How can I mutate one residue into another in pymol?
I tried the wizard--> mutagenesis-->
but nothing coming out after done.
I might understand wrong.
Please let me know.
--
Thanks and best regards,
lina
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W
eptor..pdbqt -A checkhydrogens
sh: prepare_receptor4.py: not found
can anyone provide me suggestions?
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Best Regards,
lina
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Thanks for your answering.
I will try.
On Sat, Apr 30, 2011 at 3:43 AM, Harry Jubb wrote:
> There is also something like
> Batch: prepare_receptor4.py -r /cwd/receptor_1.pdb -o
> /cwd/receptor..pdbqt -A checkhydrogens
> sh: prepare_receptor4.py: not found
>
> Dear Lina,
&g
to avoid it or the best way to make it work rather than input
'edit' ?
Thanks,
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lina
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the Z-dimension is other place.
Thanks for any advice,
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lina
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On Tue, Jul 19, 2011 at 10:29 PM, Jason Vertrees
wrote:
> Hi Lina,
>
>> I don't know how to save a NEW.pdb which based on the old one but with
>> different coordinate,
>> do I need reset the axis?
>
> Just go into Editing Mode with the mouse by clicking Mouse
On Wed, Jul 20, 2011 at 5:21 PM, Thomas Holder
wrote:
>> Thanks, but I still failed to get this new pdb.
>>
>> File -- Save molecular -->
>>
>> I wish the present coordinate will be saved as a new pdb after rotation.
>
> I guess with present coordinate you mean what you see on screen. To get this
On Thu, Jul 21, 2011 at 1:21 AM, Thomas Holder
wrote:
> Hi Lina,
>
>>> transform_by_camera_rotation
>>
>> PyMOL>transform_by_camera_rotation
>> Traceback (most recent call last):
>> File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py&qu
On Mon, Jul 25, 2011 at 1:27 AM, Thomas Holder
wrote:
> Hi lina,
>
> lina wrote, On 07/22/11 12:55:
>>
>> Thanks very much for your advice, but I don't know which part is wrong,
>> the new saved one is not the ideal one I wanted, which was supposed to
>> be
nload Logger. Secure your free ArcSight Logger TODAY!
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> Archives:
Hi,
How to add polar/aromaic hydrogen's quickly?
in A-->hydrogen -- only add all hydrogen,
thanks for any suggestions,
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Finally,
On Tue, Sep 6, 2011 at 4:27 PM, Thomas Holder
wrote:
> Hi lina,
>
> to add polar hydrogens, try this:
>
> h_add acceptors or donors
Thanks,
in my situation, is it possible to add hydrogens (polar) one in whole protein,
not consider acceptors or donors,
>
> I don'
On Tue, Sep 6, 2011 at 4:27 PM, Thomas Holder
wrote:
> Hi lina,
>
> to add polar hydrogens, try this:
>
> h_add acceptors or donors
Thanks.
it works for selections,
what if when I use h_add selections
I only want to add one H, not two H
How can I achieve this.
Thanks again.
&
Hi,
such as the atom name as
H01, H03
How can I change it to H1, H3,
Thanks for any suggestions (except modifying the .pdb file).
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Finally
ks.
before I googled, might used poor keyword to search, so did not meet this page.
Thanks again and best regards,.
lina
>
> Best regards,
> Marius
>
> --
> Dr. Marius Retegan
> Postdoctoral Fellow
>
> Département
On Wed, Sep 7, 2011 at 12:02 AM, Thomas Holder
wrote:
> Hi Lina,
>
>> Hope you won't mind this email sent to you directly.
>
> not at all, that made it finally clear what you actually want!
>
>> Here I attached the pdb,
>>
>> which I want to add the ar
users@lists.sourceforge.net/msg06211.html
is helpful for the single one selections,
here I got two.
Thanks for any suggestions,
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On Sun, Sep 11, 2011 at 3:59 AM, Thomas Holder <
spel...@users.sourceforge.net> wrote:
> Hi Lina,
>
> have a look at:
> http://pymolwiki.org/index.**php/Polarpairs<http://pymolwiki.org/index.php/Polarpairs>
>
> it takes two selections and has a state argument.
