pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] choice of color in util.cbc

[Chen, Q. <qi...@pi...>]

Thanks!

This works well. "Spectrum chain" is more flexible and powerful in this case.

Charles



________________________________
From: Thomas Holder <tho...@sc...>
Sent: Tuesday, July 14, 2020 2:24 PM
To: Chen, Qiang <qi...@pi...>
Cc: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] choice of color in util.cbc

Hi Charles,

The `first_color` argument is only active with `legacy=1`.

  util.cbc 6uwz, first_color=1, legacy=1

Other options for coloring by chain:

  spectrum chain, rainbow, 6uwz

  spectrum chain, blue green red yellow, 6uwz


Hope that helps.

Cheers,
  Thomas


> On Jul 14, 2020, at 7:18 PM, Chen, Qiang <qi...@pi...> wrote:
>
> Hi, Pymol Users
>
> Is it possible to choose different color pattern when using util.cbc?
>
> Wiki says I could use the following to choose the first_color
>
> util.cbc 6uwz, first_color=1, quiet=0
>
> 6uwz is just an example of a pentameric protein.
>
> However, there is no change when specify any other number for first_color. It always starts with cyan on the first chain.
>
> I know I can color the chain individually. I am just puzzled that util.cbc behaves this way.
>
> I am using open-source pymol2.5.0a0 running on windows 10.
>
> Thanks!
>
> Charles
> _______________________________________________
> PyMOL-users mailing list
> Archives: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&amp;data=02%7C01%7Cqic8%40pitt.edu%7C7fa17ea9f1c74b8091a208d828232bad%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637303478808757916&amp;sdata=4LxB2rIRWc%2F46YtcoayR7%2Bg48nlegyee7IVfjGGKdnc%3D&amp;reserved=0
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] choice of color in util.cbc

[Thomas H. <tho...@sc...>]

Hi Charles,

The `first_color` argument is only active with `legacy=1`.

  util.cbc 6uwz, first_color=1, legacy=1

Other options for coloring by chain:

  spectrum chain, rainbow, 6uwz

  spectrum chain, blue green red yellow, 6uwz


Hope that helps.

Cheers,
  Thomas


> On Jul 14, 2020, at 7:18 PM, Chen, Qiang <qi...@pi...> wrote:
> 
> Hi, Pymol Users
> 
> Is it possible to choose different color pattern when using util.cbc?
> 
> Wiki says I could use the following to choose the first_color
> 
> util.cbc 6uwz, first_color=1, quiet=0
> 
> 6uwz is just an example of a pentameric protein.
> 
> However, there is no change when specify any other number for first_color. It always starts with cyan on the first chain.
> 
> I know I can color the chain individually. I am just puzzled that util.cbc behaves this way.
> 
> I am using open-source pymol2.5.0a0 running on windows 10.
> 
> Thanks!
> 
> Charles 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] choice of color in util.cbc

[Chen, Q. <qi...@pi...>]

Hi, Pymol Users

Is it possible to choose different color pattern when using util.cbc?

Wiki says I could use the following to choose the first_color

util.cbc 6uwz, first_color=1, quiet=0

6uwz is just an example of a pentameric protein.

However, there is no change when specify any other number for first_color. It always starts with cyan on the first chain.

I know I can color the chain individually. I am just puzzled that util.cbc behaves this way.

I am using open-source pymol2.5.0a0 running on windows 10.

Thanks!

Charles

[PyMOL] Energy minimization in Pymol

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

I used gromacs (opls-forcefield) to simulate a peptide, attached here are
two energy minimized structures. However, em5 was 40 KJ/mol higher in
energy than em4 according to gromacs. When I minimized these two structures
using clean function in pymol builder, these structures had exactly the
same energy and the structures overlapped. Clearly, there is a change in
dihedral angles. Can someone explain what might be going on here?

Many thanks,
Neena

[PyMOL] Reading Cell Dimensions from GROMACS XTC file

[Daniel K. <dk...@pr...>]

Hello,

I would like to load a GROMACS xtc trajectory and visualize the (changing)
cell size.

My current workflow is:

load sim.pdb
load_traj sim.xtc, sim
show cell

This shows a cell/box but it is the wrong size and does not update every
frame. Is there some way to load the proper cell dimensions?

