Re: [PyMOL] where can I ask questions? Is there any forum?

[Tamas Hegedus]

Hi,

I think that you have two issues:

#1 pymol autodock/vina plugin; it should work on windows, since it is written 
in python. The issue u might encounter: it may have written in an older python 
version than the pymol install

#2 you have to perform the docking with autodock or autodock vina. I think that 
these will not run on win.
You also have to prepare the prot and small molecule w autodocktools. Some gui 
apps might have preparation wizard.

Bests



⁣Az Android BlueMail letöltése ​

2024. ápr. 1. 17:23-n, 17:23-kor, Elizabeth Tsakelidou  
ezt írta:
>
>Hey
>
>I would like to know what is the best way to install and work
>protein-ligand docking.
>I have Windows 11 and I tried Anaconda PyMOL but I think this way
>you cannot have all plugins available.
>So, what if I tried ubuntu with all is available on GitHub?
>Can I do this?
>The query arises because it is said that if you want to install linux
>in windows
>you better use cygwin.
>What do you think?
>Thanks
>
>Elizabeth
>
>Sent from Outlook
>
>
>
>
>
>
>
>
>___
>PyMOL-users mailing list
>Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>Unsubscribe:
>https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Align in PyMOL via Python script

[Tamas Hegedus]

Hi,


You probably use the script version. In this case you have to use "print"


cmd: align x, y

output: ... Executive: RMSD =4.030 (10847 to 10847 atoms)


cmd: print(cmd.align("x", "y"))
output: 
(4.0296430587768555, 10847, 5, 24.87837028503418, 13476, 1234.0, 1192)



Bests, Tamas


On 2023. 03. 02. 8:54, Irwin Selvam wrote:

Hi,

I would like to run the Align Python script found on the Align page of 
the PyMOLwiki (https://pymolwiki.org/index.php/Align). I've tweaked it 
slightly for my uses and it seems to run fine on PyMOL 2.5.0 but 
according to the wiki it should output a list of results (RMSD etc) in 
the internal feedback (or command prompt?), but it doesn't in my case. 
Does anyone know why? It does seem like there some missing lines to 
the script in order to achieve this. Apologies for the basic question!


All the best,

Irwin





___
PyMOL-users mailing list
Archives:http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] CCP4 maps not aligning to my PDB file

[Tamas Hegedus]

pls. google

https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html
https://www.cgl.ucsf.edu/chimera/data/tutorials/emfit09/emfit.html

On 4/12/21 9:25 AM, shubhashish chakraborty wrote:

Hi,
Thank you for a reply.
I am not working with cryo-EM but it's an X-ray diffraction map.
A similar kind of problem I am facing in chimera, so what could be done?

Thank you

Shubhashish Chakraborty
PhD Research Scholar (SRF)
Varma Lab
Structural and Molecular biology Lab
Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
Khargar, Navi Mumbai




On Mon, Apr 12, 2021 at 12:42 PM Tamas Hegedus <mailto:biohege...@gmail.com>> wrote:


Hi,

PyMOL seems not to primarily target working with densities.

I suggest to use Chimera if you work with cryo EM maps.
E.g. you can use it to fit your struct into the density map.
If you decide to use Chimera, be careful, a first step of
frustration could be caused by the extension of the density file.
Yes, the extension - .mrc or .map; depending on the extension the
map is aligned to the origo or not (or something like that).

Bests,
Tamas

On 4/12/21 8:34 AM, shubhashish chakraborty wrote:

Hello,
I am not able to align my pdb file with its respective electron
density map generated by CCP4i. Kindly let me know what is going
wrong.
An image is attached for better reference.

Thank you
Shubhashish Chakraborty
PhD Research Scholar (SRF)
Varma Lab
Structural and Molecular biology Lab
Advanced Centre for Treatment, Research and Education in Cancer
(ACTREC)
Khargar, Navi Mumbai




___
PyMOL-users mailing list
Archives:http://www.mail-archive.com/pymol-users@lists.sourceforge.net  
<http://www.mail-archive.com/pymol-users@lists.sourceforge.net>
Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe  
<https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>


___
PyMOL-users mailing list
Archives:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net
<http://www.mail-archive.com/pymol-users@lists.sourceforge.net>
Unsubscribe:
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
<https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>



___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] CCP4 maps not aligning to my PDB file

[Tamas Hegedus]

Hi,

PyMOL seems not to primarily target working with densities.

I suggest to use Chimera if you work with cryo EM maps.
E.g. you can use it to fit your struct into the density map.
If you decide to use Chimera, be careful, a first step of frustration 
could be caused by the extension of the density file. Yes, the extension 
- .mrc or .map; depending on the extension the map is aligned to the 
origo or not (or something like that).


