pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Edu-PyMOL Bachelor Thesis

[Vivian E. P. <viv...@ho...>]

Dear PyMOL users

I want to ask if I can use Edu-PyMOL for my bachelor thesis?
Thank you for taking the time to answer my question. I look forward to your response.
Vivian

[PyMOL] Aligning a object to camera axis

[Shyam S. <sa...@ca...>]

Hello --

I am trying to transform an object to align it's major axis with the x-axis
at z = 0 in the camera coordinate space. Sample pdb file (just a simple
scale bar) is attached.

My thought process is as follows:

1. Convert <1, 0, 0> in camera space to model space (vector A)
2. Find vector that corresponds to object's major axis (vector B)
3. Find transformation matrix C that rotates to vector B to vector A
4. Use transform_selection with C


Unfortunately, my attempts are without success (see below), perhaps due to
my lack of understanding of the pymol coordinate spaces.

I see saw two potentially relevant threads here, but I wasn't able to pull
things together successfully:

https://www.mail-archive.com/pym...@li.../msg14278.html
https://sourceforge.net/p/pymol/mailman/message/10098601/


If you have any thoughts here, please let me know!

Thanks,
Shyam


M_to_model = np.array(cmd.get_view()[:9]).reshape(3,3)
def to_model(X): return np.matmul(X, M_to_model)

# 1. xaxis in model coordinates
xaxis_mod = to_model([10, 0, 0])

# 2. major axis of scale in model coordinates
scale_orient = cmd.get_extent("scale_25")
scale_orient = np.diff(scale_orient, axis=0)[0]
print(xaxis_mod, scale_orient)

# 3. matrix to rotate scale to axis
# From scipy.spatial.transform.rotation
#
https://github.com/scipy/scipy/blob/01d8bfb6f239df4ce70c799b9b485b53733c9911/scipy/spatial/transform/rotation.py#L1854-L1982
rot, _ = align_vectors([scale_orient], [xaxis_mod])

# 4. transform scale
def reformat_3x3(rot): \
return [*rot[0], 0, \
*rot[1], 0, \
*rot[2], 0, \
0, 0, 0, 1]
cmd.transform_selection("scale_25", reformat_3x3(rot), homogenous=1)

Re: [PyMOL] Help ASPB

[David G. <dd...@uc...>]


Dear Clarisa, 


> On Sep 10, 2020, at 2:56 AM, Clarisa Alvarez <cla...@gm...> wrote:
> 
> Dear David
> Thank you very much!you do not know how much you helped me!!Thanks!
> I have two questions:



> - with you sent I only saw lateral chains, how could I see backbone?

You want to click on “H” button and hide all.
Then click on “S” ribbons to see backbone atoms.

> - I might have missed the amino acid grouping, I do not understand.

The group refer to acid and base and non-charge groups that play factor in generating the electrostatic potential. 
I am just curious have you tried this type of simple model: q1q2/4*Pier^2


Best Regards,
David 


> Thank you again!
> Have a good day.
> Clarisa.
> 
> El mié., 9 sept. 2020 a las 19:11, David Gae (<dd...@uc... <mailto:dd...@uc...>>) escribió:
> 
> select pos,(resn arg+lys+his)
> show sticks, (pos and !name c+n+o)
> color marine,pos
> disable pos
> select neg,(resn glu+asp)
> show sticks, (neg and !name c+n+o)
> color red,neg
> disable neg
> select neutral, (resn gly+ala+val+ile+leu+met+ser+cys+trp+phe+tyr+pro+gln+asn+phe)
> show sticks, (neutral and !name c+n+o)
> color yellow, neutral
> 
> I might have missed the amino acid grouping, I hope you check it before you use it.  
> Hope this helps,
> 
> 
> 
>> On Sep 9, 2020, at 4:28 AM, Clarisa Alvarez <cla...@gm... <mailto:cla...@gm...>> wrote:
>> 
>> GenScript
>> Dear all, Thanks in advance.
>> I have this problem, I have two pockets with electrostatic potential made by APSB, does anyone know how I could tell which residue contributes to each potential in each protein?
>> Thanks in advance.
>> Regards,
>> Clarisa.
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>

[PyMOL] Help APSB

[Clarisa A. <cla...@gm...>]