Best regards,
Dan Kozuch

[PyMOL] Concurrency in pymol

[achatz <ac...@wz...>]

Hello,
I need to call functions like cmd.get_area() or cmd.centerofmass() with a lot of different selection macros selecting residues. As this is quite slow I wanted to ask if it is possible to call these functions concurrently. A first test with concurrent.futures.ThreadPoolExecutor seemded to just freeze Pymol.
Or is there another method to get these informations faster in a bunch?
Thanks,
Stefan

Re: [PyMOL] How to count the number of molecules in a selection?

[Pedro L. <psl...@gm...>]

Thank you!

Em qui., 9 de jul. de 2020 às 18:40, Thomas Holder <
tho...@sc...> escreveu:

> @cmd.extend
> def count_molecules(selection="all", quiet=0):
>     tmpsele = cmd.get_unused_name("_tmp")
>     count = 0
>     if cmd.select(tmpsele, selection):
>         count += 1
>         while cmd.select(tmpsele, f'{tmpsele} &! bm. first {tmpsele}'):
>             count += 1
>     cmd.delete(tmpsele)
>     if not int(quiet):
>         print(f' Number of molecules: {count}')
>     return count
>
> Cheers,
>   Thomas
>
>
> > On Jul 9, 2020, at 9:52 PM, Pedro Lacerda <psl...@gm...> wrote:
> >
> > ... via programming
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UEFS
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

Re: [PyMOL] How to count the number of molecules in a selection?

[Thomas H. <tho...@sc...>]

@cmd.extend
def count_molecules(selection="all", quiet=0):
    tmpsele = cmd.get_unused_name("_tmp")
    count = 0
    if cmd.select(tmpsele, selection):
        count += 1
        while cmd.select(tmpsele, f'{tmpsele} &! bm. first {tmpsele}'):
            count += 1
    cmd.delete(tmpsele)
    if not int(quiet):
        print(f' Number of molecules: {count}')
    return count

Cheers,
  Thomas


> On Jul 9, 2020, at 9:52 PM, Pedro Lacerda <psl...@gm...> wrote:
> 
> ... via programming
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] How to count the number of molecules in a selection?

[Pedro L. <psl...@gm...>]

... via programming

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

[PyMOL] Question about python command in PyMOL

[Hrutvik B. <hru...@gm...>]

Hello,

My name is Vik, I'm writing a python script that allows a user to input a
TSV (tab-separated value) file of PDB's which then edits them. I'm now
trying to change the code so that it can run directly in PyMOL instead of
having to run this python script and PyMOL separately. I'm having trouble
changing the python script so that it can run 100% in Pymol. I've pasted my
script below. Please let me know if there's a way to modify my code to
actually run in PyMOL. Thank you for your help.

Sincerely, Vik

import os

print("Files present with the .tsv extension:")
for file in os.listdir():
    if file[-4:] == ".tsv":
        print(file)

userinput = input('Enter the name of the TSV file you would like to be read:')
TSVfile = open(userinput)

#empty things filled later by script
unique = set()
f = open("ColorAndAlign.pml", "a")

#Eliminates duplicate PDBs
for row in TSVfile:
    a = row.split()
    if a[0] =="pdb":
        continue
    unique.add(a[0])

Re: [PyMOL] cmd.get_fastastr()

[Pedro L. <psl...@gm...>]

Thank you for this pearl.

Em ter., 7 de jul. de 2020 às 11:23, Thomas Holder <
tho...@sc...> escreveu:

