Dear Tassos
2011/4/5 Anastassis Perrakis :
> 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 ;-)
> When I import
ing 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 Fr
have 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
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 V
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t 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 ligan
ity, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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utodock_plugin)
by Daniel Seeliger. I would use that.
Hope this helps
Folmer Fredslund
>
> please help
>
> regards
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps f
;
If I 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 wrote:
>
>>
eforge.net)
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M
are further than 5
> angstroms away from the atom I specified in the select command are
> returned. Is there some difference in the way "select within" and
> "cmd.distance", or have a confused some of the commands?
>
> Any suggestions are appreciated
>
>
orge.net)
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racts and
> register
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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)
> 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 you.
>
trk
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when 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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t fine if bg_color is black.
> >
> > Does anyone know if this is a feature or a bug?
>
> it's not a feature, for sure. We'll fix that.
>
>
OK, sounds great!
> Cheers,
> Thomas
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, I
l.
>
>
>
>
>
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Hi
Small correction to Gianlucas suggestion
">" will direct the output to a file, overwriting the contents
">>" will direct the output to a file, appending the contents
Venlig hilsen
Folmer Fredslund
Den 05/09/2014 19.16 skrev "Gianluca Santoni" :
> Do
ing list (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" :
> Hi All,
> I have installed PyMol by terminal
>
> sudo apt-get install pymol
>
> on m
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Give your users amazing mo
them (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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to 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
> wrote:
>
>> Hi there,
>>
14:07 GMT+01:00 Folmer Fredslund :
> 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 :
>
>> Hey Folmer,
>>
>>
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 :
ize is a trip for two to an Open Source event anywhere in the world
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i.org/index.php/Load)
or when using PyMOL try the help function:
help load
help isomesh
help color
hope this helps
> On Fri, Sep 26, 2008 at 5:42 PM, Folmer Fredslund wrote:
>>
>> 2008/9/26 Jhon Thomas :
>> > Hello all pymol users
>> >
>> > I am new
Hi Massimo
2008/10/13 Massimo Heitor :
> 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" (resisting off-topic joke
Dear Abhinav
2009/3/13 Abhinav Kumar :
> 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 format)?
> Alternatively, I
something like this:
http://pymolwiki.org/index.php/Get_Area
I hope this is what you are looking for?
Best regards,
Folmer Fredslund
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
ot;to do" item.
>
> Cheers,
> Warren
>
>> -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
>>
&g
work on
your normal linux distribution would make me happy.
Best regards,
Folmer Fredslund
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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] :
> Hi,
>
> Does anyone know how to get a hold of the viewport dimensions from within a
&g
Dear Andrea,
Yes it is.
http://pymolwiki.org/index.php/Select
mvh
Folmer
2009/10/22 andrea carotti :
> Hi again,
> and thanks for the support.
> I have another question. I would like to select molecules inside my pdb.
> I've seen that using the mouse selection (activating molecules in the
> rig
y – 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
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 hap
e log again with log_close.
I am not sure if this is what you found 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
se PyMOL to delete the alternate conformations thus, just retaining
one of them.
# select & remove all non A altlocs
remove not (alt ''+A)
# reset the PDB information
alter all, alt=''
taken from:
http://pymol
ongly 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
>
> Thanks in advance
>
> --
> Best Regar
many different formats.
Best regards,
Folmer Fredslund
> --
> Thank you and Regards,
>
> Vivek
>
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helps!
Best regards,
Folmer Fredslund
2010/10/29 Prince, D Bryan :
> 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 >
this when you run it.
An example file (example.pml)
load mymolecule.xyz
zoom residue 45-60
png mymolecule.png
Then do like this
pymol -c example.pml
And you get mymolecule.png
Best regards,
--
Folmer Fredslund
--
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 -> /opt/pymol-
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
accoun
s,
Folmer
Regards!!
Em sáb, 10 de jun de 2017 às 10:48, Folmer Fredslund
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 (IMHO) is to make a
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