Dear all, I need your help.
I have discrepancies when I applied APBS ramp01 on a selected pocket object
generated by myself with the electrostatic potential displayed throughout
the protein. Somebody could help me?Why could this be caused?
What are the differences between ramp01..ramp01...etc?
Thanks in advance
Regards,
Clarisa

[PyMOL] Optimize the bond distance of ligand with protein

[<mta...@ch...>]

Dear Pymol user,
I am trying to do molecular docking using Autodock vina. But when I insert
the ligand and the protein, the distance of ligand is very far from protein
(~7 angstrom)
Is there any way to decrease the distance in pymol before doing the docking?
Thank you
Maryam

[PyMOL] Calculating binding energy of ligand with protein

[<mta...@ch...>]

Hi PyMOL user,
Is this possible to calculate the binding energy of ligand with protein
using Pymol? If yes can you refer me some sources how I can do this task?
Thank you
Maryam

Re: [PyMOL] Help ASPB

[David G. <dd...@uc...>]

select pos,(resn arg+lys+his)
show sticks, (pos and !name c+n+o)
color marine,pos
disable pos
select neg,(resn glu+asp)
show sticks, (neg and !name c+n+o)
color red,neg
disable neg
select neutral, (resn gly+ala+val+ile+leu+met+ser+cys+trp+phe+tyr+pro+gln+asn+phe)
show sticks, (neutral and !name c+n+o)
color yellow, neutral

I might have missed the amino acid grouping, I hope you check it before you use it.  
Hope this helps,



> On Sep 9, 2020, at 4:28 AM, Clarisa Alvarez <cla...@gm...> wrote:
> 
> GenScript
> Dear all, Thanks in advance.
> I have this problem, I have two pockets with electrostatic potential made by APSB, does anyone know how I could tell which residue contributes to each potential in each protein?
> Thanks in advance.
> Regards,
> Clarisa.
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Help ASPB

[Clarisa A. <cla...@gm...>]

GenScript
Dear all, Thanks in advance.
I have this problem, I have two pockets with electrostatic potential made
by APSB, does anyone know how I could tell which residue contributes to
each potential in each protein?
Thanks in advance.
Regards,
Clarisa.

Re: [PyMOL] [EXTERNAL] Cmd: PyMOL lagging behind API requests...

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Petro,

PyMOL is telling you to slow down the 
issuing of your commands. PyMOL
needs time to catch up.

Try importing the time module and using the 
sleep function at strategic places in your code

https://www.datacamp.com/community/tutorials/python-time-sleep

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Piter_ [x....@gm...]
Sent: Monday, September 07, 2020 7:40 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Cmd: PyMOL lagging behind API requests...

Hi.
I try to run pymol via python in batch mode.
It works fine if I define all variables in the python file.
But it stops working when I send variables as cli arguments.
With multiple messages like :
Cmd: PyMOL lagging behind API requests...
Any hints?
Thanks.
Petro.

[PyMOL] Cmd: PyMOL lagging behind API requests...

[Piter_ <x....@gm...>]

Hi.
I try to run pymol via python in batch mode.
It works fine if I define all variables in the python file.
But it stops working when I send variables as cli arguments.
With multiple messages like :
Cmd: PyMOL lagging behind API requests...
Any hints?
Thanks.
Petro.

Re: [PyMOL] MD analysis (distance, dihedral etc)

[Baptiste L. <bap...@gm...>]

Thanks Tamas,

I will have a look on this.

Best,

Baptiste

Le 04/09/2020 à 15:55, Tamas Hegedus a écrit :
> It is.
>
> ----------
>
> Pseudo code:
> sel1 = u.select_atoms...
> sel2 = u.select_atoms... # it is important to make the selection out 
> of the loop
>
> for t in u.trajectory:
>     d = numpy.norm(sel1.center_of_geometry - sel2...)
>
> ----------
> dihedral is somwhat more complex:
>
> SEL = "resid %i and name %s"
>
> C0 = SEL % (RESI-1, 'C')
> N1 = SEL % (RESI, 'N')
> CA = SEL % (RESI, "CA")
> C1 = SEL % (RESI, "C")
> N2 = SEL % (RESI+1, "N")
>
> phiL = []
> psiL = []
>
> u = MDA.Universe(GRO, TRJ)
> phi = sum([u.select_atoms(atom) for atom in [C0, N1, CA, C1]]).dihedral
> psi = sum([u.select_atoms(atom) for atom in [N1, CA, C1, N2]]).dihedral
>
> for f in u.trajectory:
>     phiL.append(phi.value())
>     psiL.append(psi.value())
>
>
> On 9/4/20 9:02 AM, Baptiste Legrand wrote:
>> Hi all,
>>
>> Is it possible to monitor distances, dihedrals etc. in a protein 
>> trajectory? to finally plot distances or something else versus time. 
>> (as VMD or others)
>> Thanks.
>>
>> Best,
>>
>> Baptiste
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: 
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: 
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] MD analysis (distance, dihedral etc)

[Tamas H. <bio...@gm...>]

It is.