> Hi Pedro,
>
> I would probably just count CA atoms. Something like this:
>
> # Check nearby peptides
> tmpsele = pm.get_unused_name("_tmp")
> pm.select(tmpsele, f"({sim_pdb} and polymer) within 5 of "
>     f"({entry.pdb_id} and (bysegi resid {entry.ligand_resid} "
>     f"and chain {entry.ligand_chain}))")
> for chain in pm.get_chains(tmpsele):
>     if pm.count_atoms(f"guide & bs. ({tmpsele} & chain {chain})") <= 25:
>         pm.delete(sim_pdb)
>         is_apo = False
>         break
> pm.delete(tmpsele)
>
>
> Cheers,
>   Thomas
>
>
> > On Jul 6, 2020, at 10:59 PM, Pedro Lacerda <psl...@gm...> wrote:
> >
> > I used the function to check if the fasta is smaller than 25 characters.
> If it is then it is a peptide:
> >
> https://github.com/pslacerda/pymol-labimm/blob/master/scripts/peptbase/create.py#L186
> >
> > There is another way to check for peptides using only selection?
> >
> > Em seg., 6 de jul. de 2020 às 02:47, Thomas Holder <
> tho...@sc...> escreveu:
> > Hi Pedro,
> >
> > cmd.get_fastastr() always returned a FASTA formatted string. What
> changed in PyMOL 2.2 is that it now creates a record for every chain, not
> just for every object. There is a new "key" argument, you get the old
> behavior with key="model".
> >
> > print(cmd.get_fastastr(key="model"))
> >
> > If you actually want the plain sequence and not the fasta formatted
> string, then I suggest you use a function like this:
> >
> > def get_sequence(selection='all'):
> >     return ''.join(L.strip() for L in
> cmd.get_fastastr(selection).splitlines()
> >                    if not L.startswith('>'))
> >
> >
> > Cheers,
> >   Thomas
> >
> >
> > > On Jul 4, 2020, at 5:17 PM, Pedro Lacerda <psl...@gm...> wrote:
> > >
> > > Hi,
> > >
> > > The get_fastastr function changed. Before it returned the aminoacid
> sequence. Now it returns a FASTA  formatted string.
> > >
> > > How can I get the old behaviour (ie. get the aminoacid sequence)?
> > >
> > > --
> > > Pedro Sousa Lacerda
> > >
> > > Laboratório de Bioinformática e Modelagem Molecular
> > > Faculdade de Farmácia / UFBA
> > >
> > > @pslacerda
> > > +55 71 9 9981-1856
> > > http://lattes.cnpq.br/8338596525330907
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > Archives:
> http://www.mail-archive.com/pym...@li...
> > > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >
> >
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

[Thomas H. <tho...@sc...>]

Hi Vaheh,

As far as I know, any Nvidia Quadro card with a 3-pin mini-DIN connector should work. For example the Quadro P4000 or P5000.

See also:
https://nvidia.custhelp.com/app/answers/detail/a_id/4845
https://www.schrodinger.com/kb/1745

Cheers,
  Thomas

> On Jul 7, 2020, at 4:16 PM, Oganesyan, Vaheh <vah...@as...> wrote:
> 
> Hi Thomas,
>  
> Can you also mention appropriate graphics cards that pair well with the Volfoni hardware?
>  
> Thank you.
>  
> From: Thomas Holder <tho...@sc...> 
> Sent: Tuesday, July 7, 2020 10:03 AM
> To: David Krause <kr...@bi...>
> Cc: pym...@li...
> Subject: Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)
>  
> Hi David,
> 
> I won't be able to really give a future proof recommendation, but at least I can say that we have emitters and glasses from Volfoni which work so far as a suitable replacement for Nvidia's 3D vision.
> 
> emitter: Volfoni ActivHub RF one (VPES-07000)
> glasses: Volfoni EDGE RF 3D (VPEG-03210)
> 
> A new technology that we at Schrödinger are pretty excited about is the Looking Glass display. We think this has much more potential than VR to be a useful tool for drug discovery and research.
> https://lookingglassfactory.com/schrodinger
> 
> Cheers,
> Thomas
> 
> 
> > On Jul 2, 2020, at 3:48 PM, David Krause <kr...@bi...> wrote:
> > 
> > Dear List,
> > 
> > 
> > one of our research groups needs a new 3D PyMol setup.
> > Looking through the wiki (https://pymolwiki.org/index.php/Stereo_3D_Display_Options) the most prominent way to do 3D seemed through Nvidia's 3D Vision,
> > but since 3D Vision is discontinued, i struggle a bit to find a good and future proof 3D solution.
> > 
> > Can you recommend a 3D Setup?
> > Should we go VR?
> > 
> > We're planning to use the Commercial PyMol version, not the open source one.
> > 
> > 
> > -- 
> > Mit freundlichen Grüßen / With kind regards
> > 
> > David Krause
> > IT
> > Institute of Biochemistry II
> > 
> > Gustav Embden-Zentrum der Biochemie
> > Goethe University Frankfurt - Medical Faculty
> > 
> > University Hospital - Building 75
> > Theodor-Stern-Kai 7
> > 60590 Frankfurt am Main
> > Germany
> > 
> > +49 (0)69 6301 84971 (Phone)
> > +49 (0)69 6301 84975 (Fax)
> > kr...@bi...
> > 
> > 
> > 
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > 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/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] cmd.get_fastastr()

