Regards!!
Em sáb, 10 de jun de 2017 às 10:48, Folmer Fredslund
<folm...@gmail.com <mailto:folm...@gmail.com>> escreveu:
Hi João,
Yes and no.
You can not (or only with a lot of to me unnecessary tweaks) make
something like that in PyMOL.
What you should do (
Hi João,
On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9
and "--use-msgpackc=no" I get a working pymol with revision 4170.
Have you tried creating a new user and test pymol from that account?
That should help you identify if it is solely a problem with your own
Dear Ioannis,
On 2016-07-08 09:04, Ioannis Michalopoulos wrote:
> Dear PyMOL users,
>
> I use Kubuntu 14.04. I compiled PyMOL, following some instructions on the web.
> This produced the directory:
>
> /opt/pymol-svn/
>
> and a symbolic link to pymol executable:
>
> /usr/bin/pymol ->
nder them by running PyMOL on the command line like this:
pymol -c script.pml -r ray_scenes.py
Thanks to Jesper Karlsen (off-list) for pushing a bit further with this and
Tsjerk for introducing me to "invocation._argv"
Best regards,
Folmer
2016-02-01 15:19 GMT+01:00 Folmer Fredslund <
GMT+01:00 Folmer Fredslund <folm...@gmail.com>:
> Dear Tsjerk,
>
> Thanks! simply including
> if '-c' in invocation._argv
> in the script works fine for me,
>
> Best,
> Folmer
>
> 2016-01-27 12:43 GMT+01:00 Tsjerk Wassenaar <tsje...@gmail.com>:
&
(running the .pml normally) and also make raytraced png's
when the .pml is being run in commandline mode.
Best regards,
Folmer Fredslund
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check combinations, so it would be matching
> -.*c.* on the elements in _argv.
>
> There probably is a way to check for the GUI directly though.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Jan 27, 2016 at 11:49 AM, Folmer Fredslund <folm...@gmail.com>
> wrote:
/lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
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Dear Annalisa,
Perhaps you should consider installing the nvidia driver instead of using
nouveau?
Venlig hilsen
Folmer Fredslund
Den 07/11/2014 04.07 skrev Annalisa Arcella annalisa.arce...@gmail.com:
Hi All,
I have installed PyMol by terminal
sudo apt-get install pymol
on my Ubuntu14.04
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pressing ESC).
The text looks just fine if bg_color is black.
Does anyone know if this is a feature or a bug?
Best regards,
Folmer
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if this is a feature or a bug?
it's not a feature, for sure. We'll fix that.
OK, sounds great!
Cheers,
Thomas
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Hi Lapolla,
The PyMOL source is available here:
http://sourceforge.net/projects/pymol/
Hope this helps,
Folmer
2014/1/14 Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu
I thought that 1.7 was not free--that you had to pay for it. Not true? If
1.7 is free, could you give me a link? Thank
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understand correctly, what you are doing does not make any sense (I am
a protein crystallographer...)
To the best of my knowledge, what you are trying to do is not possible.
With best intentions,
Folmer
On Sun, Nov 11, 2012 at 5:22 PM, Folmer Fredslund folm...@gmail.comwrote:
Dear Amna
/Autodock_plugin)
by Daniel Seeliger. I would use that.
Hope this helps
Folmer Fredslund
please help
regards
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that the structure is not right. I didn't see much details
though, except that the atom connections seem to be wrong.
Thanks,
Ritu
On 05/23/12, Folmer Fredslund
wrote:
Hi Ritu,
Could you elaborate on some of the ligand structures get completely
messed up when viewed as sticks or lines
On 11/23/2011 01:18 PM, James Starlight wrote:
Thanks Thomas!
Those scripts works fine. Could you tell me if there any way to install
all of those scripts as the pymol plugins ( that I need not to load this
scripts every time when I sttart pymol de novo )?
James
Hi James
Jason Vertrees
your coloured helices as selections you could do
something like:
zoom helix1
pseudoatom labelhelix1
label labelhelix1, Helix 1
The position of the label can be changes using the edit mode (see e.g.
http://pymolwiki.org/index.php/MovieSchool_3#Mouse_Modes)
Hope this helps
Best regards,
Folmer
gray. This is done on the command-line.
