Hi Thomas, something strange happen when I try to load 4v99.mmtf using this
procedure (other PDB files works proprely as far as I know):
download the file from https://mmtf.rcsb.org/v1.0/full/4V99
then in script:
with open(file_path,"rb") as binary:
b = binary.read()
cmd.load(b, "str", 0, cmd.loadable.mmtfstr)
if i try to load the script with pymol, It gives this result:
...
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 6).
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 7).
Warning: map key not of type str (type 2).
Error in MMTF_parser_fetch_typed_array: length mismatch 588367 588120
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 2).
MMTF structureId: '4V99', mmtfVersion: '1.0.0'
Segmentation fault (core dumped)
The strange thing is that if I try to normally load this file in bash doing
pymol 4v99.mmtf the file is correctly loaded. Is there something I am
missing?
2017-06-22 17:52 GMT+02:00 Gianluca Tomasello <giagi...@gmail.com>:
> Thank you very much!
>
> 2017-06-22 13:11 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
>
>> Hi Gianluca,
>>
>> Yes this is possible, assuming you're using PyMOL 1.8.6. Use something
>> like this:
>>
>> def read_mmtfstr(contents, oname, state=0):
>> return cmd.load(contents, oname, state, cmd.loadable.mmtfstr)
>>
>> Cheers,
>> Thomas
>>
>> > On Jun 21, 2017, at 12:07 PM, Gianluca Tomasello <giagi...@gmail.com>
>> wrote:
>> >
>> > Hi, I am using read_pdbstr function to load a strucutres into pymol. Is
>> there a way to do the same for mmtf file formats? (I mean without using
>> temporary files)
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
>>
>
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