----------

Pseudo code:
sel1 = u.select_atoms...
sel2 = u.select_atoms... # it is important to make the selection out of 
the loop

for t in u.trajectory:
     d = numpy.norm(sel1.center_of_geometry - sel2...)

----------
dihedral is somwhat more complex:

SEL = "resid %i and name %s"

C0 = SEL % (RESI-1, 'C')
N1 = SEL % (RESI, 'N')
CA = SEL % (RESI, "CA")
C1 = SEL % (RESI, "C")
N2 = SEL % (RESI+1, "N")

phiL = []
psiL = []

u = MDA.Universe(GRO, TRJ)
phi = sum([u.select_atoms(atom) for atom in [C0, N1, CA, C1]]).dihedral
psi = sum([u.select_atoms(atom) for atom in [N1, CA, C1, N2]]).dihedral

for f in u.trajectory:
     phiL.append(phi.value())
     psiL.append(psi.value())


On 9/4/20 9:02 AM, Baptiste Legrand wrote:
> Hi all,
>
> Is it possible to monitor distances, dihedrals etc. in a protein 
> trajectory? to finally plot distances or something else versus time. 
> (as VMD or others)
> Thanks.
>
> Best,
>
> Baptiste
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: 
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] MD analysis (distance, dihedral etc)

[Baptiste L. <bap...@gm...>]

Hi all,

Is it possible to monitor distances, dihedrals etc. in a protein 
trajectory? to finally plot distances or something else versus time. (as 
VMD or others)
Thanks.

Best,

Baptiste

[PyMOL] APBSTools

[Vann, K. <KEN...@CU...>]

Hi All,

I just installed Pymol on a new computer  (Mac OS X 10.15.6 Catalina) using Homebrew. It appears that the APBS Tools 2.1 is not functioning correctly . I receive the error below when trying to run the program from the legacy plug-ins. Has anyone encountered this issue? If so, what was your solution?


2020-08-31 12:55:18.273 Python[3354:133251] -[QNSApplication _setup:]: unrecognized selector sent to instance 0x7feb78a40f70

Traceback (most recent call last):

  File "/usr/local/Cellar/pymol/2.3.0/libexec/lib/python3.8/site-packages/pmg_tk/startup/apbs_tools.py", line 322, in <lambda>

    command = lambda s=self: APBSTools2(s))

  File "/usr/local/Cellar/pymol/2.3.0/libexec/lib/python3.8/site-packages/pmg_tk/startup/apbs_tools.py", line 599, in __init__

    self.parent = app.root

  File "/usr/local/Cellar/pymol/2.3.0/libexec/lib/python3.8/site-packages/pmg_qt/mimic_pmg_tk.py", line 150, in root

    tkinter_init()

  File "/usr/local/Cellar/pymol/2.3.0/libexec/lib/python3.8/site-packages/pmg_qt/mimic_pmg_tk.py", line 15, in tkinter_init

    raise RuntimeError('tkinter init failed')

RuntimeError: tkinter init failed

Thank you in advance for any assistance that you can provide,


Kendra R. Vann, Ph.D.

Postdoctoral Fellow, Dept. of Pharmacology
Lab of Tatiana Kutateladze, Ph.D.
University of Colorado, Anschutz Medical Campus
L18-6401J

Re: [PyMOL] How to hold/wait for some time?

[Tamas H. <bio...@gm...>]

It seems that pymol refresh the screen only after the script completed.
I tried cmd.refresh(), cmd.rebuild(obj) in the loop, but they did not 
help either. I do not know the solution.