You can also use the gui (top right there is a multicolored square
with the letter C, for color) and select many different colors. This
can be done for all or individually for each object/pdb you load.
Hope this helps!
Best regards,
Folmer Fredslund
2011/7
Dear Tassos
2011/4/5 Anastassis Perrakis a.perra...@nki.nl:
Hi -
I am trying to use the script by Thomas Holder, Spectrumany
http://www.pymolwiki.org/index.php/Spectrumany
Very nice that you link to the program you use, but possibly someone
is going to ask about the PyMOL version ;-)
png mymolecule.png
Then do like this
pymol -c example.pml
And you get mymolecule.png
Best regards,
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Best regards,
Folmer Fredslund
2010/10/29 Prince, D Bryan dbryan.pri...@astrazeneca.com:
Dear PyMOL users:
I have been working my way through a tutorial on how to use PyMOL, and
working primarily from the command line. Being somewhat schooled in UNIX, I
ran into a problem and typed help show
regards,
Folmer Fredslund
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strongly advise
you to have a look at ALINE:
http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/
Here you can color the alignment and export the colors to a PyMOL script.
This is at least one way to do it.
Best regards,
Folmer Fredslund
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of them.
# select remove all non A altlocs
remove not (alt ''+A)
# reset the PDB information
alter all, alt=''
taken from:
http://pymolwiki.org/index.php/Property_Selectors#Alternate_Locations
I hope this helps.
Folmer Fredslund
earlier on, but this has
worked nicely for me everytime I've used it.
You don't mention what OS you are using, but the pwd command will give
you your current path (at least on linux) and it should be relatively
easy to find the output file afterwards.
Best regards,
Folmer Fredslund
Thanks
Hi John,
Please be aware that there is a difference between a python script
that allows you to define some functionality you can use in PyMOL
(usually with a .py ending), and a script that will read coordinates
and do some PyMOL stuff (which I usually apply a .pml ending).
So, what I think is
– sequence function. Is
there any script to/load/select/highlight specific molecule from one object?
Please reply back
I don't think you need a script to do this.
Look into this link
http://pymolwiki.org/index.php/States
and I think you will understand.
Best regards,
Folmer Fredslund
Hi Carsten,
Is this what you are looking for?
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html
Best regards,
Folmer Fredslund
2009/9/24 Schubert, Carsten [PRDUS] cschu...@its.jnj.com:
Hi,
Does anyone know how to get a hold of the viewport dimensions from within
that will work on
your normal linux distribution would make me happy.
Best regards,
Folmer Fredslund
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-Original Message-
From: Folmer Fredslund [mailto:folm...@gmail.com]
Sent: Thursday, July 09, 2009 6:33 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Label coordinates
Dear all,
Is there a way to get the coordinates for manually shifted
Dear all,
Is there a way to get the coordinates for manually shifted labels?
What I want to do is to include the label positions in my script
instead of moving the labels each time I update my figure.
Thanks in advance,
Folmer Fredslund
found something like this:
http://pymolwiki.org/index.php/Get_Area
I hope this is what you are looking for?
Best regards,
Folmer Fredslund
Dear Abhinav
2009/3/13 Abhinav Kumar abhin...@slac.stanford.edu:
Hi,
I need to make figures in tiff format with at least 600 dpi resolution
as required by the journal. The default resolution in Pymol figures is
72. Is there a simple way to increase the resolution (and save it in
tiff
Hi Massimo
2008/10/13 Massimo Heitor massimohei...@gmail.com:
I am looking at the residue sequence for a protein that I'm studying for a
class and I have a few questions.
I understand the regular amino acid codes (CYS, ARG, LEU, etc...).
What is NAG? I see one sequence NAG NAG NAG NAG
=/
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try the help function:
help load
help isomesh
help color
hope this helps
On Fri, Sep 26, 2008 at 5:42 PM, Folmer Fredslund folm...@gmail.com wrote:
2008/9/26 Jhon Thomas jhon1.tho...@gmail.com:
Hello all pymol users
I am new to pymol and trying to open a .xplor map file in pymol to get
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