[PyMOL] Fw: symmetry and pdb remark
Dear All, Here I make my question much clear. 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 However by getting the mate coordinates of 2zam and 2zan by Coot or Chimera, you will find their 6 mates arrange differently ( viewed by Chimera or by Pymol). For 2zan, the 6 mates were separated with each other, but for 2zam the 6 mates were connected. Can you explain to me why their 6 mates arrange differently? What is more, by pymol I align 2zan onto 2zam, and I get the PDB for 2zan fitted to 2zam (no any text information from the pdb file left after pymol saving, except the coordinates). Then I add all the text information from 2zan (except the coordinates) to the PDB for 2zan fitted to 2zam, and then I get the mate coordinates by Chimera or Coort and then view the mates got by Chimera or Coot for the text information added PDB for 2zan fitted to 2zam, I find the 6 mates arrange like 2zam, rather like 2zan (viewed by Chimera). Thus, will you please explain which remark information decide 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" <smith_liu...@163.com> Date: 2017-02-02 12:06:16 To: pymol-users@lists.sourceforge.net Subject: symmetry and pdb remark 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 However by getting the mates of 2zam and 2zan, you will find their 6 mates arrange differently ( viewed by Chimera). Can you explain to me why their 6 mates arrange differently? What is more, by pymol I align 2zan onto 2zam, and I get the PDB for 2zan fitted to 2zam (no any remark information left after pymol saving). Then I add all the remark information from 2zan to the PDB for 2zan fitted to 2zam, and then I view the mates for the remark added PDB for 2zan fitted to 2zam, I find the 6 mates arrange like 2zam, rather like 2zan (viewed by Chimera). Thus, will you please explain which remark information decide 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-- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] symmetry and pdb remark
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 However by getting the mates of 2zam and 2zan, you will find their 6 mates arrange differently ( viewed by Chimera). Can you explain to me why their 6 mates arrange differently? What is more, by pymol I align 2zan onto 2zam, and I get the PDB for 2zan fitted to 2zam (no any remark information left after pymol saving). Then I add all the remark information from 2zan to the PDB for 2zan fitted to 2zam, and then I view the mates for the remark added PDB for 2zan fitted to 2zam, I find the 6 mates arrange like 2zam, rather like 2zan (viewed by Chimera). Thus, will you please explain which remark information decide 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-- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on the generate symmetry mates function
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 the P 65 mates molecules? Why the original pdb input did not exist as 1 of the 6 mates molecules? I am looking forward to getting a reply from you. Smith-- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] a special phenomenon on using pymol
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 phenomenon can occur? Smith-- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on the alignment command
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? Smith-- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on contact surface and domain angle
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 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] calculation of the contact surface between subunits
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? Smith-- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to close displaying a molecule
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 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Fw: on load new B-factors
in addition, now it occurs "[Errno 2] No such file or directory: 'newBfactors.txt', although I have specified the directory of 'newBfactors.txt'. It seems this error message has no relation with which directory I put 'newBfactors.txt'. Any advice? Smith Forwarding messages 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, [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] TypeError: ‘NoneType' object is unsubscriptable" Will you please tell me how to clear this error? In addition, for the newBfactors.txt, each line was for one residue rather than for the one atom, right? If my PDB starting at resi 100 ending at resi 400, the newBfactors.txt should start at resi 1 and end at resi 400 in order to have pymol color the whole molecule correctly based on new B-factors, am I right or not? Smith -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on load new B-factors
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] TypeError: ‘NoneType' object is unsubscriptable" Will you please tell me how to clear this error? In addition, for the newBfactors.txt, each line was for one residue rather than for the one atom, right? If my PDB starting at resi 100 ending at resi 400, the newBfactors.txt should start at resi 1 and end at resi 400 in order to have pymol color the whole molecule correctly based on new B-factors, am I right or not? Smith -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] color based on residue sequence
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 Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to separate the complex subunits
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 extend the full subunit so that each helix can be easily visible in pymol, without breaking the whole subunit from N-terminal to C-terminal into separated and disjoined parts? Smith-- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on axis of the subunit
Dear All, Will you please show me how to display an axis of a subunit or a domain by pymol? Smith-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] save_transformed.py
Dear Thomas,
I do not know I still do something wrong.
