Re: [ccp4bb] ligands found in ChEBI...

2022-12-08 Thread Harry Powell 
Hi folks

it seems that the “easiest” way to get my coords if I know the ChEBI identifier 
is to do something like this in Python3 (note this snippet has no error 
checking!):

> import sys # only needed to parse the command-line arguments
> chebi = sys.argv[1] # expect ChEBI identifier without the leading “CHEBI:" 
> import pubchempy # have to pip install or conda install, whatever for your 
> environment
> pubchempy.download("SDF", f“ChEBI_{chebi}.sdf", f”CHEBI:{chebi}", "name", 
> record_type="3d", overwrite=True)

and running that with “64119” as the argument gives me a file ChEBI_64119.sdf 
with 3D coords.

Many thanks to all who got me out of my hole!

Harry

> On 6 Dec 2022, at 12:19, Harry Powell  wrote:
> 
> Hi Julie
> 
> Ta.
> 
> Do you know if there’s an API (pref. Python 3.9 or later) for downloading the 
> 3D coordinates from ChemSpider?
> 
> Harry
> 
>> On 6 Dec 2022, at 12:04, Julie Tucker 
>> <20908adb55d7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Chemspider can also provide you with a .mol file amongst other things.
>> http://www.chemspider.com/Chemical-Structure.2424.html?rid=281bd645-a2c9-4d07-af08-c3148b323194
>> Best wishes
>> Julie
>> 
>> On Tue, 6 Dec 2022 at 11:55, Oliver Smart  wrote:
>> Hi Harry,
>> 
>> The SDF found at ChEBI is a 2D SDF with the coordinates used for the 
>> diagram. I do not think that ChEBI has
>> 3D coordinates. Why not use PubChem instead as this does provide 3D sdf 
>> files?
>> 
>> For your caffeine example:
>> 
>> https://pubchem.ncbi.nlm.nih.gov/compound/64119 
>> 
>> There 
>> 
>> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d_type=save_basename=Conformer3D_CID_2519
>>  
>> 
>> Provides a  SDF file.
>> 
>> Hope this helps
>> 
>> Oliver
>> 
>> p.s. I you are stuck with ChEBI identifiers it would be possible to 
>> programatically find the equivalent PubChem CID.
>> 
>> 
>> 
>> 
>>> On 6 Dec 2022, at 11:31, Harry Powell 
>>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> 
>>> Hi folks
>>> 
>>> Can anyone help with this?
>>> 
>>> I must have missed something in the documentation, because I don’t 
>>> understand why the .mol and .sdf files downloaded from 
>>> 
>>> https://www.ebi.ac.uk/chebi
>>> 
>>> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades 
>>> now since I solved any small molecule structures, but something around 
>>> 1.395Å rings a faint bell).
>>> 
>>> I need to have ligands that have realistic sizes, and while I’m perfectly 
>>> at ease scaling the models to what I think are sensible sizes, I can’t help 
>>> but think that this isn’t necessary and I’ve missed something somewhere.
>>> 
>>> Here’s an example of a molecule that I used this morning - 
>>> 
>>> 
>>> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true=31332=0
>>> 
>>> contents of downloaded file - 
 
 Marvin  01140911122D  
 
 15 15  0  0  0  0999 V2000
  -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
  -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
   0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
   0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
   0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
   0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
   1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
   1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
   1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
   0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
   0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
   1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
   2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
 10  1  2  0  0  0  0
 1  2  1  0  0  0  0
 14  2  1  0  0  0  0
 8  3  1  0  0  0  0
 4  3  2  0  0  0  0
 7  4  1  0  0  0  0
 1  5  1  0  0  0  0
 5  3  1  0  0  0  0
 12  5  1  0  0  0  0
 6  2  1  0  0  0  0
 6  4  1  0  0  0  0
 11  6  2  0  0  0  0
 9  7  1  0  0  0  0
 13  7  1  0  0  0  0
 9  8  2  0  0  0  0
 M  END
 
>>> 
>>> Harry
>>> 
>>> 
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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Re: [ccp4bb] ligands found in ChEBI...