Bests,
Tamas

On 4/12/21 8:34 AM, shubhashish chakraborty wrote:

Hello,
I am not able to align my pdb file with its respective electron 
density map generated by CCP4i. Kindly let me know what is going wrong.

An image is attached for better reference.

Thank you
Shubhashish Chakraborty
PhD Research Scholar (SRF)
Varma Lab
Structural and Molecular biology Lab
Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
Khargar, Navi Mumbai




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Selecting the water within a protein channel

[Tamas Hegedus]

Hi,

I would run HOLE, which detects the tunnel/channel and generates a file 
for you (SPH?) which is a pdb file with SPH (sphere) atoms corresponding 
to the tunnel/channel volume.

You can select water molecules (or anything else) around these SPH atoms.

Suggestion: the ends of the tunnel are broadening with a lot of spheres; 
you most likely want to remove those SHP atoms...


Bests,
Tamas

On 3/19/21 6:31 PM, Jason Mosier wrote:
Hello, I was wondering if someone could help me screen for which 
molecules are being found within the inside of a protein channel / 
near the protein channel. I know I can search for the molecules within 
3.5 A of the protein, but this also results in finding the ones on the 
outside. I know this is pretty specific and might be difficult to do, 
but it would increase our accuracy a bunch because at the moment we 
are hand picking which water molecules "seem" to be close to the 
channel and our numbers are very inconsistent. Here is the current 
code we are using: https://pastebin.com/1iBZ7rKi 



Best,
Jason M.


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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

[Tamas Hegedus]

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/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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

[Tamas Hegedus]

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" ;
*Date:* Tue, Sep 1, 2020 02:21 AM
*To:* "pymol-users";
*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/pymol-users@lists.sourceforge.net
Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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

[Tamas Hegedus]

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/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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 Hegedus]

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)" ;
*Date:* Mon, Aug 31, 2020 06:13 PM
*To:* "ZHANG 
Cheng"<272699...@qq.com>;"pymol-users";
*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 [272699...@qq.com]
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/pymol-users@lists.sourceforge.net
Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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 Hegedus]

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)" ;
*Date:* Mon, Aug 31, 2020 06:13 PM
*To:* "ZHANG 
Cheng"<272699...@qq.com>;"pymol-users";
*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 [272699...@qq.com]
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/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] extract monomer from trimer structure

[Tamas Hegedus]

Hi,

I think that:
* You have a couple chains in a monomer.
* You have to know which chains build a monomer.
* Then you create a new object from these chains. E.g. create monomer, 
chain A1 or chain B1 or chain C1 or etc... (here the "or" is an operator 
and it does not indicate that I do not know which chain you need)
* You can likely simplify the selection; I guess that all chains with 
the same digit/number build a monomer, thus you can use a wild char for 
selection:

  create monomer1, chain *1
  create monomer2, chain *2
* Then file, save molecule, and select the "monomer" object for saving

Bests, tamas

On 7/4/20 7:58 AM, Dr. Subramanian, Senthil Kumar wrote:


Hello,

I am new to PyMOL. I would like to work with the monomer structure of 
PDB id: 5zf0, not the entire structure of how they have shown (two 
trimers against each other). Is there any way I could extract monomer 
from trimers structure and save it as a PDB? Your help is very much 
appreciated.


Thank you.

Kind regards,

Senthil



___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] tertiary structure/protein folding

[Tamas Hegedus]

Hi,

Predicting tertiary structure with high accuracy is the holy grail...
I can suggest to perform homology modeling. See Modeller.
If your target is small, you can use molecular dynamics (w replica 
exchange).


Tamas

On 2020. 05. 21. 18:49, Grace Ciabattoni wrote:

Hello,
I am trying to model my protein of interest using the builder function 
in version 2.3. Is there a way to induce protein folding to properly 
mimic tertiary structure, or is secondary structure the highest 
manipulatable level of protein order in PyMol?

Thank you,
Grace


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



--
This email has been checked for viruses by AVG.
https://www.avg.com
___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Extract all phi and psi angles

[Tamas Hegedus]

Hi,

For this type of analysis I would use MDAnalysis (Python):
https://www.mdanalysis.org/
https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html

Tamas

On 5/9/20 5:08 PM, Neena Susan Eappen wrote:

Hi Jarrett,

Thank you for your reply. However, that command gives phi and psi 
angles for only one atom (when only one atom is selected). Is there 
one command we can use to extract all phi and psi angles?


