[PyMOL] unable to initialize pymol plugin

Dear Users, Could someone help to solve the following initializing problem? I am using a Toshiba Qosmio laptop. Also how can I see 3d here? Thank you in advance. Hena PyMOL(TM) Molecular Graphics System, Version 1.7.2.1. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warre

Re: [PyMOL] slow pymol-v1.7.4.0-Linux-x86_64 in ubuntu 14.04 LTS

gt; *OpenGL graphics engine:* > * GL_VENDOR: NVIDIA Corporation* > * GL_RENDERER: Quadro K2200/PCIe/SSE2* > * GL_VERSION: 4.5.0 NVIDIA 352.39* > *Adapting to Quadro hardware.* > *Detected 24 CPU cores. Enabled multithreaded rendering.* > > Kind regards, > Thibault. > >

[PyMOL] slow pymol-v1.7.4.0-Linux-x86_64 in ubuntu 14.04 LTS

Dear Pymol members, I have a hard time to use pymol-v1.7.4.0-Linux-x86_64 in ubuntu 14.04 LTS which I need to use very often. Although other graphics programs like COOT, CCP4MG are running just fine. After I load the pdb file, it just taking too much time for any operation like zoom in or out, rota

[PyMOL] plugin errors in pymol 1.7.2.1

Dear Pymol Users, I installed pymol 1.7.2.1 in my laptop (windows 8.1) and found some errors. Please see the highlighted portion below. How can I see stereo, although it has been enabled? I installed Openbabel, but some plug-in are not being initialized. Could you please suggest how can I solve th

[PyMOL] attribute error

Dear Pymol users, I am getting two problems with pymol at this moment. After I measure a distance between two atoms, the dashed line with label displayed. Then I was trying to change the color of the dashed line using the color menu at the last column and it did not work. It is showing 'attribute

[PyMOL] label unit cell

Hi, I can display the unit cell by typing 'show cell'. How can I label the unit cell? I want to see the origin and unit cell axes a, b, c. Looking forward to hearing from you..., hena -- Slashdot TV. Video for Nerds. Stu

Re: [PyMOL] Cartoon_oval_length

com> wrote: > nice! Glad you could solve it. > > Could you write a brief reply to the pymol-users list so that other people > know that the issue is solved and the problem was cartoon_fancy_helices? > Thanks! > > --Thomas > > On 25 Aug 2014, at 13:27, Hena Dutta wrote:

[PyMOL] Cartoon_oval_length

Hi, I am trying to change the cartoon oval length using the command set cartoon_oval_length, 0.6 But, it is not showing any change. I am using pymol 1.6.0.0 in windows 8.1 Can someone help me? Regards, Hena -- Slashdot TV.

[PyMOL] make bond between two atoms

Hi, I created two objects as follows: pseudoatom A1, pos=[10.0, 10.0, 100.0] pseudoatom A2, pos=[10.0, 10.0, -200.0] I want to create a bond between these two atoms. Could you please help me? I need to display a 2 fold axis passing through these points. I tried to use make and fuse command. Migh

Re: [PyMOL] displaying cartoon helix and sheet in multiple identical chains

> > -- > Jared Sampson > Xiangpeng Kong Lab > NYU Langone Medical Center > 550 First Ave MSB 398 > New York, NY 10016 > 212-263-7898 > http://kong.med.nyu.edu/ > > On Jul 10, 2012, at 1:39 PM, Hena Dutta wrote: > > Hi, > > Sorry, I forgot

[PyMOL] displaying cartoon helix and sheet in multiple identical chains

Hi, Sorry, I forgot to mention that, I have only C-alpha coordinates of 60 chains in one pdb file. I have 60 identical chains. Each chain is about 140 residues. Residues from 10-36 is helix and residues from 50-56 is beta sheet. I want to prepare a cartoon diagram displaying helix and sheet in re

[PyMOL] displaying fancy helix and beta sheet in multiple identical chains

Hi, I have 60 identical chains. Each chain is about 140 residues. Residues from 10-36 is helix and residues from 50-56 is beta sheet. I want to prepare a cartoon diagram displaying helix and sheet in red and yellow color respectively and the rest part(loop) in white. I need to do this for all 60 c

[PyMOL] measuring helix angle

Hi, Can anyone guide me how to use the pymol script to calculate the angle between two helices? Where and how to edit the script? I have 2 helices in a pdb file as follows: protein.pdb hel1 is chain A: 6-20 hel2 is chain A: 26-39 Thanking you in advance... Hena --