2022-12-06 Thread Julie Tucker 
Maybe more information on that here: https://developer.rsc.org/?
I'm not an expert and only used it interactively...
Julie

On Tue, 6 Dec 2022 at 12:19, Harry Powell 
wrote:

> Hi Julie
>
> Ta.
>
> Do you know if there’s an API (pref. Python 3.9 or later) for downloading
> the 3D coordinates from ChemSpider?
>
> Harry
>
> > On 6 Dec 2022, at 12:04, Julie Tucker <
> 20908adb55d7-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Chemspider can also provide you with a .mol file amongst other things.
> >
> http://www.chemspider.com/Chemical-Structure.2424.html?rid=281bd645-a2c9-4d07-af08-c3148b323194
> > Best wishes
> > Julie
> >
> > On Tue, 6 Dec 2022 at 11:55, Oliver Smart 
> wrote:
> > Hi Harry,
> >
> > The SDF found at ChEBI is a 2D SDF with the coordinates used for the
> diagram. I do not think that ChEBI has
> > 3D coordinates. Why not use PubChem instead as this does provide 3D sdf
> files?
> >
> > For your caffeine example:
> >
> > https://pubchem.ncbi.nlm.nih.gov/compound/64119
> >
> > There
> >
> >
> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d_type=save_basename=Conformer3D_CID_2519
> >
> > Provides a  SDF file.
> >
> > Hope this helps
> >
> > Oliver
> >
> > p.s. I you are stuck with ChEBI identifiers it would be possible to
> programatically find the equivalent PubChem CID.
> >
> >
> >
> >
> >> On 6 Dec 2022, at 11:31, Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> >>
> >> Hi folks
> >>
> >> Can anyone help with this?
> >>
> >> I must have missed something in the documentation, because I don’t
> understand why the .mol and .sdf files downloaded from
> >>
> >>  https://www.ebi.ac.uk/chebi
> >>
> >> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few
> decades now since I solved any small molecule structures, but something
> around 1.395Å rings a faint bell).
> >>
> >> I need to have ligands that have realistic sizes, and while I’m
> perfectly at ease scaling the models to what I think are sensible sizes, I
> can’t help but think that this isn’t necessary and I’ve missed something
> somewhere.
> >>
> >> Here’s an example of a molecule that I used this morning -
> >>
> >>
> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true=31332=0
> >>
> >> contents of downloaded file -
> >>>
> >>>  Marvin  01140911122D
> >>>
> >>> 15 15  0  0  0  0999 V2000
> >>>   -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
> >>>   -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
> >>>0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
> >>>0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
> >>>0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
> >>>0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
> >>>1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
> >>>1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
> >>>1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
> >>>   -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
> >>>0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
> >>>0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
> >>>1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
> >>>   -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
> >>>2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
> >>> 10  1  2  0  0  0  0
> >>>  1  2  1  0  0  0  0
> >>> 14  2  1  0  0  0  0
> >>>  8  3  1  0  0  0  0
> >>>  4  3  2  0  0  0  0
> >>>  7  4  1  0  0  0  0
> >>>  1  5  1  0  0  0  0
> >>>  5  3  1  0  0  0  0
> >>> 12  5  1  0  0  0  0
> >>>  6  2  1  0  0  0  0
> >>>  6  4  1  0  0  0  0
> >>> 11  6  2  0  0  0  0
> >>>  9  7  1  0  0  0  0
> >>> 13  7  1  0  0  0  0
> >>>  9  8  2  0  0  0  0
> >>> M  END
> >>>
> >>
> >> Harry
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>
> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >
> >
> > --
> > Julie Tucker
> > York Biomedical Research Institute
> > Department of Biology and HYMS
> > University of York
> >
> > My normal working days are Monday-Tuesday and Thursday-Friday. Please be
> patient if you do not hear from me promptly. I choose to work flexibly;
> please only respond to this message when convenient for you to do so.
> >
> > Email disclaimer
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> >

Re: [ccp4bb] ligands found in ChEBI...

2022-12-06 Thread Harry Powell 
Hi Oliver

I’d just worked that out when I tried an obviously non-planar molecule (that I 
didn’t include with my breakfast this morning)!

PubChem looks like a useful way forward - many thanks.