On 8/31/20 8:33 PM, ZHANG Cheng wrote:
> Not work.
>
> time.sleep( 5 )
> did not outpput any error, but freeze for a few seconds. However, 
> nothing come out on the Pymol interface.
>
> ------------------ Original ------------------
> *From:* "Tamas Hegedus" <bio...@gm...>;
> *Date:* Tue, Sep 1, 2020 02:21 AM
> *To:* "pymol-users"<pym...@li...>;
> *Subject:* Re: [PyMOL] How to hold/wait for some time?
>
> This one?
> https://www.tutorialspoint.com/python/time_sleep.htm
>
> On 8/31/20 7:51 PM, ZHANG Cheng wrote:
>> I use the command below, trying to display the object one by one, 
>> with 2 seconds in between. So how to "wait for 2 seconds"?
>>
>> from pymol import cmd
>> cmd.enable('protein_1')
>> # how to hold for 2 seconds?
>> cmd.disable('protein_1')
>> cmd.enable('protein_2')
>> # how to hold for 2 seconds?
>> cmd.disable('protein_2')
>>
>> Thank you!
>>
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives:http://www.mail-archive.com/pym...@li...
>> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Re: [PyMOL] How to hold/wait for some time?

[<272...@qq...>]

Not work.


time.sleep( 5 ) 
did not outpput any error, but freeze for a few seconds. However, nothing come out on the Pymol interface.


------------------ Original ------------------
From:                                                                                                                        "Tamas Hegedus"                                                                                    <bio...@gm...&gt;;
Date:&nbsp;Tue, Sep 1, 2020 02:21 AM
To:&nbsp;"pymol-users"<pym...@li...&gt;;

Subject:&nbsp;Re: [PyMOL] How to hold/wait for some time?



                   This one?
     https://www.tutorialspoint.com/python/time_sleep.htm
     
     On 8/31/20 7:51 PM, ZHANG Cheng wrote:
     
                   I use the command below, trying to display the object one by         one, with 2 seconds in between. So how to "wait for 2 seconds"?
       
       
                from pymol import cmd
         cmd.enable('protein_1')
         # how to hold for 2 seconds?&nbsp;
         cmd.disable('protein_1')
         cmd.enable('protein_2')
         # how to hold for 2 seconds?&nbsp;&nbsp;
         cmd.disable('protein_2')
       
       
       
       Thank you!
       
       
       
       
       
              
              _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li... Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] How to hold/wait for some time?

[Tamas H. <bio...@gm...>]

This one?
https://www.tutorialspoint.com/python/time_sleep.htm

On 8/31/20 7:51 PM, ZHANG Cheng wrote:
> I use the command below, trying to display the object one by one, with 
> 2 seconds in between. So how to "wait for 2 seconds"?
>
> from pymol import cmd
> cmd.enable('protein_1')
> # how to hold for 2 seconds?
> cmd.disable('protein_1')
> cmd.enable('protein_2')
> # how to hold for 2 seconds?
> cmd.disable('protein_2')
>
> Thank you!
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] How to hold/wait for some time?

[<272...@qq...>]

I use the command below, trying to display the object one by one, with 2 seconds in between. So how to "wait for 2 seconds"?


from pymol import cmd
cmd.enable('protein_1')
# how to hold for 2 seconds? 
cmd.disable('protein_1')
cmd.enable('protein_2')
# how to hold for 2 seconds?  
cmd.disable('protein_2')



Thank you!

[PyMOL] Quad-Buffered Stereo 3D in Windows and Windowed Mode?

[Shintaro A. <shi...@gm...>]

Dear Pymol Team,

I have been playing around with stereo view using NVIDIA 3D vision 2 system
on Windows. I am using a RTX 2070, together with pymol 2.3.3.

Long story short I have managed to get it to work, but exclusively in
Fullscreen mode. When the session is in a windowed mode, it does not engage
the 3D mode. While I should probably walk away with this as a victory, I
couldn't stop noticing that this behavior is somewhat similar to what I
experienced in Linux with compositing desktop environments (MATE vs GNOME),
and was wondering if there was something I could tweak in Windows 10 to get
the hardware stereo to also work when the session is not fullscreen.

Best wishes
Shintaro

Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?

[<272...@qq...>]

Also, "join_states multitest, (test*)" could not achieve the purpose. The multiple objects can be combined into one object, but the b-factor in this object is all the same as the last frame.




------------------ Original ------------------
From:                                                                                                                        "ZHANG Cheng"                                                                                    <272...@qq...&gt;;
Date:&nbsp;Mon, Aug 31, 2020 08:58 PM
To:&nbsp;"Mooers, Blaine H.M.  (HSC)"<Bla...@ou...&gt;;"pymol-users"<pym...@li...&gt;;

Subject:&nbsp;Re:RE: Re:RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?



