, 2015 at 6:14 PM, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
wrote:

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

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