[Thomas H. <tho...@sc...>]

Hi Pedro,

I would probably just count CA atoms. Something like this:

# Check nearby peptides
tmpsele = pm.get_unused_name("_tmp")
pm.select(tmpsele, f"({sim_pdb} and polymer) within 5 of "
    f"({entry.pdb_id} and (bysegi resid {entry.ligand_resid} "
    f"and chain {entry.ligand_chain}))")
for chain in pm.get_chains(tmpsele):
    if pm.count_atoms(f"guide & bs. ({tmpsele} & chain {chain})") <= 25:
        pm.delete(sim_pdb)
        is_apo = False
        break
pm.delete(tmpsele)


Cheers,
  Thomas


> On Jul 6, 2020, at 10:59 PM, Pedro Lacerda <psl...@gm...> wrote:
> 
> I used the function to check if the fasta is smaller than 25 characters. If it is then it is a peptide:
> https://github.com/pslacerda/pymol-labimm/blob/master/scripts/peptbase/create.py#L186
> 
> There is another way to check for peptides using only selection?
> 
> Em seg., 6 de jul. de 2020 às 02:47, Thomas Holder <tho...@sc...> escreveu:
> Hi Pedro,
> 
> cmd.get_fastastr() always returned a FASTA formatted string. What changed in PyMOL 2.2 is that it now creates a record for every chain, not just for every object. There is a new "key" argument, you get the old behavior with key="model".
> 
> print(cmd.get_fastastr(key="model"))
> 
> If you actually want the plain sequence and not the fasta formatted string, then I suggest you use a function like this:
> 
> def get_sequence(selection='all'):
>     return ''.join(L.strip() for L in cmd.get_fastastr(selection).splitlines()
>                    if not L.startswith('>'))
> 
> 
> Cheers,
>   Thomas
> 
> 
> > On Jul 4, 2020, at 5:17 PM, Pedro Lacerda <psl...@gm...> wrote:
> > 
> > Hi,
> > 
> > The get_fastastr function changed. Before it returned the aminoacid sequence. Now it returns a FASTA  formatted string.
> > 
> > How can I get the old behaviour (ie. get the aminoacid sequence)?
> > 
> > -- 
> > Pedro Sousa Lacerda
> > 
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> > 
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

[Oganesyan, V. <vah...@as...>]

Hi Thomas,

Can you also mention appropriate graphics cards that pair well with the Volfoni hardware?

Thank you.

From: Thomas Holder <tho...@sc...>
Sent: Tuesday, July 7, 2020 10:03 AM
To: David Krause <kr...@bi...>
Cc: pym...@li...
Subject: Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

Hi David,

I won't be able to really give a future proof recommendation, but at least I can say that we have emitters and glasses from Volfoni which work so far as a suitable replacement for Nvidia's 3D vision.

emitter: Volfoni ActivHub RF one (VPES-07000)
glasses: Volfoni EDGE RF 3D (VPEG-03210)

A new technology that we at Schrödinger are pretty excited about is the Looking Glass display. We think this has much more potential than VR to be a useful tool for drug discovery and research.
https://lookingglassfactory.com/schrodinger<https://lookingglassfactory.com/schrodinger>

