Hi,
The actual implementation in C is at layer1/Ray.c .
Best regards,
Takanori Nakane
On 2014-05-12 14:17, Riccardo wrote:
> Hello to the PyMOL mailing list.
>
> I'm searching for the place where the "get_vrml()" function (which
> seems to be involved to export a wrl file) has been defined, in
Hi,
This is because PyMOL does not read SSBOND records
in PDB files. Actually, PyMOL determines if a bond
is present based on atomic distances and CONECT records.
http://www.pymolwiki.org/index.php/Connect_mode
PyMOL does not write SSBOND records when saving a
PDB file.
Best regards,
Takanori N
Dear Thomas,
Thank you very much for your investigation.
I agree with you. PyMOL is doing right;
SCALEn should be the identity matrix, or CRYST1 expanded.
CRYST1 is defined to be "1 1 1 90 90 90" for
structures determined by non-crystallographic methods.
Thanks to the increased resolution of cry
Hi,
And you can use get_raw_distances script at
http://www.pymolwiki.org/index.php/Get_raw_distances
to get detailed information about contacts.
Best regards,
Takanori Nakane
On 2014-05-27 15:24, Sampson, Jared wrote:
> Hi Merlin -
>
> Try limiting the distances shown to those between atoms in
Hi,
Unfortunately, no.
PyMOL simply skips these lines and does not store
them in memory.
Best regards,
Takanori Nakane
On 2014-05-27 21:20, Lesburg, Charles wrote:
> Hi PyMOLers,
>
> Does anyone know if it's possible to access the REMARK (and other non
> ATOM/HETATM) lines of a PDB file *afte
Hi,
If the linear arrangement is defined as 'biological assembly'
in the PDB file, you can use "Biological Unit" script in
http://www.pymolwiki.org/index.php/BiologicalUnit
to quickly generate it.
Best regards,
Takanori Nakane
On 2014-08-27 11:57, Spencer Bliven wrote:
> Sometimes it is easier
Hi,
> I tried writing a macro where I woul use load *.mol2 but that doesn't
> work either.
You can use glob in Python. An example is in the
"User Comments/Examples" section of
http://www.pymolwiki.org/index.php/Load .
Best regards,
Takanori Nakane
On 2014-09-10 08:56, ashika torikora wrote:
>
Hi,
Try the following in PyMOL's command prompt.
from glob import glob
for file in glob("path/to/data/*.mol2"): cmd.load(file)
Takanori Nakane
On 2014-09-10 11:10, ashika torikora wrote:
> I don't think I understand what glob does or how to use it.
>
> 2014-09
Hi,
In GUI, [Color]-[spectrum]-[rainbow].
From command line,
util.chainbow("name")
Best regards,
Takanori Nakane
On 2014-10-14 13:55, sunyeping wrote:
> Dear pymol user,
>
> Could you tell me how to color a polypeptide continuously from N- to
> C-terminal by continuous spectrum such as red