First I load a PDB in pymol, then I input orient (with orient input the
molecule really moved significantly in display), then I input
transform_by_camera_rotation, then I input save /tmp/withneworientation.pdb,
the withneworientation.pdb was really saved, but the newly saved
withneworientation.pdb has the all atom orientations (x,y,z) exactly same as
those of the original PDB I initially input to the pymol for the process I
obtained the withneworientation.pdb.
Smith
At 2015-11-30 08:08:52, "Thomas Holder" <thomas.hol...@schrodinger.com> wrote:
>Hi Smith, and everybody who tried to help you so far,
>
>Short answer: copy and paste this into the PyMOL command line, it will save
>the view-transformed object to "transformed.pdb" in your home folder.
>
>cv=list(cmd.get_view())
>cmd.transform_selection("all", \
> cv[0:3]+[0.0]+ \
> cv[3:6]+[0.0]+ \
> cv[6:9]+[0.0]+ \
> cv[12:15]+[1.0], transpose=1)
>cmd.save('~/transformed.pdb')
>
>To comment on the many emails that have been posted so far:
>
>1) I think you haven't used the script correct. Instead of "run
>save_trannsforme.py all, newpdb.pdb", you have to do "run
>save_transformed.py", followed by "save_transformed all, newpdb.pdb"
>2) The script is actually wrong (missing transpose=1)
>3) A correct solution has been posted 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 purpose. All
>> orient does is move the camera. It does not do anything to the x,y,z
>> coordinates of the PDB.
>>> On Nov 27, 2015, at 11:49 PM, Smith Liu <smith_liu...@163.com> wrote:
>>>
>>> Dear Jordan,
>>>
>>> To save a new view is not my purpose, my purpose is to save a new set of
>>> PDB. For example， if the original PDB does not orient well by pymol by
>>> default, first I input "orient", and I want to save a set of new pdb, when
>>> I display by pymol the new pdb, it will display as "oriented“. Is any way
>>> we can get this oriented pdb?
>>>
>>> Smith
>>>
>>>
>>> At 2015-11-28 15:37:10, "Jordan Willis" <jwillis0...@gmail.com> wrote:
>>> get view takes in camera coordinates. You can’t open a PDB and it have know
>>> anything about the camera view. You will have to grab 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 will display the new position as
>>>> default.
>>>>
>>>> The script is
>>>>
>>>> "# Adds the command save_transformed
>>>> # Usage: save_transformed object, file
>>>> def save_transformed(object,file):
>>>> m = cmd.get_view(0)
>>>> ttt = [m[0], m[1], m[2], 0.0,
>>>>m[3], m[4], m[5], 0.0,
>>>>m[6], m[7], m[8], 0.0,
>>>>0.0, 0.0, 0.0, 1.0]
>>>> cmd.transform_object(object,ttt)
>>>> cmd.save(file,object)
>>>> cmd.extend('save_transformed',save_transformed)"
>>>>
>>>> shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures
>>>>
>>>> Here I notice that once load a pdb, you move it a little, then you input
>>>> "get_view", you will get the matrix like
>>>> 0.448818117, 0.886667669, -0.111277729
>>>> -0.889764965, 0.454960942, 0.036454394
>>>>
>>>> which should be the m[0] to m[5] in the above script.
>>>>
>>>> In addition, in http://www.pymolwiki.org/index.php/Transform_odb, there is
>>>> also a transcript. For matrix it uses *.odb file. Is this *.odb same as
>>>> the get_view matrix, if not, can we convert get_view matrix to *.odb?
>>>>
>>>> Besides, in http://www.pymolwiki.org/index.php/Transform_selection there
>>>> is another script.
>>>>
>>>> I do not know how to use this scripts to realize my purpose.
>>>>
>>>> Smit
Re: [PyMOL] on PDB
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
"orient" after load the pdb, then I input command "run save_trannsforme.py all,
newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find
newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My
pymol is Linux Open-Source PyMOL 1.6.X.
I am looking forward to getting a reply from you on how to get the oriented
pdb, which should be different from the original PDB I load.
