Re: [PyMOL] draw sticks between given coordinates

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

Re: [PyMOL] Custom surface?

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

Re: [PyMOL] pymol to webGL?

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 Martin wrote

Re: [PyMOL] Is it possible to write PNG images in PyMOL of higher resolution than the viewing window?

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 resolution (in terms

Re: [PyMOL] Coloring c-alpha atoms makes cartoons colored too

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 anas...@mbu.iisc.ernet.in wrote: Hi everyone, I want to color C-alpha atoms of a selection in a specified colour (red

Re: [PyMOL] View Matrix operation

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. l.j.feit...@uu.nl wrote: Hi all, I have a small question about transformations with the view matrix

Re: [PyMOL] pymol_tube and pymol_loop

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 cartoon_tube or cartoon_loop described

Re: [PyMOL] Drawing lines

to ray-trace your scene to see the effect. Best regards, Takanori Nakane -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint

Re: [PyMOL] pdb to string

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 -- LIMITED TIME SALE

Re: [PyMOL] remote access-pymol can not work

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

Re: [PyMOL] Managing Viewport Location

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 script works just fine. As I don't use Windows version of PyMOL, I cannot test more. Best regards, Takanori Nakane

Re: [PyMOL] Managing Viewport Location

, size, defocus, focus, maximize, show Best regards, Takanori Nakane -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http

Re: [PyMOL] Reducing VRML file size

for details. Best regards, Takanori Nakane -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc

Re: [PyMOL] Label on top of molecules?

of its original position. Best regards, Takanori Nakane -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct

[PyMOL] Dynamic Isomesh (like COOT)

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 1HWK, 1hwk_map, type

Re: [PyMOL] writing out the surface

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 -- Live Security

Re: [PyMOL] how to remap mouse wheel?

Hi, You can use button command. In this case, button wheel, None, MovZ will do the job. Best regards, Takanori Nakane -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security

Re: [PyMOL] Exporting distance objects from PyMOL en masse in text

Hi, You can use get_raw_distances script http://pymolwiki.org/index.php/Get_raw_distances Best regards, Takanori Nakane -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security

Re: [PyMOL] Line thickness for show as cell

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 Nakane

Re: [PyMOL] Get event click in a residue in a script/plugin and launch function

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 -- Virtualization Cloud Management Using Capacity

Re: [PyMOL] list of polar contacts

and undocumented APIs. Already I have many fragments of memos but it will take some time to put them together. Best regards, Takanori Nakane -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive

Re: [PyMOL] list of polar contacts

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 points = obj[5][2][0][1] ret

Re: [PyMOL] Scene exporter for Web

contribute by writing documentations for undocumented APIs and settings, such as cmd.dump, get_session, etc. Best regards, Takanori Nakane -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online

[PyMOL] Scene exporter for Web

this script useful, I will put it on Pymol wiki. Best regards, Takanori Nakane -- RSA(R) Conference 2012 Mar 27 - Feb 2 Save $400 by Jan. 27 Register now! http://p.sf.net/sfu/rsa-sfdev2dev2

Re: [PyMOL] Convert PyMOL isomesh or isosurface to cgo?

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.split('\n\n'): CGOobj.append(BEGIN

Re: [PyMOL] selection within object

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. With Citrix VDI-in-a-Box, you don't need a complex

Re: [PyMOL] Color states as rainbow

+ cmd.count_states())) part. Best regards, Takanori Nakane -- Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event for developers. It will provide a great way