Harry

> On 6 Dec 2022, at 11:55, Oliver Smart  wrote:
> 
> Hi Harry,
> 
> The SDF found at ChEBI is a 2D SDF with the coordinates used for the diagram. 
> I do not think that ChEBI has
> 3D coordinates. Why not use PubChem instead as this does provide 3D sdf files?
> 
> For your caffeine example:
> 
> https://pubchem.ncbi.nlm.nih.gov/compound/64119 
> 
> There 
> 
> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d_type=save_basename=Conformer3D_CID_2519
>  
> 
> Provides a  SDF file.
> 
> Hope this helps
> 
> Oliver
> 
> p.s. I you are stuck with ChEBI identifiers it would be possible to 
> programatically find the equivalent PubChem CID.
> 
> 
> 
> 
>> On 6 Dec 2022, at 11:31, Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hi folks
>> 
>> Can anyone help with this?
>> 
>> I must have missed something in the documentation, because I don’t 
>> understand why the .mol and .sdf files downloaded from 
>> 
>>  https://www.ebi.ac.uk/chebi
>> 
>> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades 
>> now since I solved any small molecule structures, but something around 
>> 1.395Å rings a faint bell).
>> 
>> I need to have ligands that have realistic sizes, and while I’m perfectly at 
>> ease scaling the models to what I think are sensible sizes, I can’t help but 
>> think that this isn’t necessary and I’ve missed something somewhere.
>> 
>> Here’s an example of a molecule that I used this morning - 
>> 
>>  
>> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true=31332=0
>> 
>> contents of downloaded file - 
>>> 
>>>  Marvin  01140911122D  
>>> 
>>> 15 15  0  0  0  0999 V2000
>>>   -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
>>>0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>>2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
>>> 10  1  2  0  0  0  0
>>>  1  2  1  0  0  0  0
>>> 14  2  1  0  0  0  0
>>>  8  3  1  0  0  0  0
>>>  4  3  2  0  0  0  0
>>>  7  4  1  0  0  0  0
>>>  1  5  1  0  0  0  0
>>>  5  3  1  0  0  0  0
>>> 12  5  1  0  0  0  0
>>>  6  2  1  0  0  0  0
>>>  6  4  1  0  0  0  0
>>> 11  6  2  0  0  0  0
>>>  9  7  1  0  0  0  0
>>> 13  7  1  0  0  0  0
>>>  9  8  2  0  0  0  0
>>> M  END
>>> 
>> 
>> Harry
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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> 



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Re: [ccp4bb] ligands found in ChEBI...

2022-12-06 Thread Julie Tucker 
Chemspider can also provide you with a .mol file amongst other things.
http://www.chemspider.com/Chemical-Structure.2424.html?rid=281bd645-a2c9-4d07-af08-c3148b323194
Best wishes
Julie

On Tue, 6 Dec 2022 at 11:55, Oliver Smart  wrote:

> Hi Harry,
>
> The SDF found at ChEBI is a 2D SDF with the coordinates used for the
> diagram. I do not think that ChEBI has
> 3D coordinates. Why not use PubChem instead as this does provide 3D sdf
> files?
>
> For your caffeine example:
>
> https://pubchem.ncbi.nlm.nih.gov/compound/64119
>
> There
>
>
> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d_type=save_basename=Conformer3D_CID_2519
>
>
> Provides a  SDF file.
>
> Hope this helps
>
> Oliver
>
> p.s. I you are stuck with ChEBI identifiers it would be possible to
> programatically find the equivalent PubChem CID.
>
>
>
>
> On 6 Dec 2022, at 11:31, Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi folks
>
> Can anyone help with this?
>
> I must have missed something in the documentation, because I don’t
> understand why the .mol and .sdf files downloaded from
>
> https://www.ebi.ac.uk/chebi
>
> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades
> now since I solved any small molecule structures, but something around
> 1.395Å rings a faint bell).
>
> I need to have ligands that have realistic sizes, and while I’m perfectly
> at ease scaling the models to what I think are sensible sizes, I can’t help
> but think that this isn’t necessary and I’ve missed something somewhere.
>
> Here’s an example of a molecule that I used this morning -
>
>
> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true=31332=0
>
> contents of downloaded file -
>
>
>  Marvin  01140911122D
>
> 15 15  0  0  0  0999 V2000
>   -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>   -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
>0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
>0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
>1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
>1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>   -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
>0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
>0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
>1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
>   -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
> 10  1  2  0  0  0  0
>  1  2  1  0  0  0  0
> 14  2  1  0  0  0  0
>  8  3  1  0  0  0  0
>  4  3  2  0  0  0  0
>  7  4  1  0  0  0  0
>  1  5  1  0  0  0  0
>  5  3  1  0  0  0  0
> 12  5  1  0  0  0  0
>  6  2  1  0  0  0  0
>  6  4  1  0  0  0  0
> 11  6  2  0  0  0  0
>  9  7  1  0  0  0  0
> 13  7  1  0  0  0  0
>  9  8  2  0  0  0  0
> M  END
>
>
> Harry
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>


-- 
Julie Tucker
York Biomedical Research Institute
Department of Biology and HYMS
University of York

*My normal working days are Monday-Tuesday and Thursday-Friday. Please be
patient if you do not hear from me promptly. I choose to work flexibly;
please only respond to this message when convenient for you to do so.*

Email disclaimer




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Re: [ccp4bb] ligands found in ChEBI...

2022-12-06 Thread Oliver Smart 
Hi Harry,

The SDF found at ChEBI is a 2D SDF with the coordinates used for the diagram. I 
do not think that ChEBI has
3D coordinates. Why not use PubChem instead as this does provide 3D sdf files?

For your caffeine example:

https://pubchem.ncbi.nlm.nih.gov/compound/64119 
 

There 

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d_type=save_basename=Conformer3D_CID_2519
 

 

Provides a  SDF file.

