Hi,
If you are getting unwanted PyMOL standard errors you can turn them off
using the cmd.feedback() commands:
cmd.feedback('disable', 'selector', 'everything')
cmd.feedback('disable', 'executive', 'everything')
to turn them on again:
cmd.feedback('enable', 'selector', 'everything')
cmd.fee
Kostas,
This command:
dist name, sel1, sel2, mode=3D2
doesn't work because the move value should be a whole number ie. 1,2,3 etc.
Also unless you have some objects actually called sel1 and sel2 you
won't get anything meaningful back.
something like this:
dist name, resn lys, resn glu, mode=
Hello All,
Can someone tell me wether it is possible to use a stand-alone python
installation alongside the latest PyMol releases? I have a few things
set up in my main python installation which an older (python free)
version of Pymol was happy to use, having installed the newer version it
us
' is the model id you want to
align all others against. Written by Jules Jacobsen
(jacob...@ebi.ac.uk). Feel free to do whatever you like with this code."""
id = id.lower()
pdbList = cmd.get_names()
for entry in pdbList[:]:
entry = entry.strip()
#x27;' is the model id you want to
align all others against. Written by Jules Jacobsen
(jacob...@ebi.ac.uk). Feel free to do whatever you like with this code."""
id = id.lower()
pdbList = cmd.get_names()
for entry in pdbList[:]:
entry = entry.strip
al Message
Subject: 0.98 beta 18 Selecting
Date: Tue, 23 Nov 2004 11:05:01 +0000
From: Jules Jacobsen
To: pymol-users@lists.sourceforge.net
Hi all,
Has anyone else had the problem of not being able to select several
identical residue types in aligned structures? eg in the .pse included,
if you s
Hi Matthew,
You want: 'set ribbon_trace,1'
or 'set cartoon_trace,1'
Jules
Matthew Bowler wrote:
Dear All,
I am trying display a c-alpha model in pymol (1qo1), when the file
is opened all the atoms are displayed as non-bonded. Is there a way to
tell pymol that this is a c-alpha trace an
Hi Kostas,
What you need to do is create a new object based on the part you wish to
view, then centre the view on that object.
select objectName, resi 1-55
center objectName
alternatively use the 'zoom' command instead of 'center'.
As for treating models of an NMR ensemble seperately use the
Hello List,
I'm trying to make a plugin which will load various features from a
swissprot entry onto a model loaded in PyMol but need to know a few
things such as:
Where are the sequences of the models stored in pymol and how do I
retrieve them?
Are these taken from the ATOM or SEQRES sect
Yes, I've got the same problem.
Jules
Daniel Rigden wrote:
Hi all
When I visualise sequences, all Glu residues (as well as all Asp
residues) are shown as D!
Has anyone else seen this?
Daniel
Mark,
You don't have to reboot, go to the process tab of windows task manager
and end the python image underlying PyMOl.
Jules
Mark Wilke wrote:
Is there any way of stopping a ray trace once it has been started without
closing pymol? Some of my ray trace jobs take too long and I want to sto
Yes, i've had the same problem too.
Jules
On Mon, 5 Apr 2004, Tom Lee wrote:
> I have trouble installing PyMOL using pymol-0_95-bin-win32-py23.zip. Here
> is the message I got.
>
> The installer is unable to locate Python. Python must be installed before
> PyMOL. Do you wish to abort?
>
> I h
Hello Pymol types,
I have a quick question- has anyone had any trouble printing out images
in word using version 0.9 in word XP?
The images look fine when viewed on the screen yet when it comes to
printing them out they appear as negatives, including the white
background which becomes black.
Jules Moore wrote:
PyMOLians and Warren,
I am using Redhat Linux 7.1 to run PyMOL. It seems
to be slightly lagging. Is this just because of the
graphics card? On another computer, a Mac, it runs
quickly and smoothly. Does anyone have any advice on
how to spice up the beauty that is P
| From: "Warren L. DeLano"
| To:
| Date: Thu, 10 Jul 2003 12:40:23 -0700
| Subject: [PyMOL] New Map Formats Coming...
|
| PyMOLers,
|
| In response to user requests, I have added support for BRIX ("O" maps)
| and FLD (AVS Field) map formats in the current development version.
| Are there any ot
Hi Warren,
I was just wondering about a few features that pymol is currently
lacking and if/when you were planning on implementing them.
