VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Thu Oct 23 2014 - 13:01:11 CDT

You will have to convert the cif to mtz which can be done with other phenix
tools such as phenix.reflection_file_converter or phenix.cif_as_mtz

On Thu, Oct 23, 2014 at 12:52 PM, Jonathan Gough <jonathan.d.gough_at_gmail.com
> wrote:

> is the cif file in the MTZ format?
>
> On Thu, Oct 23, 2014 at 1:45 PM, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
> wrote:
>
>> You could try using phenix to create a .ccp4 map which can be read by
>> VMD. You can use the phenix.mtz2map function (
>> https://www.phenix-online.org/documentation/reference/mtz2map.html) to
>> do this.
>>
>> On Thu, Oct 23, 2014 at 11:58 AM, Jonathan Gough <
>> jonathan.d.gough_at_gmail.com> wrote:
>>
>>> Hi All,
>>>
>>> It seems that VMD can read several different types of volumetric
>>> data/density/potential map (
>>> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/).
>>>
>>> the PDB has mmCIF and structure factor sf files. They also have a
>>> conversion tool (http://sf-tool.rcsb.org/) that will convert the files
>>> to XPLOR or CNS. However, VMD can't seem to read these files, even though
>>> they are supported.
>>>
>>> Does anyone know how to convert the cif (from the PDB) to a vmd readable
>>> file?
>>>
>>> Thanks,
>>> Jonathan
>>>
>>
>>
>