Hope this helps

Oliver

p.s. I you are stuck with ChEBI identifiers it would be possible to 
programatically find the equivalent PubChem CID.




> On 6 Dec 2022, at 11:31, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi folks
> 
> Can anyone help with this?
> 
> I must have missed something in the documentation, because I don’t understand 
> why the .mol and .sdf files downloaded from 
> 
>   https://www.ebi.ac.uk/chebi
> 
> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now 
> since I solved any small molecule structures, but something around 1.395Å 
> rings a faint bell).
> 
> I need to have ligands that have realistic sizes, and while I’m perfectly at 
> ease scaling the models to what I think are sensible sizes, I can’t help but 
> think that this isn’t necessary and I’ve missed something somewhere.
> 
> Here’s an example of a molecule that I used this morning - 
> 
>   
> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true=31332=0
> 
> contents of downloaded file - 
>> 
>>  Marvin  01140911122D  
>> 
>> 15 15  0  0  0  0999 V2000
>>   -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
>>0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
>>0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
>>1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
>>1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
>>0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
>>0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
>>1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
>> 10  1  2  0  0  0  0
>>  1  2  1  0  0  0  0
>> 14  2  1  0  0  0  0
>>  8  3  1  0  0  0  0
>>  4  3  2  0  0  0  0
>>  7  4  1  0  0  0  0
>>  1  5  1  0  0  0  0
>>  5  3  1  0  0  0  0
>> 12  5  1  0  0  0  0
>>  6  2  1  0  0  0  0
>>  6  4  1  0  0  0  0
>> 11  6  2  0  0  0  0
>>  9  7  1  0  0  0  0
>> 13  7  1  0  0  0  0
>>  9  8  2  0  0  0  0
>> M  END
>> 
> 
> Harry
> 
> 
> 
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Re: [ccp4bb] ligands found in ChEBI...

2022-12-06 Thread Harry Powell 
Whoops. 

It looks like these entries are not supposed to be 3D models, but 
representations of 2D line drawings (which I noticed when I had a look at an 
obviously non-planar molecule).

Which is a shame, because I was hoping I could use them in 3D modelling…

Sorry for polluting your inboxes!

Harry

> On 6 Dec 2022, at 11:31, Harry Powell  wrote:
> 
> Hi folks
> 
> Can anyone help with this?
> 
> I must have missed something in the documentation, because I don’t understand 
> why the .mol and .sdf files downloaded from 
> 
>   https://www.ebi.ac.uk/chebi
> 
> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now 
> since I solved any small molecule structures, but something around 1.395Å 
> rings a faint bell).
> 
> I need to have ligands that have realistic sizes, and while I’m perfectly at 
> ease scaling the models to what I think are sensible sizes, I can’t help but 
> think that this isn’t necessary and I’ve missed something somewhere.
> 
> Here’s an example of a molecule that I used this morning - 
> 
>   
> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true=31332=0
> 
> contents of downloaded file - 
>> 
>>  Marvin  01140911122D  
>> 
>> 15 15  0  0  0  0999 V2000
>>   -0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -0.71450.41250. N   0  0  0  0  0  0  0  0  0  0  0  0
>>0.7145   -0.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>0.71450.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>>0.   -0.82500. N   0  0  0  0  0  0  0  0  0  0  0  0
>>0.0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>1.49920.66740. N   0  0  0  0  0  0  0  0  0  0  0  0
>>1.4992   -0.66750. N   0  0  0  0  0  0  0  0  0  0  0  0
>>1.98410.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -1.4289   -0.82500. O   0  0  0  0  0  0  0  0  0  0  0  0
>>0.00011.65000. O   0  0  0  0  0  0  0  0  0  0  0  0
>>0.0001   -1.65000. C   0  0  0  0  0  0  0  0  0  0  0  0
>>1.75411.45200. C   0  0  0  0  0  0  0  0  0  0  0  0
>>   -1.42890.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>>2.0809   -1.53650. O   0  0  0  0  0  0  0  0  0  0  0  0
>> 10  1  2  0  0  0  0
>>  1  2  1  0  0  0  0
>> 14  2  1  0  0  0  0
>>  8  3  1  0  0  0  0
>>  4  3  2  0  0  0  0
>>  7  4  1  0  0  0  0
>>  1  5  1  0  0  0  0
>>  5  3  1  0  0  0  0
>> 12  5  1  0  0  0  0
>>  6  2  1  0  0  0  0
>>  6  4  1  0  0  0  0
>> 11  6  2  0  0  0  0
>>  9  7  1  0  0  0  0
>> 13  7  1  0  0  0  0
>>  9  8  2  0  0  0  0
>> M  END
>> 
> 
> Harry
> 
> 



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