Smith
At 2015-11-28 00:44:07, "Shane Caldwell" <shane.caldwel...@gmail.com> wrote:
Hi Smith,
It will be in whatever folder pymol is launched from. If you launched pymol
from a specific place, it will be that folder. If not, it might be in the
system 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", then I
input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the
oriented newpdb.pdb.
Will you please show me how to get the oriented newpdb.pdb?
Smith
At 2015-11-26 18:58:48, "Spencer Bliven" <spencer.bli...@gmail.com> wrote:
Smith–
The code is intended to be saved to a file ("save_transformed.py") and then
loaded into pymol using `run /path/to/save_transformed.py`. There's some
general info on running pymol scripts: Simple_ScriptingRunning_Scripts
The script defines a new command which can be run e.g. `save_transformed
, `. You don't have to replace anything in the script yourself.
Note that the save_transformed command modifies the object it's run on, so you
might want to run it on a backup copy by first calling `create _backup,
`
-Spencer
On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smith_liu...@163.com> wrote:
Dear All,
For get view, we get something like
set_view (\
0.999876618, -0.000452542, -0.015699286,\
0.000446742,0.99821, -0.000372844,\
0.015699454,0.000365782,0.999876678,\
0.0,0.0, -150.258514404,\
11.842411041, 20.648729324,8.775371552,\
118.464958191, 182.052062988,0.0 )
For save trasformed pdb file, we need sonething like
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
Will you please show me how to replace m[0], m[1] from what we get by
get_view? Which item is which item?
In addition, for the save_transformed.py, the last sentence is
"cmd.extend('save_transformed',save_transformed)". Should we replace the second
save_transformed with something, for example *.pdb? Ortherwise how to get the
output modified PDB?
I am looking forward to getting a reply from you.
Smith
At 2015-11-26 14:24:15, "Andreas Forster" <docandr...@gmail.com> wrote:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
Andreas
On 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...@gmail.com> wrote:
Hi Smith,
You can type
>get_view
and copy the 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. Once we have it oriented by pymol,
is any way we can save the new PDB oriented?
Smith
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Re: [PyMOL] save_transformed.py
Dear Jordan,
To save a new view is not my purpose, my purpose is to save a new set of PDB.
For example， if the original PDB does not orient well by pymol by default,
first I input "orient", and I want to save a set of new pdb, when I display by
pymol the new pdb, it will display as "oriented“. Is any way we can get this
oriented pdb?
Smith
At 2015-11-28 15:37:10, "Jordan Willis" <jwillis0...@gmail.com> wrote:
get view takes in camera coordinates. You can’t open a PDB and it have know
anything about the camera view. You will have to grab 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 will display the new position as default.
The script is
"# Adds the command save_transformed
# Usage: save_transformed object, file
def save_transformed(object,file):
m = cmd.get_view(0)
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
cmd.transform_object(object,ttt)
cmd.save(file,object)
cmd.extend('save_transformed',save_transformed)"
shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures
Here I notice that once load a pdb, you move it a little, then you input
"get_view", you will get the matrix like
0.448818117, 0.886667669, -0.111277729
-0.889764965, 0.454960942, 0.036454394
which should be the m[0] to m[5] in the above script.
In addition, in http://www.pymolwiki.org/index.php/Transform_odb, there is also
a transcript. For matrix it uses *.odb file. Is this *.odb same as the
get_view matrix, if not, can we convert get_view matrix to *.odb?
Besides, in http://www.pymolwiki.org/index.php/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 <smith_liu...@163.com> wrote:
By Jordan,
by
find ~/ -name “newpdb.pdb” or by
find / -name “newpdb.pdb”
still does not work. Is any possibility the original "save_transformed.py" does
not work?
Smith
At 2015-11-28 13:11:25, "Jordan Willis" <jwillis0...@gmail.com> wrote:
try 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
"orient" after load the pdb, then I input command "run save_trannsforme.py all,
newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find
newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My
pymol is Linux Open-Source PyMOL 1.6.X.
I am looking forward to getting a reply from you on how to get the oriented
pdb, which should be different from the original PDB I load.