Dear Blaine,


I tried "split_states protein, prefix=test", it can output multiple objects, with each object having 1 frame.


However, when each object (test0001, test0002, ...) is saved as PDB, I found that the b-factor values are all the same as the last frame of the protein.pdb.


Best
Cheng




------------------ Original ------------------
From:                                                                                                                        "Mooers, Blaine H.M.  (HSC)"                                                                                    <Bla...@ou...&gt;;
Date:&nbsp;Mon, Aug 31, 2020 08:29 PM
To:&nbsp;"ZHANG Cheng"<272...@qq...&gt;;"pymol-users"<pym...@li...&gt;;

Subject:&nbsp;RE: Re:RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?



Dear Cheng,

Please note that the original split_states code that I posted
has a typo (the dangers of posting a reply before dawn!)
&nbsp;The semicolon after pdb should be a comma.

split_states protein, prefix=test;

Thank you Tamas for the pseudo code for iterating the application of spectrum!!!

After applying the spectrum with Tamas's code,
you will want to combine the 1000 objects into one file.

join_states multitest, (test*)

And then you will want to save the multistate object

multisave multitest.pdb,multitest,0

Best regards,

Blaine


Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: ZHANG Cheng [272...@qq...]
Sent: Monday, August 31, 2020 5:56 AM
To: Mooers, Blaine H.M.&nbsp; (HSC); pymol-users
Subject: Re:RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

Hi Blaine,

Thank you for your suggestion. "set all_states, on" could not work.

For splitting the object, it is an alternatve. But I have 1000 frames in the object, and I want to show a movie by playing the frames.

Best
Cheng


------------------ Original ------------------
From: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...&gt;;
Date: Mon, Aug 31, 2020 06:13 PM
To: "ZHANG Cheng"<272...@qq...&gt;;"pymol-users"<pym...@li...&gt;;
Subject: RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

Hi ZHANG Cheng,

Did you try?

set all_states, on;spectrum b

Another approach would to split the states into separate objects and then apply the
spectrum command to each object.

split_states protein.pdb; prefix=test;spectrum b,,test*

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: ZHANG Cheng [272...@qq...]
Sent: Sunday, August 30, 2020 4:40 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

I load a protein.pdb file into Pymol. This file has multiple frames (or states), and with different b-factor values at different frames at the PDB file b-factor columns.

After running the "spectrum b" command, the colouring is only based on the last state of the object.

So can I colour the frames differently using their corresponding b-factor values? In that case, I can see the colour changing throughout the frame playing.

Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Dear Cheng,

Please note that the original split_states code that I posted
has a typo (the dangers of posting a reply before dawn!)
 The semicolon after pdb should be a comma.

split_states protein, prefix=test;

Thank you Tamas for the pseudo code for iterating the application of spectrum!!!

After applying the spectrum with Tamas's code,
you will want to combine the 1000 objects into one file.

join_states multitest, (test*)

And then you will want to save the multistate object

multisave multitest.pdb,multitest,0

Best regards,

Blaine


Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: ZHANG Cheng [272...@qq...]
Sent: Monday, August 31, 2020 5:56 AM
To: Mooers, Blaine H.M.  (HSC); pymol-users
Subject: Re:RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

Hi Blaine,

Thank you for your suggestion. "set all_states, on" could not work.

For splitting the object, it is an alternatve. But I have 1000 frames in the object, and I want to show a movie by playing the frames.

Best
Cheng


------------------ Original ------------------
From: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...>;
Date: Mon, Aug 31, 2020 06:13 PM
To: "ZHANG Cheng"<272...@qq...>;"pymol-users"<pym...@li...>;
Subject: RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

Hi ZHANG Cheng,

Did you try?

set all_states, on;spectrum b

Another approach would to split the states into separate objects and then apply the
spectrum command to each object.

split_states protein.pdb; prefix=test;spectrum b,,test*

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: ZHANG Cheng [272...@qq...]
Sent: Sunday, August 30, 2020 4:40 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

I load a protein.pdb file into Pymol. This file has multiple frames (or states), and with different b-factor values at different frames at the PDB file b-factor columns.

After running the "spectrum b" command, the colouring is only based on the last state of the object.

So can I colour the frames differently using their corresponding b-factor values? In that case, I can see the colour changing throughout the frame playing.

Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?

[<272...@qq...>]

Dear Blaine,


I tried "split_states protein, prefix=test", it can output multiple objects, with each object having 1 frame.


However, when each object (test0001, test0002, ...) is saved as PDB, I found that the b-factor values are all the same as the last frame of the protein.pdb.


Best
Cheng




------------------ Original ------------------
From:                                                                                                                        "Mooers, Blaine H.M.  (HSC)"                                                                                    <Bla...@ou...&gt;;
Date:&nbsp;Mon, Aug 31, 2020 08:29 PM
To:&nbsp;"ZHANG Cheng"<272...@qq...&gt;;"pymol-users"<pym...@li...&gt;;

Subject:&nbsp;RE: Re:RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?



Dear Cheng,

Please note that the original split_states code that I posted
has a typo (the dangers of posting a reply before dawn!)
&nbsp;The semicolon after pdb should be a comma.

split_states protein, prefix=test;

Thank you Tamas for the pseudo code for iterating the application of spectrum!!!

After applying the spectrum with Tamas's code,
you will want to combine the 1000 objects into one file.

join_states multitest, (test*)

And then you will want to save the multistate object

multisave multitest.pdb,multitest,0

Best regards,

Blaine


Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: ZHANG Cheng [272...@qq...]
Sent: Monday, August 31, 2020 5:56 AM
To: Mooers, Blaine H.M.&nbsp; (HSC); pymol-users
Subject: Re:RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

Hi Blaine,

Thank you for your suggestion. "set all_states, on" could not work.

For splitting the object, it is an alternatve. But I have 1000 frames in the object, and I want to show a movie by playing the frames.

Best
Cheng


------------------ Original ------------------
From: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...&gt;;
Date: Mon, Aug 31, 2020 06:13 PM
To: "ZHANG Cheng"<272...@qq...&gt;;"pymol-users"<pym...@li...&gt;;
Subject: RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

Hi ZHANG Cheng,

Did you try?

set all_states, on;spectrum b

Another approach would to split the states into separate objects and then apply the
spectrum command to each object.

split_states protein.pdb; prefix=test;spectrum b,,test*

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: ZHANG Cheng [272...@qq...]
Sent: Sunday, August 30, 2020 4:40 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

I load a protein.pdb file into Pymol. This file has multiple frames (or states), and with different b-factor values at different frames at the PDB file b-factor columns.

After running the "spectrum b" command, the colouring is only based on the last state of the object.

So can I colour the frames differently using their corresponding b-factor values? In that case, I can see the colour changing throughout the frame playing.

Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?

[Tamas H. <bio...@gm...>]

you can also try not to split and
set/activate the given frame in the for loop

it could happen that spectrum works on the active frame (which was the 
last one in your case)
https://pymolwiki.org/index.php/Frame

On 8/31/20 2:16 PM, ZHANG Cheng wrote:
> Thank you, this could be a solution. I would still like not splitting 
> the object if possible.
>


On 8/31/20 1:54 PM, Tamas Hegedus wrote:
> You may write and use a script after splitting the object.
>
> a pseudo code:
>
> for i in range(1, 1001):
>     spectrum b, rainbow, frame_i
>     enable frame_i
>     sleep sometime
>     disable frame_i
>
> On 8/31/20 12:56 PM, ZHANG Cheng wrote:
>> Hi Blaine,
>>
>> Thank you for your suggestion. "set all_states, on" could not work.
>>
>> For splitting the object, it is an alternatve. But I have 1000 frames 
>> in the object, and I want to show a movie by playing the frames.
>>
>> Best
>> Cheng
>>
>>
>> ------------------ Original ------------------
>> *From:* "Mooers, Blaine H.M. (HSC)" <Bla...@ou...>;
>> *Date:* Mon, Aug 31, 2020 06:13 PM
>> *To:* "ZHANG 
>> Cheng"<272...@qq...>;"pymol-users"<pym...@li...>;
>> *Subject:* RE: [EXTERNAL] [PyMOL] How to color based on b-factor for 
>> all the frames in one object in Pymol?
>>
>> Hi ZHANG Cheng,
>>
>> Did you try?
>>
>> set all_states, on;spectrum b
>>
>> Another approach would to split the states into separate objects and 
>> then apply the
>> spectrum command to each object.
>>
>> split_states protein.pdb; prefix=test;spectrum b,,test*
>>
>> Best regards,
>>
>> Blaine
>>
>> Blaine Mooers, Ph.D.
>> Associate Professor
>> Department of Biochemistry and Molecular Biology
>> College of Medicine
>> University of Oklahoma Health Sciences Center
>> S.L. Young Biomedical Research Center (BRC) Rm. 466
>> 975 NE 10th Street, BRC 466
>> Oklahoma City, OK 73104-5419
>>
>> ________________________________________
>> From: ZHANG Cheng [272...@qq...]
>> Sent: Sunday, August 30, 2020 4:40 PM
>> To: pymol-users
>> Subject: [EXTERNAL] [PyMOL] How to color based on b-factor for all 
>> the frames in one object in Pymol?
>>
>> I load a protein.pdb file into Pymol. This file has multiple frames 
>> (or states), and with different b-factor values at different frames 
>> at the PDB file b-factor columns.
>>
>> After running the "spectrum b" command, the colouring is only based 
>> on the last state of the object.
>>
>> So can I colour the frames differently using their corresponding 
>> b-factor values? In that case, I can see the colour changing 
>> throughout the frame playing.
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives:http://www.mail-archive.com/pym...@li...
>> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?

