Dear All,
in the pymol default color based on b-factor spectrum, will you please tell me
how pymol determines the specific color based on the b-factor leve? For
example, in which scope of b-factors the protein part would be in red and in
which scope of b-factors the protein part would be in
Dear All，
Is any simple method by pymol we can color residues based on the residue
conservation?
Best regards.
Smith--
Presto, an open source distributed SQL query engine for big data, initially
developed by
Dear All,
If there is a cleft (looks like letter "C", which is not totally closed) formed
by 2 subunits, will you please tell me by pymol how to measure the volume of
the cleft formed?
Best regards.
Smith--
Dear All,
Pymol has the function to measure the distance betweeen 2 atoms. In addition,
if 2 hydrophobic residues are close enough, there will be hydrophobic
interactions betweem them. But will you please tell me how to measure the
distance between 2 hydrophobic residues by pymol?
Best
to do, or something more complex? Could
you provide more details about your problem?
Cheers,
Osvaldo.
On Wed, Jul 8, 2015 at 12:33 PM, Smith Liu smith_liu...@163.com wrote:
Dear All,
Pymol has the function to measure the distance betweeen 2 atoms. In addition,
if 2 hydrophobic residues
Dear All,
Will you please tell me how to process so that a long helix will be shown as a
long rod (pr long bar） by pymol?
Best regards.
Smith--
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Dear All,
Suppose a protein contains 2 subunits. Will you please introduce to me by pymol
how to represent helix in one subunit as cylindrical helix, and helix in
another subunit as regular helix?
Best regards.
Dear All，
For my windows version of pymol, I cannot locate the surface function under the
setting button. Will you please tell me how can I make my surface cavity pocket
function workable?
Best regards.
Smith--
Dear All,
Suppose I have a protein complex displayed by pymol, is any way pymol can
separate its subunits in a fixed and beautiful patten of arrangement in the
pymol window?
If the subunit contains may alpha helices too dense for display each helix
visibly by pymol, is any way pymol can
Dear All,
Is any way by pymol we color the protein based on residue sequence, for example
from red starting resi 1 gradually to blue at residue 1000?
Smith--
Go from Idea to Many App Stores Faster with Intel(R) XDK
Dear All,
Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb and
have only A.pdb displayed?
Smith
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sages
From: "Smith Liu" <smith_liu...@163.com>
Date: 2015-12-10 22:27:03
To: "pymol-users@lists.sourceforge.net" <pymol-users@lists.sourceforge.net>
Subject: [PyMOL] on load new B-factors
Dear All,
When I use "loadBfacts mol, [startaa, [source, [v
Dear All,
When I use "loadBfacts mol, [startaa, [source, [visual Y/N]]]", I meet the
following error message,
"File "Some_directory\parse.py", line 250, in parse
self.result=app(layer.kw[0],layer.args,layer.kw_args)
File "loadBfacts.py",line 16, in loadBfacts
obj=cmd.get_object_list(mol)[0]
e output into a txt file for later use. The output set_view command
will return the window to the same camera settings
Shane
Shane Caldwell
McGill University
On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smith_liu...@163.com> wrote:
Dear All,
Suppose the original PDB was not oriented.
Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smith_liu...@163.com> wrote:
Dear Shane,
get_view is a nice command. Is any way to change the original PDB based on what
we get by set_view to get the new pdb?
Smith
At 2015-11-26 03:54:32, "Shane Caldwell" <shane.caldwel..
m files for pymol, which will depend on your operating system and
architecture.
Shane
Shane Caldwell
McGill University
On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smith_liu...@163.com> wrote:
Dear All，
Once a molecule displayed in pymol, first I input command "orient"
ab the view, save it
somewhere, and then load it. You can’t code a view change within the PDB.
On Nov 27, 2015, at 11:27 PM, Smith Liu <smith_liu...@163.com> wrote:
Dear Jordan,
My purpose is, once you move a molecule in pymol, I want to save a new pdb,
when we open the new pdb, pymol wil
/Transform_selection there is
another script.
I do not know how to use this scripts to realize my purpose.
Smith
At 2015-11-28 15:07:18, "Jordan Willis" <jwillis0...@gmail.com> wrote:
very possible, can you send me the script?