Smith
At 2015-11-28 00:44:07, "Shane Caldwell" <shane.caldwel...@gmail.com> wrote:
Hi Smith,
It will be in whatever folder pymol is launched from. If you launched pymol
from a specific place, it will be that folder. If not, it might be in the
system 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", then I
input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the
oriented newpdb.pdb.
Will you please show me how to get the oriented newpdb.pdb?
Smith
At 2015-11-26 18:58:48, "Spencer Bliven" <spencer.bli...@gmail.com> wrote:
Smith–
The code is intended to be saved to a file ("save_transformed.py") and then
loaded into pymol using `run /path/to/save_transformed.py`. There's some
general info on running pymol scripts: Simple_ScriptingRunning_Scripts
The script defines a new command which can be run e.g. `save_transformed
, `. You don't have to replace anything in the script yourself.
Note that the save_transformed command modifies the object it's run on, so you
might want to run it on a backup copy by first calling `create _backup,
`
-Spencer
On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smith_liu...@163.com> wrote:
Dear All,
For get view, we get something like
set_view (\
0.999876618, -0.000452542, -0.015699286,\
0.000446742,0.99821, -0.000372844,\
Re: [PyMOL] save_transformed.py
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 will display the new position as default.
The script is
"# Adds the command save_transformed
# Usage: save_transformed object, file
def save_transformed(object,file):
m = cmd.get_view(0)
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
cmd.transform_object(object,ttt)
cmd.save(file,object)
cmd.extend('save_transformed',save_transformed)"
shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures
Here I notice that once load a pdb, you move it a little, then you input
"get_view", you will get the matrix like
0.448818117, 0.886667669, -0.111277729
-0.889764965, 0.454960942, 0.036454394
which should be the m[0] to m[5] in the above script.
In addition, in http://www.pymolwiki.org/index.php/Transform_odb, there is also
a transcript. For matrix it uses *.odb file. Is this *.odb same as the
get_view matrix, if not, can we convert get_view matrix to *.odb?
Besides, in http://www.pymolwiki.org/index.php/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 <smith_liu...@163.com> wrote:
By Jordan,
by
find ~/ -name “newpdb.pdb” or by
find / -name “newpdb.pdb”
still does not work. Is any possibility the original "save_transformed.py" does
not work?
Smith
At 2015-11-28 13:11:25, "Jordan Willis" <jwillis0...@gmail.com> wrote:
try 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
"orient" after load the pdb, then I input command "run save_trannsforme.py all,
newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find
newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My
pymol is Linux Open-Source PyMOL 1.6.X.
I am looking forward to getting a reply from you on how to get the oriented
pdb, which should be different from the original PDB I load.
Smith
At 2015-11-28 00:44:07, "Shane Caldwell" <shane.caldwel...@gmail.com> wrote:
Hi Smith,
It will be in whatever folder pymol is launched from. If you launched pymol
from a specific place, it will be that folder. If not, it might be in the
system 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", then I
input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the
oriented newpdb.pdb.
Will you please show me how to get the oriented newpdb.pdb?
Smith
At 2015-11-26 18:58:48, "Spencer Bliven" <spencer.bli...@gmail.com> wrote:
Smith–
The code is intended to be saved to a file ("save_transformed.py") and then
loaded into pymol using `run /path/to/save_transformed.py`. There's some
general info on running pymol scripts: Simple_ScriptingRunning_Scripts
The script defines a new command which can be run e.g. `save_transformed
, `. You don't have to replace anything in the script yourself.
Note that the save_transformed command modifies the object it's run on, so you
might want to run it on a backup copy by first calling `create _backup,
`
-Spencer
On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smith_liu...@163.com> wrote:
Dear All,
For get view, we get something like
set_view (\
0.999876618, -0.000452542, -0.015699286,\
0.000446742,0.99821, -0.000372844,\
0.015699454,0.000365782,0.999876678,\
0.0,0.0, -150.258514404,\
11.842411041, 20.648729324,8.775371552,\
118.464958191, 182.052062988,0.0 )
For save trasformed pdb file, we need sonething like
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
Will you please show me how to replace m[0], m[1] from what we get by
get_view? Which item is which item?
