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')
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,
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
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()
if entry not in id:
cmd.do('align %s, %s\n'%(entry
Subject: 0.98 beta 18 Selecting
Date: Tue, 23 Nov 2004 11:05:01 +
From: Jules Jacobsen jo...@hermes.cam.ac.uk
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
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
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
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
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 have
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
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
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
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
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
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
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