&g
Hi,
when I tried to set something,
let's say
set stick_radius, 0.5
found not ideal, and I wanna be back to default setting,
how do I check the default settings very quickly.
above just an example, not real case,
Thanks for any suggestions,
--
Best Regards,
Hi,
a quick question,
how can update the ss for all states, not check one by one,
and run dssp and update ...
Thanks for any advice,
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lina
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On Sat, Sep 17, 2011 at 1:01 AM, Thomas Holder <
spel...@users.sourceforge.net> wrote:
> Hi Lina,
>
Hi Thomas,
Thanks for your answering.
>
> as far as I know the secondary structure atom property is not state
> specific, so you cannot assign per state. But you can split s
On Sat, Sep 17, 2011 at 4:03 AM, Thomas Holder <
spel...@users.sourceforge.net> wrote:
> Hi Lina,
>
> >> I can also offer you my own dssp script which works with multiple
> objects, see
> >> attachment. It provides the PyMOL commands "dssp" and "
Hi,
Is it possible to output the sequence roughly following the skeleton of protein
structure?
Or are there some other good way handling it.
I tried aline (seem this name) before and also manually. It's headache to
arrange large molecules.
Thanks for any suggestions.
OL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
>
> --
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> http://p
Hi,
Just a quick Q:
How can I better organize those *.py I mainly obtained from pymol wiki,
not those can be installed by the plugins,
pymol run in different directory each time.
Thanks,
--
Best Regards,
lina
On Mon, Sep 19, 2011 at 12:41 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Hi Lina,
>
> First, download the one-letter and three-letter amino acid converters
> (http://www.pymolwiki.org/index.php/Aa_codes) and run it or copy/paste
> it into PyMOL. It's
On Mon, Sep 19, 2011 at 3:56 PM, Thomas Holder <
spel...@users.sourceforge.net> wrote:
> Hi Lina,
>
>
> Another question here,
>>
>> can I show the whole residue as a ball, and different residues connect by
>> (virtual) bonds.
>>
>
> combine r
Hi,
I tried to zoom in, make it large,
but seems not work, neither,
zoom
zoom complete 1 or 0
zoom center
Thanks for some suggestions,
--
Best Regards,
lina
--
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On Wed, Sep 21, 2011 at 11:02 PM, Thomas Holder <
spel...@users.sourceforge.net> wrote:
> Hi Lina,
>
> if you are looking for a way to "zoom in", use your right mouse button or
> type:
>
Thanks, are there some command is equal to the right mouse button?
just curi
Hi,
how can I get the atoms name (except label)
when I use
select o, name o
not work.
Here I will the .pse file in the following email.
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lina
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Hi,
how can I change the atom such as
H01 to H22 in command
Thanks ahead,
--
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lina
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Hi,
How can I print the small ligand's atoms name quickly, not by label,
just interesting their names,
Thanks ahead,
--
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lina
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All the data continuously generated in your IT infrastructure conta
Hi,
How do I use the history input in the make_ndx prompt,
such as before I input
name 32 A2
name 33 A3
up arrow showed me: > ^[[A
Alt+up arrow showed me: > ^[[1;3A
Just curious,
Thanks,
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Sorry,
send to the wrong list.
Please ignore.
On Sat, Oct 8, 2011 at 11:18 PM, lina wrote:
> Hi,
>
> How do I use the history input in the make_ndx prompt,
>
> such as before I input
>
> name 32 A2
> name 33 A3
>
> up arrow showed me: > ^[[A
> Alt+up
Hi,
The picture in
http://www.pymol.org/
is gorgeous, just wonder how did it produce such purple cloud effect?
Thanks for any hint.
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Why? It c
Hi,
I met the following error after recently update some (other) package.
once start pymol, it would show lines of the same
Setting-Error: type read mismatch (float) -1
later, for every move I took in using it, it would show:
Setting-Error: type read mismatch (int) 667
except those Setting-Er
On Sun, Oct 9, 2011 at 10:50 PM, lina wrote:
> Hi,
>
> I met the following error after recently update some (other) package.