In addition, for the save_transformed.py, the last sentence is
"cmd.extend('save_transformed',save_transformed)". Should we replace the second
save_transformed with something, for example *.pdb? Ortherwise how to get the
output modified PDB?
I am l
[PyMOL] save_transformed.py
By Jordan,
by
find ~/ -name “newpdb.pdb” or by
find / -name “newpdb.pdb”
still does not work. Is any possibility the original "save_transformed.py" does
not work?
Smith
At 2015-11-28 13:11:25, "Jordan Willis" <jwillis0...@gmail.com> wrote:
try 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
"orient" after load the pdb, then I input command "run save_trannsforme.py all,
newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find
newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My
pymol is Linux Open-Source PyMOL 1.6.X.
I am looking forward to getting a reply from you on how to get the oriented
pdb, which should be different from the original PDB I load.
Smith
At 2015-11-28 00:44:07, "Shane Caldwell" <shane.caldwel...@gmail.com> wrote:
Hi Smith,
It will be in whatever folder pymol is launched from. If you launched pymol
from a specific place, it will be that folder. If not, it might be in the
system 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", then I
input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the
oriented newpdb.pdb.
Will you please show me how to get the oriented newpdb.pdb?
Smith
At 2015-11-26 18:58:48, "Spencer Bliven" <spencer.bli...@gmail.com> wrote:
Smith–
The code is intended to be saved to a file ("save_transformed.py") and then
loaded into pymol using `run /path/to/save_transformed.py`. There's some
general info on running pymol scripts: Simple_ScriptingRunning_Scripts
The script defines a new command which can be run e.g. `save_transformed
, `. You don't have to replace anything in the script yourself.
Note that the save_transformed command modifies the object it's run on, so you
might want to run it on a backup copy by first calling `create _backup,
`
-Spencer
On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smith_liu...@163.com> wrote:
Dear All,
For get view, we get something like
set_view (\
0.999876618, -0.000452542, -0.015699286,\
0.000446742,0.99821, -0.000372844,\
0.015699454,0.000365782,0.999876678,\
0.0,0.0, -150.258514404,\
11.842411041, 20.648729324,8.775371552,\
118.464958191, 182.052062988,0.0 )
For save trasformed pdb file, we need sonething like
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
Will you please show me how to replace m[0], m[1] from what we get by
get_view? Which item is which item?
In addition, for the save_transformed.py, the last sentence is
"cmd.extend('save_transformed',save_transformed)". Should we replace the second
save_transformed with something, for example *.pdb? Ortherwise how to get the
output modified PDB?
I am looking forward to getting a reply from you.
Smith
At 2015-11-26 14:24:15, "Andreas Forster" <docandr...@gmail.com> wrote:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
Andreas
On 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...@gmail.com> wrote:
Hi Smith,
You can type
>get_view
and copy the 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. Once we have it oriented by pymol,
is any way we can save the new PDB oriented?
Smith
--
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Re: [PyMOL] on PDB
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...@gmail.com> wrote: Hi Smith, You can type >get_view and copy the 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. 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 amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551=/4140 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] on PDB
Dear All,
For get view, we get something like
set_view (\
0.999876618, -0.000452542, -0.015699286,\
0.000446742,0.99821, -0.000372844,\
0.015699454,0.000365782,0.999876678,\
0.0,0.0, -150.258514404,\
11.842411041, 20.648729324,8.775371552,\
118.464958191, 182.052062988,0.0 )
For save trasformed pdb file, we need sonething like
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
Will you please show me how to replace m[0], m[1] from what we get by
get_view? Which item is which item?
In addition, for the save_transformed.py, the last sentence is
"cmd.extend('save_transformed',save_transformed)". Should we replace the second
save_transformed with something, for example *.pdb? Ortherwise how to get the
output modified PDB?
I am looking forward to getting a reply from you.
Smith
At 2015-11-26 14:24:15, "Andreas Forster" <docandr...@gmail.com> wrote:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
Andreas
On 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...@gmail.com> wrote:
Hi Smith,
You can type
>get_view
and copy the 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. Once we have it oriented by pymol,
is any way we can save the new PDB oriented?
