Re: [PyMOL] Load mmtf data

[Gianluca T. <gia...@gm...>]

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 <gia...@gm...>:

> Thank you very much!
>
> 2017-06-22 13:11 GMT+02:00 Thomas Holder <tho...@sc...>:
>
>> 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 <gia...@gm...>
>> 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.
>>
>>
>