Re: [PyMOL] MacPymol + Missing Features (APBS?)

he "A > generate" menu. > > http://pymolwiki.org/index.php/psico > > Cheers, > Thomas > > João Rodrigues wrote, On 02/13/14 14:44: > > Dear all, > > > > I had the incentive version installed for a while (v1.7 beta2) and I was > > surprised to s

[PyMOL] MacPymol + Missing Features (APBS?)

Dear all, I had the incentive version installed for a while (v1.7 beta2) and I was surprised to see that in the [A] menu, under 'generate' there was an option to generate an electrostatic map with apbs. Unfortunately my laptop HD died, and when I reinstalled everything today this option is missin

Re: [PyMOL] accurate way to change/process b-factor in PDB

Hi Afonso, PyMOL allows for Python scripting so in principle you could do something like: import math alter structure, b=math.log(b, 10) Just make sure not to have 0.0 bfactors in there! Cheers, João 2013/7/4 Afonso Duarte > Dear All, > > > I have a pdb file composed by several chains wher

Re: [PyMOL] How to avoid the protonation of a particular atom

Hi, Protonate everyone, deprotonate that particular atom Cheers, João 2013/4/1 > Hello, > > I'm working with a receptor that has a catalytic Zn and i have to > protonate everything except this atom. I have proved everything to avoid > this protonation (put Zn2+ on the pdb, change the protona

[PyMOL] Zoom + Fading simultaneously in movie

Hi all, I'm trying to make a short movie here and I came across something I can't find on the internet how to do it.. I want to zoom in a region of the protein (done easily) and at the same time fade its surface (also easily done on its own, thanks Tsjerk). Is this possible or we cannot have two

Re: [PyMOL] Using cmd.png with ray=False still ray traces the image

k to ray tracing, since it is the only way to > obtain a figure in this mode. So, in a script, I shouldn't use ray. I should just use png directly and allow it to ray. It worked. Cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 18 de Abril de 2012 09:38, Thom

Re: [PyMOL] Using cmd.png with ray=False still ray traces the image

m a bit out of ideas.. Cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 17 de Abril de 2012 22:33, Jason Vertrees < jason.vertr...@schrodinger.com> escreveu: > João, > > I'm not sure why this is giving you problems. Why do you have > renderer=2? Why not the def

Re: [PyMOL] Using cmd.png with ray=False still ray traces the image

Same result Jason, i also tried =false... No dia 17 de Abr de 2012 20:45, "Jason Vertrees" < jason.vertr...@schrodinger.com> escreveu: > Hi João, > > What about > > cmd.png(default_name+'.png', dpi=300, ray=0) > > Cheers, > > -- Jason &

[PyMOL] Using cmd.png with ray=False still ray traces the image

ames): cmd.ray(width, height, renderer=2) > cmd.png(default_name+'.png', dpi=300, ray=False) This actually renders my scene *twice. *I've tried cmd.do and it does the same.. am I missing something or is this not supposed to happen? Thanks and cheers, João [...] Rodr

Re: [PyMOL] how to select whole residues around an object?

Use byres(). select neighbours, byres( chain A w. 4A of chain B) Cheers, João -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Vis

Re: [PyMOL] atom structure

Hi, You can set something like this: set sphere_scale, 0.2 set stick_radius, 0.15 show spheres show sticks I usually use lines for the bonds though. Best, João -- Try before you buy = See our experts in action! The mo

Re: [PyMOL] To build protein structure model?

Try MODELLER. -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style A

Re: [PyMOL] Editing of the pdb structure

s are very weak... My opinion only. João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 27 de Janeiro de 2012 09:50, James Starlight escreveu: > Arne, Thomas > > Thanks alot. Bond works finw > > > I'd like just to ask what about geometry optimisation of the new stru

Re: [PyMOL] Create a dimer from predicted monomer

Hello Karen, Predicting protein complexes structures is "docking". Pymol should not be used for this. I would advise you to look at docking software that allows for symmetrical molecules, such as HADDOCK (http://haddocking.org/) or SymmDock (http://bioinfo3d.cs.tau.ac.il/SymmDock/). B

Re: [PyMOL] (HB) dotted line with out distance number

Hey Leila, The distance is a Label, so if you hide the labels for the distance object is should disappear. Regards, João -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the

Re: [PyMOL] PyMOL Help

Hello Matthew, You write something like and chain A. To select chain A. In your case, doing select catalytic, resi 2 and chain E should do the trick Best! João [...] Rodrigues @ http://doeidoei.wordpress.org On Tue, Jul 13, 2010 at 5:28 AM, Matthew Jenner wrote: > Hi PyMOL, > > Th

Re: [PyMOL] How does PyMol add hydrogen atoms?

Hey Jason, Thanks! I'd "traced" add_H to that function before but my knowledge of C is rudimentary so I was quite overwhelmed. Yet, I think I managed to understand a bit better what's going on, but correct me if I'm wrong. It seems PyMol looks for neighbours first, derives a "bonding network" fro

Re: [PyMOL] How does PyMol add hydrogen atoms?

Hey Jason! Thanks for the reply, no problem at all with the delay :) I got my hands around the code and I *think* I got it to add hydrogens to a protein (including checking that random effect). My only question is, how PyMol determines which atoms lack hydrogens. I checked the hetatm.py and prot

[PyMOL] How does PyMol add hydrogen atoms?

when it comes to H-addition? How are H-s added to say, Methane? (given a single C). Best! João [...] Rodrigues @ http://doeidoei.wordpress.org -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Fa