>
> once start pymol, it would show lines of the same
>
> Setting-Error: type read mismatch (float) -1
>
> later, for every move I took
On Oct 10, 2011, at 1:04, Tsjerk Wassenaar wrote:
> Hi Lina,
>
> Can you tell more? What version are you using, what system are you on, do you
> use a .pymolrc, and what exactly do you do?
>
Version 1.4.
Debian amd64
I did use .pymolrc.
Please kindly notice the problem
On Mon, Oct 10, 2011 at 2:58 AM, Tsjerk Wassenaar wrote:
> Hey Lina,
>
> It most likely is a consequence of the update. But the error comes
> from the settings code, so I assumed that you set some settings at
> startup, which brings a .pymolrc in mind. Not loading that file woul
On Mon, Oct 10, 2011 at 2:58 AM, Tsjerk Wassenaar wrote:
> Hey Lina,
>
> It most likely is a consequence of the update. But the error comes
>
Hi Tsjerk,
Right now I downgrade the pymol from 1.4.1-1+b1 to 1.4.1-1. It works.
I was kinda of lazy sometimes, should have carefully che
Hi,
I wish to change
ATOM822 H01 PDB 1 32.103 36.531 -0.203 -0.11 0.02 .296
H
ATOM823 C12 PDB 1 34.140 35.147 -0.218 -0.18 -0.01 .122
C
to:
ATOM822 H01 PDB 1 32.103 36.531 -0.203 -0.11
0.02 H
ATOM823 C12 PDB 1
gt; s/^\(.\{72\}\)/\1/ :: Subsitute the first 72 characters and
>> the following four by the first 72 and four spaces. '\1' refers to the
>> 72 stored characters: \(.\{72\}\}
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>>
>> On Tue
On Tue, Oct 11, 2011 at 4:41 PM, Marius Retegan
wrote:
> Dear Lina,
>
> I don't want to be rude, but you should read this part of a document
> on how to ask questions on a mailing list
> http://catb.org/~esr/faqs/smart-questions.html#before.
> Some of the question that you
On Tue, Oct 11, 2011 at 8:13 PM, Francis E Reyes wrote:
> The column editing mode of vim will do this in a jiffy.
>
> Ctrl-V, select the column(s), hit D.
>
Thanks, very nice. I did not realize that the vim can choose block.
>
> F
>
> On Oct 11, 2011, at 1:59
On Wed, Oct 12, 2011 at 5:04 AM, Peter D Simone wrote:
> I'm having this same problem with PyMOL 1.4.1. Ray tracing doesn't make
> any difference. Changing label_font_id also seems to not affect anything,
> normal or ray traced. They both work on PyMOL 0.99 on Windows.
>
Hmm...
FYI: The PyMOL
On Tue, Oct 18, 2011 at 12:08 AM, Tao-wei Huang wrote:
> Hi all,
>
> I have problems with starting pymol in ubuntu. When I started it from
> terminal, I just received the error message: Segmentation fault. I
> tried googling pymol segmentation fault, but I don't find effective
> information to fix
d Windows 7.
> Maybe I misunderstood your question?
> regards,
Thanks,
> hongbo
>
> On 16.09.2011 5:45, lina wrote:
>
> Hi,
>
> a quick question,
>
> how can update the ss for all states, not check one by one,
>
> and run dssp and update .
Hi,
I went through the pymolwiki and cross this page:
http://www.pymolwiki.org/index.php/Display_CCP4_Maps
I have some questions:
1] do I need generate the map from ccp4
(I have already installed the ccp4i, but seems not easy to know how
to get the map)
2] For small molecular (ligand), the c
On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder
wrote:
> Hi Lina,
>
> do you already have any electron density or reflection file (*.map, *.mtz,
> ...) or do you want to create a "fake" density from your structure? It's not
I don't have the reference electr
On Wednesday 26,October,2011 12:55 AM, Jason Vertrees wrote:
Hi Lina,
1] do I need generate the map from ccp4
(I have already installed the ccp4i, but seems not easy to know how
to get the map)
The CCP4 file is a map. Once the map is loaded into PyMOL you can
choose how you
On Mon, Oct 31, 2011 at 2:21 AM, James Starlight wrote:
> Dear PyMol users!
>
> I want to prepare my pdb structure for MD simulation with gromacs
You may ask in gmx list.