Smith
--
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[PyMOL] on PDB
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 amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on save_transformed.py
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? Smith-- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on PDB display and calculation
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 axis and cross-section？ Smith -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on async
Dear All, Will you please tell me the meaning of "async"in pymol script? Smith-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on using pymol scripts
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-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] what is wrong on my using centroid.py
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
---
See more here: http://www.pymolwiki.org/index.php/centroid
DESCRIPTION
get the centroid (geometric center) of a selection or move selection
to the origin.
ARGUMENTS
selection = string: a valid PyMOL selection {default: all}
center = 0 or 1: if center=1 center the selection {default: 0}
returns: centroid: [ x, y, z ]
SEE ALSO
get_extent, get_position, http://pymolwiki.org/index.php/Center_Of_Mass
# @AUTHOR: Jason Vertrees
# Copyright (c) 2008, Jason Vertrees
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following
# conditions are met:
#
# * Redistributions of source code must retain the above copyright notice,
this list of conditions and the following
# * disclaimer.
# * Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following
# * disclaimer in the documentation and/or other materials provided with
the distribution.
# * Neither the name of the nor the names of its
contributors may be used to endorse or promote products derived
# * from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
# THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# DATE : 2008-09-26
# REV : 1
'''
from pymol import cmd
from pymol import stored
from chempy import cpv
def centroid(selection='all', center=0, quiet=1):
model = cmd.get_model(selection)
nAtom = len(model.atom)
centroid = cpv.get_null()
for a in model.atom:
centroid = cpv.add(centroid, a.coord)
centroid = cpv.scale(centroid, 1. / nAtom)
if not int(quiet):
print ' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid)
if int(move):
cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)",
space={'centroid': centroid, 'sub': cpv.sub})
return centroid
cmd.extend("centroid", centroid)
--
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[PyMOL] on coloring residues based on y values in the x y z coordinates
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 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] on coloring residues based on y values in the x y z coordinates
Dear David, I am unfamiliar with the pymol scripts so I do not understands where your scripts end at each line. Can we write this way, stored.y=[] iterate_state 1, prot, stored.y.append(y) alter prot, b=stored.y.pop(0) which means those from % in your scripts will be not used in each line for pymol reading? Can you introduce a website to introduce the pymol scripts? For stored.y=， following y= is it the file name of file stores y for each coordinates? Can you introduce to me a server or software which can extract y coordinates from the PDB and save it as another file? Can you introduce to me a server of software which can delete the original b-factors in the original PDB and have the ys pasted on the b-factors positions in the PDB file? Smith At 2015-11-18 21:13:05, "David Hall" <li...@cowsandmilk.net> wrote: I forgot: spectrum b at the end. On Wed, Nov 18, 2015 at 8:11 AM, David Hall <li...@cowsandmilk.net> wrote: Assuming you are ok with overwriting the B-factors stored.y=[] iterate_state 1, prot, stored.y.append(y) % prot here should be replaced with your pymol object name alter prot, b=stored.y.pop(0) % 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 atoms) with equivalent position in the primary sequence but has a y-axis shift in the 3-D structure? Smith -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on coloring residues based on residue conservation
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 Facebook, enables you to easily query your data on Hadoop in a more interactive manner. Teradata is also now providing full enterprise support for Presto. Download a free open source copy now. http://pubads.g.doubleclick.net/gampad/clk?id=250295911=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] volume measurement
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-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on surface function in the setting
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-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on cylindrical helix presentation
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. Smith-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] a command related to pymol show as
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-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to measure the distance of 2 hydrophobic residues
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 regards. Smith-- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to measure the distance of 2 hydrophobic residues
Dear Osvaldo, I want to know whether hydrophobic interactions between 2 residues exist, thus I want know the distance between the 2 residues, rather than the distance between the atom of each of the 2 residues. Is any sense and method we measure the distance between 2 residues? Best regards. Smith At 2015-07-09 00:52:32, Osvaldo Martin aloctavo...@gmail.com wrote: Hi Smith, If you want to measure the distance between two residues (hydrophobic or not) you could choose and atom from each residue and measure the distance between those two atoms. Is this what you want 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 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 regards. Smith -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on color based on b-factor spectrum
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 green, yellow and blue? Smith-- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