[Tamas H. <bio...@gm...>]

You may write and use a script after splitting the object.

a pseudo code:

for i in range(1, 1001):
     spectrum b, rainbow, frame_i
     enable frame_i
     sleep sometime
     disable frame_i

On 8/31/20 12:56 PM, ZHANG Cheng wrote:
> Hi Blaine,
>
> Thank you for your suggestion. "set all_states, on" could not work.
>
> For splitting the object, it is an alternatve. But I have 1000 frames 
> in the object, and I want to show a movie by playing the frames.
>
> Best
> Cheng
>
>
> ------------------ Original ------------------
> *From:* "Mooers, Blaine H.M. (HSC)" <Bla...@ou...>;
> *Date:* Mon, Aug 31, 2020 06:13 PM
> *To:* "ZHANG 
> Cheng"<272...@qq...>;"pymol-users"<pym...@li...>;
> *Subject:* RE: [EXTERNAL] [PyMOL] How to color based on b-factor for 
> all the frames in one object in Pymol?
>
> Hi ZHANG Cheng,
>
> Did you try?
>
> set all_states, on;spectrum b
>
> Another approach would to split the states into separate objects and 
> then apply the
> spectrum command to each object.
>
> split_states protein.pdb; prefix=test;spectrum b,,test*
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> ________________________________________
> From: ZHANG Cheng [272...@qq...]
> Sent: Sunday, August 30, 2020 4:40 PM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] How to color based on b-factor for all the 
> frames in one object in Pymol?
>
> I load a protein.pdb file into Pymol. This file has multiple frames 
> (or states), and with different b-factor values at different frames at 
> the PDB file b-factor columns.
>
> After running the "spectrum b" command, the colouring is only based on 
> the last state of the object.
>
> So can I colour the frames differently using their corresponding 
> b-factor values? In that case, I can see the colour changing 
> throughout the frame playing.
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?

[<272...@qq...>]

Hi Blaine,


Thank you for your suggestion. "set all_states, on" could not work.


For splitting the object, it is an alternatve. But I have 1000 frames in the object, and I want to show a movie by playing the frames.


Best
Cheng




------------------ Original ------------------
From:                                                                                                                        "Mooers, Blaine H.M.  (HSC)"                                                                                    <Bla...@ou...&gt;;
Date:&nbsp;Mon, Aug 31, 2020 06:13 PM
To:&nbsp;"ZHANG Cheng"<272...@qq...&gt;;"pymol-users"<pym...@li...&gt;;

Subject:&nbsp;RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?



Hi ZHANG Cheng,

Did you try?

set all_states, on;spectrum b

Another approach would to split the states into separate objects and then apply the 
spectrum command to each object. 

split_states protein.pdb; prefix=test;spectrum b,,test*

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: ZHANG Cheng [272...@qq...]
Sent: Sunday, August 30, 2020 4:40 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

I load a protein.pdb file into Pymol. This file has multiple frames (or states), and with different b-factor values at different frames at the PDB file b-factor columns.

After running the "spectrum b" command, the colouring is only based on the last state of the object.

So can I colour the frames differently using their corresponding b-factor values? In that case, I can see the colour changing throughout the frame playing.