Cheers,
Thomas


> On Jul 2, 2020, at 3:48 PM, David Krause <kr...@bi...<mailto:kr...@bi...>> wrote:
>
> Dear List,
>
>
> one of our research groups needs a new 3D PyMol setup.
> Looking through the wiki (https://pymolwiki.org/index.php/Stereo_3D_Display_Options<https://pymolwiki.org/index.php/Stereo_3D_Display_Options>) the most prominent way to do 3D seemed through Nvidia's 3D Vision,
> but since 3D Vision is discontinued, i struggle a bit to find a good and future proof 3D solution.
>
> Can you recommend a 3D Setup?
> Should we go VR?
>
> We're planning to use the Commercial PyMol version, not the open source one.
>
>
> --
> Mit freundlichen Grüßen / With kind regards
>
> David Krause
> IT
> Institute of Biochemistry II
>
> Gustav Embden-Zentrum der Biochemie
> Goethe University Frankfurt - Medical Faculty
>
> University Hospital - Building 75
> Theodor-Stern-Kai 7
> 60590 Frankfurt am Main
> Germany
>
> +49 (0)69 6301 84971 (Phone)
> +49 (0)69 6301 84975 (Fax)
> kr...@bi...<mailto:kr...@bi...>
>
>
>
> _______________________________________________
> 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>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



_______________________________________________
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Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

[Thomas H. <tho...@sc...>]

Hi David,

I won't be able to really give a future proof recommendation, but at least I can say that we have emitters and glasses from Volfoni which work so far as a suitable replacement for Nvidia's 3D vision.

emitter: Volfoni ActivHub RF one (VPES-07000)
glasses: Volfoni EDGE RF 3D (VPEG-03210)

A new technology that we at Schrödinger are pretty excited about is the Looking Glass display. We think this has much more potential than VR to be a useful tool for drug discovery and research.
https://lookingglassfactory.com/schrodinger

Cheers,
  Thomas


> On Jul 2, 2020, at 3:48 PM, David Krause <kr...@bi...> wrote:
> 
> Dear List,
> 
> 
> one of our research groups needs a new 3D PyMol setup.
> Looking through the wiki (https://pymolwiki.org/index.php/Stereo_3D_Display_Options) the most prominent way to do 3D seemed through Nvidia's 3D Vision,
> but since 3D Vision is discontinued, i struggle a bit to find a good and future proof 3D solution.
> 
> Can you recommend a 3D Setup?
> Should we go VR?
> 
> We're planning to use the Commercial PyMol version, not the open source one.
> 
> 
> -- 
> Mit freundlichen Grüßen / With kind regards
> 
> David Krause
> IT
> Institute of Biochemistry II
> 
> Gustav Embden-Zentrum der Biochemie
> Goethe University Frankfurt - Medical Faculty
> 
> University Hospital - Building 75
> Theodor-Stern-Kai 7
> 60590 Frankfurt am Main
> Germany
> 
> +49 (0)69 6301 84971 (Phone)
> +49 (0)69 6301 84975 (Fax)
> kr...@bi...
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] cmd.get_fastastr()

[Pedro L. <psl...@gm...>]

I used the function to check if the fasta is smaller than 25 characters. If
it is then it is a peptide:
https://github.com/pslacerda/pymol-labimm/blob/master/scripts/peptbase/create.py#L186

There is another way to check for peptides using only selection?

Em seg., 6 de jul. de 2020 às 02:47, Thomas Holder <
tho...@sc...> escreveu:

> Hi Pedro,
>
> cmd.get_fastastr() always returned a FASTA formatted string. What changed
> in PyMOL 2.2 is that it now creates a record for every chain, not just for
> every object. There is a new "key" argument, you get the old behavior with
> key="model".
>
> print(cmd.get_fastastr(key="model"))
>
> If you actually want the plain sequence and not the fasta formatted
> string, then I suggest you use a function like this:
>
> def get_sequence(selection='all'):
>     return ''.join(L.strip() for L in
> cmd.get_fastastr(selection).splitlines()
>                    if not L.startswith('>'))
>
>
> Cheers,
>   Thomas
>
>
> > On Jul 4, 2020, at 5:17 PM, Pedro Lacerda <psl...@gm...> wrote:
> >
> > Hi,
> >
> > The get_fastastr function changed. Before it returned the aminoacid
> sequence. Now it returns a FASTA  formatted string.
> >
> > How can I get the old behaviour (ie. get the aminoacid sequence)?
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

Re: [PyMOL] 2 proteins plus ligand

[Pedro L. <psl...@gm...>]

Hi Larry,

My guess is that you need a docking tool (like DOCKTHOR server;
https://dockthor.lncc.br/v2/).