Thanks,
Neena



On Mon, 27 Apr 2020 at 22:01, Jarrett Johnson 
> wrote:


Hi Neena,

Is this command sufficient?

https://pymol.org/dokuwiki/doku.php?id=command:phi_psi

Best,
Jarrett J

On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen
mailto:neenasusan...@gmail.com>> wrote:

Hello PyMOL users,

How to extract all peptide dihedral angles (phi and psi) in PyMOL?

Many thanks,
Neena
___
PyMOL-users mailing list
Archives:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 


*Jarrett Johnson* | Senior Developer

Schrodinger Logo 



___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Wait for processing to complete before invoking new commands

[Tamas Hegedus]

Something is fishy... as I do not expect this to happen. I have never 
experienced this problem.

I made different types of mistakes resulting in such a phenomenon.
* using a for loop and in the command, loading the ligand, I did not 
inserted the loop variable into the file name

(e.g. I used lig_1.pdb instead of "lig_%i.pdb" % ix)
* it was not with vina (difficult to imagine this situation), but once I 
generated a set of pdb files with the same coordinates


On the other hand:
https://pymolwiki.org/index.php/Sync



On 4/30/20 5:09 AM, leifepeter...@sbcglobal.net wrote:


I am writing png images for many docked ligands but all the png files 
have the same image – even though the file names are different for the 
ligand_out.pdbqt files.   So PyMol is getting ahead of itself and 
quickly looping through all the code and dumping the same image but 
with different files names since the image buffer never caught up.   
Thus, I will need to programatically wait for each png to be 
generated, and once the png command is finished, I can move to the 
next ligand.


What command can be used to instruct PyMol to finish its processing 
before taking on new commands, either that or e.g. 5 sec pause? I will 
need to use this command right after the png command.




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Number of parameters is off for cmd.set_view?

[Tamas Hegedus]

please see 
https://pymolwiki.org/index.php/Set_View

set_view (...)  where ... is 18 floating point numbers
cmd.set_view(string-or-sequence view) !!! you provided 18 floating point 
numbers here and not a string or sequence.


On 4/29/20 8:40 PM, leifepeter...@sbcglobal.net wrote:


In the GUI command line, I entered get_view and got the following

set_view (\

    -0.219962522,    0.763355076, -0.607366502,\

 0.878539860,    0.425617725, 0.216765702,\

 0.423973948,   -0.485916167, -0.764265418,\

 0.001047601,    0.000947788, -48.208724976,\

   -24.094066620,  -41.117546082, 2.001868963,\

   -84.735671997,  181.151062012,  -20.0 )

However, in my filename.py, use of the command

cmd.set_view (\

    -0.219962522,    0.763355076, -0.607366502,\

 0.878539860,    0.425617725, 0.216765702,\

 0.423973948,   -0.485916167, -0.764265418,\

 0.001047601,    0.000947788, -48.208724976,\

   -24.094066620,  -41.117546082, 2.001868963,\

   -84.735671997,  181.151062012,  -20.0 )

Returned the error message:

TypeError: set_view() takes from 1 to 5 positional arguments but 18 were given



___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Script for drawing docked ligand-active site pics

[Tamas Hegedus]

Hi,

I do not provide a full solution...
I suggest
* try every particular step in pymol, in the command window
* if one step is successful, then put it (finally everything) into a file
* use python commands (not pymol; e.g. cmd.color("blue", "lig_01"))
* run the file either using "run python.file.py" in pymol; in this case 
you can set "argumuments" as regular python variables before running 
"run ..."
* run the file from the shell "pymol -c python.file.py -- arg1 arg_i 
view1.pkl
* if you have several poses in the vina output, I suggest to split them 
(vina_split) convert to pdb (e.g. openbabel) and then load them 
individually into pymol in a for cycle
* before saving png, try/test "ray x, y"; later this can be set in the 
"png" command

* READ the documentation
* use GOOGLE; e.g. "pymol find polar contacts"

You can save your view:
pickle.dump(cmd.get_view(), open(fname, 'wb'))
Load it back:
cmd.set_view(pickle.load(open(fname, 'rb')))


On 4/29/20 6:29 PM, leifepeter...@sbcglobal.net wrote:


I have two receptors and their active sites for which I need to draw 
about 70 separate ligand-active site images (.png).  Both active sites 
are saved in session files (.pse) based on 3D coordinates from pdbqt 
files after prepping for Vina docking.   The ligand 3D coordinates are 
based on *_out.pdbqt files from docking with Vina.


