Hi,
Open the map in Coot and select [File]-[Export Map].
This allows you to save the map in .ccp4 (= .mrc)
format, which PyMOL can read.
Best regards,
Takanori Nakane
On 7/30/24 20:17, Urban Leitgeb via PyMOL-users wrote:
Hi,
I calculated anomalous difference maps with shelx and got .phs
regards,
Takanori Nakane
On 2/7/24 19:25, Daniele Notarmuzi wrote:
Hello!
I am trying to draw sticks given a set of coordinates and sometimes I
succeed, sometimes I do not. In my silly mind, what I would like to do
is to give two set of 3D coordinates and have a stick drawn between
them. For
Hi,
This can be achieved with CGO
http://pymol.sourceforge.net/newman/user/S0500cgo.html.
CGO_grid script https://pymolwiki.org/index.php/Cgo_grid will be a good
starting point for your work.
Best regards,
Takanori Nakane
On 2020/09/17 15:07, Piter_ wrote:
Hi everybody.
Is it possible to
mage pixel.
Did you take that into the account? Probably you don't need 2400 dpi
or 1200 dpi.
https://en.wikipedia.org/wiki/Dots_per_inch#/media/File:DPI_and_PPI.png
Best regards,
Takanori Nakane
Am 2016年05月10日 um 09:34 schrieb Stephen Kerry:
> Thank you for trying this out on a workstati
Hi,
It looks like the structure of PyMOL session (what
we got from cmd.get_session) has changed in recent upgrades.
I have to rewrite the program.
Does anyone know if there is a setting to export in the 'old' format?
Best regards,
Takanori Nakane
On 2015/10/18 1:47, Osvaldo Ma
Hi,
Yes.
See http://www.pymolwiki.org/index.php/Ray and
http://www.pymolwiki.org/index.php/Png .
Best regards,
Takanori Nakane
On 2015年01月05日 16:39, Brenton Horne wrote:
> Hi,
>
> I'd like to know if it is possible to save PNG images of a structure
> that have a higher resolu
Hi,
set sphere_color, grey, "x"
instead of "color red, x" will do what you want.
Best regards,
Takanori Nakane
On Tue, 2 Dec 2014 16:39:56 +0530 (IST) "Anasuya Dighe"
wrote:
> Hi everyone,
>
> I want to color C-alpha atoms of a selection in a speci
Dear Louris,
Probably "axes" script at http://www.pymolwiki.org/index.php/Axes
is a good staring point to study.
Best regards,
Takanori Nakane
On Wed, 19 Nov 2014 12:14:29 + "Feitsma, L.J." wrote:
> Hi all,
>
> I have a small question about transformations
Hi,
This page would be useful:
http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#cut
However, showing intact spheres above the clip plane for the surface
can be difficult. I am not sure if it is possible to set different
clipping planes to each object.
Best regards,
Takanori Nakane
0 0.0010000.0
When they are deleted, the model can be loaded correctly.
According to the PDB format specification
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#SCALEn ,
SCALEn records should not affect real space (orthogonal) coordinates.
Best regards,
Hi,
"cartoon tube" is a separate command from "show".
i.e.
show cartoon
cartoon tube
will show all the protein in the 'tube' representation.
Best regards,
Takanori Nakane
(2014/04/19 4:18), sunyeping wrote:
> Dear all, I want to show my protein in carto
Hi,
> I want to dump a loaded pdb file to a string, the inverse of the function
> read_pdbstr(). There is such a function available?
cmd.get_pdbstr() will do the job.
Best regards,
Takanori Nakane
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.0)
You might need to ray-trace your scene to see the effect.
Best regards,
Takanori Nakane
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Hi,
I have successfully used VirtualGL http://www.virtualgl.org/
to run PyMOL remotely on Ubuntu 12.04 LTS.
The client is Mac OS Mountain Lion.
The performance is satisfactory.
Best regards,
Takanori Nakane
;)
> time.sleep(1)
> pymol.cmd.window("position", 500, 300)
>
> ...in Python, Pymol freezes. If I remove the sleep command, it freezes
> before even displaying the test water molecules.
I couldn't reproduce it.
On my Ubuntu with PyMOL 1.5.0.1 & Python 2.7, your
th, int height)
"action" is one of the following, judging from the error message.
box, fit, hide, position, size, defocus, focus, maximize, show
Best regards,
Takanori Nakane
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lender for details.
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Takanori Nakane
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stroms in front of its original position.
Best regards,
Takanori Nakane
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Hi,
How about using "split_states 3iyw" instead of "set all_states, on"?
Best regards,
Takanori Nakane
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Use cmd.selection_sc for setting names (like 'line_width'),
cmd.map_sc for maps, cmd,repres_sc for representations
(sticks, lines, etc).
By the way, update is another way to set values to Python's Dict.
auto_arg[0]['test'] = [some, thing, s] is same as
auto_arg[0].update([
tron density maps.
Comments and suggestions are welcome.
Best regards,
Takanori Nakane
=== SCRIPT START (save as dynamic_mesh.py) ===
# Dynamic Mesh by Takanori Nakane
# version 0.1: 20120819
'''
This script was tested on PyMOL 1.2 and 1.5.
Example:
fetch 1HWK, async=1
fetch 1
tex normal vector, which can be rendered as GL_TRIANGLES.
Please examine my old post for a script example.
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10012.html
Best regards,
Takanori Nakane
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Hi,
You can use "button" command.
In this case,
button wheel, None, MovZ
will do the job.
Best regards,
Takanori Nakane
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Hi,
You can use get_raw_distances script
http://pymolwiki.org/index.php/Get_raw_distances
Best regards,
Takanori Nakane
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Dear Gudrun,
> How can I draw a thicker line when using show as cell, please?
Internally, unit cell is drawn as a CGO object.
Therefore, you can change its line width by
set cgo_line_width, N
where N = 1 is the default.
Best regards,
Takanori Nak
where can I get some example or explanation for
> that.
You can use "wizard" framework.
Please examine "examples/devel/click_ordered_list.py" in Pymol source tree.
Best regards,
Takanori Nakane
--
V
Hi Sean,
> I was wondering if it were possible to have a selection update itself for
> every frame.
You can use mdo command for that.
http://www.pymolwiki.org/index.php/Mdo
Best regards,
Takanori Nakane
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rnal
data structure and undocumented APIs.
Already I have many fragments of memos but it will take some
time to put them together.
Best regards,
Takanori Nakane
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The
convert it to atom name.
Save the script to somewhere and
run script_name.py
list_dist
will do the job.
Takanori Nakane
=== Script start ===
from pymol import cmd
def parseDistObj(obj):
if (obj[5][0][3][10] != 1): # 'show dashed' flag
return ""
l, I think I can contribute by
writing documentations for "undocumented" APIs and settings,
such as cmd.dump, get_session, etc.
Best regards,
Takanori Nakane
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think this script useful, I will put it on Pymol wiki.
Best regards,
Takanori Nakane
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bility issue. Please let me know
if it doesn't work.
Takanori Nakane
SCRIPT ===
from pymol import cmd
from pymol.cgo import *
def dump2surfaceCGO():
CGOobj = []
dumpedFile = open("dump.tmp").read()
for block in dumpedFile.s
lection
within a selection.
select chain A and ss 's'
will do it. If you have already selected monomer A, then
select (sele) and ss 's'
will also do.
Takanori Nakane
--
Ridiculously easy VDI. Wit
ing
"0x%02x00ff" % (i * 255 / (2 + cmd.count_states()))
part.
Best regards,
Takanori Nakane
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