So you pulled the protein structures from the web... the coordinates from
one is arbitrary to the other. If they interact in a way that forms a
protein-protein interface (PPI) then you need a PPI docking software also
to get the complex. But my guess is that you don't need the complex and the
small ligand will bind to only one of the proteins... I don't know.

Hope it helps,
Abraços,

Em seg., 6 de jul. de 2020 às 15:09, Larry Mahan <di...@gm...>
escreveu:

> Hello,
> Like others, I am new to Pymol.  I am interested in seeing if a small
> molecule (.mol2) "ligand" has a binding site on one of two proteins (2KAV
> and 5FEB) but since they are known to interact, it might be something
> between the two.  While I am also looking into/learning Autodock Vina, in
> Pymol I tried pulling up one protein (successful), then the other
> (successful) and interestingly they came up somewhat "intertwined" next to
> each other.  Then I brought in the small molecule (300MW) and it jumped to
> an orientation with one end next to an a.a. of one protein and the other
> end next to an a.a. of the other. And some of the side groups made possible
> sense (e.g. H-bonding).  No matter which order I pull up the proteins or
> molecule, they always configure this same way.
>
> So my question is ... are these alignments just fortuitous? (then why the
> same each permutation of adding) or is Pymol suggesting an optimal
> alignment for the 2 proteins and "suggesting" a binding site for the small
> molecule?
> Is there a better way to look at this?
> Thanks for any insights!
>
> Larry (pymol newbie)
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

[PyMOL] 2 proteins plus ligand

[Larry M. <di...@gm...>]

Hello,
Like others, I am new to Pymol.  I am interested in seeing if a small
molecule (.mol2) "ligand" has a binding site on one of two proteins (2KAV
and 5FEB) but since they are known to interact, it might be something
between the two.  While I am also looking into/learning Autodock Vina, in
Pymol I tried pulling up one protein (successful), then the other
(successful) and interestingly they came up somewhat "intertwined" next to
each other.  Then I brought in the small molecule (300MW) and it jumped to
an orientation with one end next to an a.a. of one protein and the other
end next to an a.a. of the other. And some of the side groups made possible
sense (e.g. H-bonding).  No matter which order I pull up the proteins or
molecule, they always configure this same way.

So my question is ... are these alignments just fortuitous? (then why the
same each permutation of adding) or is Pymol suggesting an optimal
alignment for the 2 proteins and "suggesting" a binding site for the small
molecule?
Is there a better way to look at this?
Thanks for any insights!

Larry (pymol newbie)

Re: [PyMOL] cmd.get_fastastr()

[Thomas H. <tho...@sc...>]

Hi Pedro,

cmd.get_fastastr() always returned a FASTA formatted string. What changed in PyMOL 2.2 is that it now creates a record for every chain, not just for every object. There is a new "key" argument, you get the old behavior with key="model".

print(cmd.get_fastastr(key="model"))

If you actually want the plain sequence and not the fasta formatted string, then I suggest you use a function like this:

def get_sequence(selection='all'):
    return ''.join(L.strip() for L in cmd.get_fastastr(selection).splitlines()
                   if not L.startswith('>'))


Cheers,
  Thomas


> On Jul 4, 2020, at 5:17 PM, Pedro Lacerda <psl...@gm...> wrote:
> 
> Hi,
> 
> The get_fastastr function changed. Before it returned the aminoacid sequence. Now it returns a FASTA  formatted string.
> 
> How can I get the old behaviour (ie. get the aminoacid sequence)?
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Running PyMol (Linux) on Chromebook

[Wink, D. J <dw...@ui...>]

Dr. Willis:

Thank you very much for the suggestion. I will proceed to share it with the students and we will gladly report back what happens.

As for the instruction line you mention: I assume this input on the (base) environment line indicated within the instalpython3.com/chromebook instructions. Or should we do it on the command line that appears *after* starting python?

Best wishes
Donald Wink

From: Jordan Willis <jwi...@gm...>
Sent: Sunday, July 5, 2020 8:15 PM
To: Wink, Donald J <dw...@ui...>
Cc: pym...@li...
Subject: Re: [PyMOL] Running PyMol (Linux) on Chromebook

Might I recommend a conda based solution.

https://installpython3.com/chromebook/

Install miniconda on your Chromebook using the attached link.