On Nov 27, 2015, at 10:58 PM, Smith Liu <s
running
find ~/ -name “newpdb.pdb”
On Nov 27, 2015, at 9:08 PM, Smith Liu <smith_liu...@163.com> wrote:
Dear All,
Osvaldo is new here for this question, so I repeat it a little. By pymol I open
a pdb and orient it and I want to save the oriented pdb. First I input command
"ori
Dear All,
Will you please show me how to display an axis of a subunit or a domain by
pymol?
Smith--
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Dear All,
Suppose the original PDB was not oriented. Once we have it oriented by pymol,
is any way we can save the new PDB oriented?
Smith--
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users
for example here:
>https://sourceforge.net/p/pymol/mailman/message/27824450/
>
>Hope that helps.
>
>Cheers,
> Thomas
>
>On 28 Nov 2015, at 02:52, Jordan Willis <jwillis0...@gmail.com> wrote:
>
>> Yes, but what you are describing, saving a new view is your purp
Dear All,
Is any way we can colour the molecule by pymol based on the y values in the z y
z coordinates, so that we can view easily the residues (or atoms) with
equivalent position in the primary sequence but has a y-axis shift in the 3-D
structure?
Smith
% again, replace prot with your pymol object name
On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu <smith_liu...@163.com> wrote:
Dear All,
Is any way we can colour the molecule by pymol based on the y values in the z y
z coordinates, so that we can view easily the residues (or atom
Dear All,
If I want to use a pymol script, for example the script on centroid, will you
please tell me how to download the corresponding script from the pymol website?
Smith--
Dear All,
When I run the centroid.py, I have the following error message: "NameError:
global name 'move' is not defined". My centroid.py script downloaded (have I
misdone or miseddited something?) is as following. Will you please tell me how
to solve the error message issue?
Smith
---
Dear All,
Once I have displayed a tetramer PDB by pymol, is any way I can get the central
axis of the tetramer and display it? Is any way I can get the cross-section of
the tetramer (perpendicular to the central axis) and display it? If the
tetramer is asymmetric, then how to get the central
Dear All,
In http://pymolwiki.org/index.php/Modeling_and_Editing_Structures there is
"save_transformed.py". Will you please show me how to use this script? There is
no problem to do "run save_transformed.py". But after click that command, how
to get and save the transformed pdb file?
Dear All,
Will you please tell me the meaning of "async"in pymol script?
Smith--
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Dear All,
Suppose my protein A PDB contains chian A, B, C, D, and my protein B PDB
contains chain E, F, G, H, I want to align all protein A without chain D, with
all protein B without chain H, will you please tell me the align command?
Dear All,
Will you please tell me the pymol command for calculation of the contact
surface between subunits of a protein complex? And what is the command for
calculation of the cavity volume surrounded by the protein complex?
Dear All,
Will you please tell me the command to calculate the contact surface area
between 2 sub-units in the protein complex? Will you please also tell me the
command to calculate the angle in degree between 2 domains in a sub-unit?
Smith
Dear All,
Today as every day I do, I align 2 pdb files by pymol. After a moment, I find
the aligned 2 molecules start to rock back and forth continuously in the pymol
window (from about 45 degree to -45 degree). Today I never used the rotate or
rock command.
Will you please explain why this
Dear All,
I have a symmetry problem, which I hope I can get your help.
For both PDB 2zan and 2zam, they are for the same protein, they conformation
were similar except that 2zam was apo and 2zam was ATP binding. 2zaz was got by
soaking the 2zam crystal with ATP. Both were P65 space group
the mate
arrangement, as in the remark added PDB for 2zan fitted to 2zam? Why after
pymol alignment, the same remark information leads to different mates
arrangement?
I am looking forward to getting a reply from you.
Smith
Forwarding messages
From: "Smith Liu"
Dear All,
Once load a pdb with space group P 65 by pymol, I click action then generate
symmetry mates within 4 A, I find in the pymol windows, there were 7 molecules
displayed (one was the original pdb) . Here I want to ask, in the 7 molecules
displayed, all the other 6 molecules were really
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