1- calculation of surface potentials- will this be coming soon?
2- Are you thinking of including any kind of sequence viewer and
sequence alignment tools to
Hi Steven,
Just go to the movies menue and click 'show all states'.
Jules
On Sun, 8 Jun 2003, Stephan Tatzel wrote:
> I have a pdb file containing several states of a Ligand, separated with the
> MODEL and ENDMDL keywords.
> Opening that file, PyMol creates an object and than loads every Model
I agree, what are the exact criteria for fitting in pymol? Currently i'm
using SwissPDB viewer for quick fitting as this is pretty robust and
usually comes up with something sensible. This is satisfactory for
viewing but saving a swiss pdb fit for use in pymol is not. Pymol still
seems to have prob
Wouldn't an easier way to do this be to have a command whereby you tell
pymol to rotate/translate all seperate molecules relative to their own
centres rather than the group or last loaded molecule centre as it does
currently? That way you only need one pymol open and wouldn't need to have
a master/
Hi Dirk
This might actually be a hardware affect rather than a software effect.
The GeForce4
is undoubtably quicker that the GeForce 2 bu there comes a time when the
actual CPU is lagging behind in the amount of data it can pass to the GPU-
this also includes other limitations such as the graphics
be tightly integrated
with the PDB databank for their structural checking procedures prior to
accepting a model it would make sense that this be used as an industrial
standard.
Jules
Jules Jacobsen
MRC Centre for Protein Engineering
Cambridge Laboratory of Molecular Biology
On Thu, 12 Dec 2002
Hi Michael,
If I understand you right you already can do this- make sure that no atoms
are selected first then click on the mouse menu so that when you press
'shift' RotF and MovF are implemented. Then all you have to do is move the
mouse over the molecule you want to move/rotate whilst holding do
Hi Eric,
Try:
set transparency=0.5
show sticks
transparency values from 0-1
hope this helps
Jules
On Sun, 8 Dec 2002, eric hu wrote:
> Hi, I am kinda new to pymol. I wonder if I can show
> both ligand and the surface around it. In other word,
> can I increase the transparency of the surface
Hi Luca,
To create new objects of chains try this:
select R= chain R
this will create an object named R from the atoms of chain R. Where chain
R is specified in the PDB file.
Sorry, i can't help with the Z-plane clipping thing.
Jules
On Fri, 29 Nov 2002, Luca Fenu wrote:
> dear Pymolers,
>
>
Hi Kristl
The problem is that the secondary structure of your protein hasn't been
defined in the PDB file. This is why the cartoon looks ike a tube. What
you need to do is type util.ss into the command line and this will
calculate some sort of secondary structure for you although it's not
that acc
Does anyone know of a way to dock (read move independantly) two or more
molecules in one window? I am aware of the rotate and translate commands
but these are really not quick or easy to use. If there isn't any way of
doing this can i then add this to a wish list of functions for future
releases. T
you can change most of the parameters using set dash_n where n= length,
width, gap, radius. Unfortunately dash_color doesn't exist.
hope this helps
Jules
On Tue, 22 Oct 2002, franck coste wrote:
> Hi,
> I'd like to know if it's possible to change the parameters of the
> DISTANCE command (color,
Have you tried using both left and right mouse buttons at the same time
instead of the middle button?
Jules
On Mon, 14 Oct 2002, J. Evan Sadler wrote:
> I have a microsoft intellimouse explorer, OS 10.2.1, and can't seem to get
> the mouse to function as a three button mouse. I have apparently n
Wed, 3 Jul 2002, Jules Jacobsen wrote:
>
> > Does anyone know how to display an ensemble of NMR structures without the
> > entire ensemble being amalgamated into one big mess?
>
> If you have MODEL entries in the PDB file, PyMOL will automatically
> separate them into separate
Hi,
Does anyone know how to display an ensemble of NMR structures without the
entire ensemble being amalgamated into one big mess?
cheers
Jules
30 matches
Mail list logo