After opening a .pse file to show the surface of the active site, the 
following automated steps are needed:


 1. Open a ligand docking output file, ligandname_out.pdbqt, and
automatically orient the active site (the site coordinates jump a
little as soon as each ligand docking output file is opened).   So
the same active site orientation is needed so images are consistent.
 2. Adjust the brightness level (mouse thumbwheel) so that each saved
image has a consistent look.
 3. On the ligand, removes valence.
 4. Change the color of the ligand using ColoràElementsàGreen (carbon)
 5. On the ligand, FindàPolar contactsàTo any atom (is there away to
get counts of H-bonds)
 6. Save PNG using ligand name.

(need to also programmatically hit Return after code is pasted into 
command line)


Once I get something that works after pasting the code for the above 6 
steps into the command line, and discover that the image is saved, I 
can then write my own code to clone the commands, and substitute all 
the ligand file names.


Certainly, someone has already written code to autodraw a docked 
ligand (from Vina) sitting in an active site?




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Grid mode problem

[Tamas Hegedus]

alter 3n7h, b=0.0

On 4/24/20 4:09 PM, George Tzotzos wrote:

Thank you both,

Below are the first 3 lines of my script

select 3n7h
alter all, b=0.0
set_color color0, [0.30196078431372547,0.0,0.29411764705882354]

I introduced line 1 for the selection of the protein (similarly in the second 
script).
Is this line correct because it didn’t get rid of the problem?




On 24 Apr 2020, at 14:39, Tamas Hegedus  wrote:

Use a selection in your commands in your scripts. Set the selection to one of 
your proteins in one of your script and the selection to the other one in the 
other script.


On 4/24/20 3:02 PM, George Tzotzos via PyMOL-users wrote:

Below is a summary of a task I’m trying to implement in pymol

1. Load 2 proteins
2. Align them (align prt1, prt2)
3. Use grid_slot to display the proteins side by side
4. Load two different scripts (one for each protein)

Step 4 is where I get stuck. Each script is applied to both proteins.

Is there a way to apply each script to one grid only?

Thanks in advance for any suggestions

___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Grid mode problem

[Tamas Hegedus]

Use a selection in your commands in your scripts. Set the selection to 
one of your proteins in one of your script and the selection to the 
other one in the other script.



On 4/24/20 3:02 PM, George Tzotzos via PyMOL-users wrote:

Below is a summary of a task I’m trying to implement in pymol

1. Load 2 proteins
2. Align them (align prt1, prt2)
3. Use grid_slot to display the proteins side by side
4. Load two different scripts (one for each protein)

Step 4 is where I get stuck. Each script is applied to both proteins.

Is there a way to apply each script to one grid only?

Thanks in advance for any suggestions

___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] floating external gui

[Tamas Hegedus]

Hi,

I am using a compiled version of pymol.
I like the floating window.

The CNTR-E does not work to toggle floating, I have to use the mouse (display, 
external gui, toggle floating).
Is it possible to start pymol with floating external gui?

Thanks, Tamas

___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] click and select bug in 2.2

[Tamas Hegedus]

Hi Thomas,

Thanks a lot.

In the last 15 years I tried to compile pymol several times without 
success. Now installing from the source was like a charm. Till now I did 
not find that bug in the github version.


(6 months were not enough to get used to the new interface. I am trying 
to use it with decoupled windows, but somehow the two windows are pretty 
inconvenient in this version.)


Cheers,
Thomas

--
Tamas Hegedus, PhD
Senior Research Fellow
Department of Biophysics and Radiation Biology
Semmelweis University | phone: (36) 1-459 1500/60233
Tuzolto utca 37-47| mailto:ta...@hegelab.org
Budapest, 1094, Hungary   | http://www.hegelab.org

On 1/10/20 5:35 PM, Thomas Holder wrote:

Hi Tamas,

Sounds like one of these bugs:

https://github.com/schrodinger/pymol-open-source/issues/11
https://github.com/schrodinger/pymol-open-source/issues/35

Can you install the latest version from source, like described here?

https://pymolwiki.org/index.php/Linux_Install#Install_from_source

Cheers,
   Thomas


On Jan 10, 2020, at 4:15 PM, Tamas Hegedus  wrote:

Hi,

I use pymol 2.2 (debian stable release).
Sometimes pymol starts to behave in a strange way. Clicking to an amino acid 
select a residue somewhere else in the protein.
(This is not caused by me missing the click in the 3D)

I would be happy not to downgrade pymol if you have a solution to get around 
this bug.

Thanks,
Tamas


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.




___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] click and select bug in 2.2

[Tamas Hegedus]

Hi,

I use pymol 2.2 (debian stable release).
Sometimes pymol starts to behave in a strange way. Clicking to an amino 
acid select a residue somewhere else in the protein.

(This is not caused by me missing the click in the 3D)

I would be happy not to downgrade pymol if you have a solution to get 
around this bug.


Thanks,
Tamas


___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe