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

ld 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 b

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

Dear All, I have a pdb file composed by several chains where the b-factor column was replaced by a physical property of the proteins. I am now trying to color according to b-factor and to obtain a better representation of the properties described. i.e. I am interested in calculating the log of th

[PyMOL] how to obtain the values from ramp_new

Deal All, I am using the ramp_new command to obtain a hotspot interaction pattern between 2 proteins (like Surface Colored by Distance from a Point from http://www.pymolwiki.org/index.php/Ramp_New). It works fine but now I want to check the values that originate this coloring in the surface of t

Re: [PyMOL] how to create a custom rainbow according to residue number

, lime green forest, chain A+C+E > PyMOL> spectrumany resi, lightblue blue density, chain B+D+F > > Hope that helps. > > Cheers, > Thomas > > Afonso Duarte wrote, On 09/04/12 15:15: >> >> Dear All, >> >> I'm using Pymol1.4 in windows and I

[PyMOL] how to create a custom rainbow according to residue number

r in Pymol ? Best Afonso ####### Afonso Duarte ITQB-UNL Portugal -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how

Re: [PyMOL] how to change the color of ramps?

map(lambda x,y: diff_len(x,y), stored.distCoord, stored.origCoord) > > # put them into the b-factor of the protein > > alter 1hug, b=newB.pop(0) > > # color by rainbow_rev or any other > # palette listed in "help spectrum" > > spectrum b, rainbow_rev, 1hug > >

[PyMOL] how to change the color of ramps?

Dear All, I am using the ramp_new command to color the surface of protein A according to the distance of protein B (i.e. like in the wiki example ramp_new proximityRamp, pOrig, 1hug, range=[5,65], color=rainbow). However I would like to color the surface of protein A in the inverse rainbow color..

Re: [PyMOL] Problem when running APBS 1.1.0 in Pymol 1.3 - protein is misplaced

> Dear All, > > I am running APBS 1.1.0. via the "APBS Tools2" plugin on Pymol 1.3 (either on > Linux or Vista). > As usual i fetch a pdb structure and then do a "set grid" and then "run APBS". > This works fine for most of the proteins I am working on, however I found out > that in some of the p

Re: [PyMOL] Strange pattern on the cartoon representation

, > a wholly owned subsidiary of Eli Lilly & Company > 180 Varick Street, 6th floor > New York, NY 10014 > phone:(917)606-4116 fax:(212)645-2054 > > > > -Original Message- > > From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] > > Sent: Tuesday, May 1

Re: [PyMOL] Strange pattern on the cartoon representation

(oh, and use reply-to-all to keep the discussion on the list :)) > > Cheers, > > Tsjerk > > On Tue, May 18, 2010 at 1:04 PM, Afonso Duarte > wrote: > > Hi Tsjerk, > > > > You are completely right ... I should have included an example. > > This picture was m

[PyMOL] Strange pattern on the cartoon representation

Dear All, I am making some figures using ray. When the processing is finished I get a strange pattern (like newspaper paper pattern) in my cartoon representations, Spheres and sticks representations are OK only the cartoon. I have tried to change the options on the cartoon representation but with

Re: [PyMOL] how to create a new .pdb from 3 pdb's?

ected_from_object2 > > Hope it helps, > > Tsjerk > > On Sun, Mar 28, 2010 at 4:33 PM, Afonso Duarte > wrote: >> Dear All, >> >> I want to create molecule in Pymol by combining 3 different pdbs. >> Two of them are form the pdb data bank and one was create

[PyMOL] how to create a new .pdb from 3 pdb's?

Dear All, I want to create molecule in Pymol by combining 3 different pdbs. Two of them are form the pdb data bank and one was created via pymol. I have the 3 of them open in pymol but now I am trying to figure out how to connect the termini of the polypeptides in pymol. I searched the wiki/manua