>
> 1- I want to place some CAP groups like ACE or NH2 to N and C termii of 1
> and last residue of my protein, respectyally.
Hi,
a quick question, how to keep the volume during ray.
the volume is here,
but after ray,
it's gone,
what's kinda of special settings I need to take care?
Thanks with best regards,
--
All the data continuously gene
On Tue, Nov 29, 2011 at 11:34 PM, Jason Vertrees
wrote:
> Hi Lina,
>
> set ray_volume, on
Thanks,
is the ray_volume some new feature in latest version?
seems Version 1.4. no ray_volume feature.
Best regards,
>
> Cheers,
>
> -- Jason
>
> On Tue, Nov 29, 2011 at 1
ome unmet dependencies on my box, so I have to stick to 1.4
for a while and will try again in future.
Thanks and best regards,
>
> Thanks,
> David
>
> On Tue, Nov 29, 2011 at 10:34 AM, Jason Vertrees
> wrote:
>> Hi Lina,
>>
>> set ray_volume, on
>>
>>
on a build of the latest open source code in SVN.
>>
>> Thanks,
>> David
>>
>> On Tue, Nov 29, 2011 at 10:34 AM, Jason Vertrees
>> wrote:
>>> Hi Lina,
>>>
>>> set ray_volume, on
>>>
>>> Cheers,
>>>
>>&g
Hi,
suppose I have 201 states,
how can I quick jump to 101 states.
or how can I split the 100 and 101 states out, when I used split_states, protein
it all split out.
Thanks for any suggestions,
Best regards,
--
10 Ti
If you have fink,
you can have an alternative way of installation.
fink install pymol-py27
It works well.
On Wed, Dec 21, 2011 at 4:19 AM, Lauren Porter wrote:
> Pymol 1.3 is still available online, but it doesn't work with any versions
> of python greater than 2.5. If I try to install Pymol
On Tuesday 10,January,2012 09:43 PM, James Starlight wrote:
> Deal all!
>
> I'm intresting about representation of the polarr contacts between
> ligand and protein
>
> 1) Usually I'm ussing Present-> Ligand sites option for that purposes
> but in my current case I'm working with GFP where tree resi
Hi,
I met following error once update some packages days ago.
CmdException Exception in Tk callback
Function: at 0x46fdde8> (type: )
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
return apply(self.fu
Hi,
Surprisingly the pymol menu windows was gone, only the pymol viewer,
any clues?
Thanks,
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ow. do you know any command to
issue the menu window?
Thanks.
>
>
> With the information you provide I'm not sure that anyone can help you.
>
> Best regards,
> Folmer
>
>
> 2013/3/21 lina mailto:lina.lastn...@gmail.com>>
>
> Hi,
>
> Su
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/pymol/__init__.py", line 452,
in launch_gui
sys.modules[self.invocation.options.gui].__init__(self,poll,skin)
TypeError: module.__init__() takes at most 2 arguments (3 given)
-
On Friday 22,March,2013 12:09 PM, lina wrote:
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/pymol/__init__.py", line 452,
> in launch_gui
> sys.modules[self.invocation.options.gui].__init__(self,poll,skin)
> TypeError: module._
The way I did:
1] sudo pymol
PyMol -- > Plugin --> Manage Plugins --> install
install the pymol_dssp_stride.py
2] restart pymol
Plugin--> DSSP & Stride
On Saturday 23,March,2013 11:46 PM, James Starlight wrote:
> Dear PyMOl users!
>
> I've forced with the proble
get those contact
residues output into a file simply, without examine one by one using eyes.
Thanks for any answer,
lina
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Consolidation -- Increasing the use
n output stream: 24
> PyMOL: abrupt program termination.
>
After I installed the fglrx driver, it popped up this issue.
but seems that without driver, the pymol can't get 3D accelerate and the
waiting sometimes so slow.
If anyone has some ideas please let me know.
stler [AMD
Radeon HD 6600M Series]
Debian Squeeze AMD64.
Thanks and best regards,
lina
On Sun, Apr 17, 2011 at 10:51 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Hi Zhao,
>
> The ATI drivers are a bit tricky on Linux. First, can you run
> "glxgears
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