Then you can simply use conda to install pymol


conda install -c schrodinger pymol

Jordan Willis, PhD


On Jul 5, 2020, at 4:36 PM, Wink, Donald J <dw...@ui...<mailto:dw...@ui...>> wrote:

I am a university (UIC) faculty member who is directing some entering college students in a structured research programs. Things are going pretty well for those with MacOS or Windows computers. But I have a couple of students with Chromebooks who are attempting to install and run the Linux version.

We’ve downloaded and extracted the tar files but encountered some library issues that are apparently blocking startup.

If there are users with experience in managing this environment, I’d love to pose some more detailed questions.

Thanks
Donald Wink


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

Re: [PyMOL] Running PyMol (Linux) on Chromebook

[J.R. W <jwi...@gm...>]

> I assume this input on the (base) environment line indicated within the instalpython3.com/chromebook <http://instalpython3.com/chromebook> instructions.



This one. This is the command line terminal for instructions to send to the computer. Not to be confused with the Python Interpreter REPL (the >>> that comes up after typing “python”)

Jordan


> On Jul 5, 2020, at 8:28 PM, Wink, Donald J <dw...@ui...> wrote:
> 
> Dr. Willis:
> 
> Thank you very much for the suggestion. I will proceed to share it with the students and we will gladly report back what happens.
>  
> As for the instruction line you mention:  Or should we do it on the command line that appears *after* starting python?
>  
> Best wishes
> Donald Wink
>  
> From: Jordan Willis <jwi...@gm...> 
> Sent: Sunday, July 5, 2020 8:15 PM
> To: Wink, Donald J <dw...@ui...>
> Cc: pym...@li...
> Subject: Re: [PyMOL] Running PyMol (Linux) on Chromebook
>  
> Might I recommend a conda based solution. 
>  
> https://installpython3.com/chromebook/ <https://installpython3.com/chromebook/>
>  
> Install miniconda on your Chromebook using the attached link. 
>  
> Then you can simply use conda to install pymol
>  
>  
> conda install -c schrodinger pymol
>  
> Jordan Willis, PhD
> 
> 
> On Jul 5, 2020, at 4:36 PM, Wink, Donald J <dw...@ui... <mailto:dw...@ui...>> wrote:
>  
> I am a university (UIC) faculty member who is directing some entering college students in a structured research programs. Things are going pretty well for those with MacOS or Windows computers. But I have a couple of students with Chromebooks who are attempting to install and run the Linux version.
>  
> We’ve downloaded and extracted the tar files but encountered some library issues that are apparently blocking startup.
>  
> If there are users with experience in managing this environment, I’d love to pose some more detailed questions.
>  
> Thanks
> Donald Wink
>  
>  
> _______________________________________________
> 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>

Re: [PyMOL] Multi sequence edition simultaneously

[sepehr d. <dej...@gm...>]

Simultaneous multi-sequence edition

Hi all,

I have a question regarding adding peptide sequence to the original
sequence in PyMOL. I have an original structure of a nanoparticle
consisting of 420 monomers and I like to add a similar peptide sequence to
each monomer. Is that any easy way to apply a sequence addition/ change to
one monomer and apply it to the. whole structure rather than going and
adding the sequence manually 420 times in PyMOL?

On Sun, Jul 5, 2020 at 7:53 AM sepehr dejdar <dej...@gm...> wrote:

>
> Hi,
>
> I have a question regarding adding peptide sequence to the original
> sequence in PyMOL. I have an original structure of a nanoparticle
> consisting of 420 monomers and I like to add a similar peptide sequence to
> each monomer. Is that any easy way to apply a sequence addition/ change to
> one monomer and apply it to the. whole structure rather than going and
> adding the sequence manually 420 times in PyMOL?
>
> Sincerely,
> Sepehr
> Sent from my iPhone

Re: [PyMOL] Running PyMol (Linux) on Chromebook

[Jordan W. <jwi...@gm...>]

Might I recommend a conda based solution. 

https://installpython3.com/chromebook/ <https://installpython3.com/chromebook/>

Install miniconda on your Chromebook using the attached link. 

Then you can simply use conda to install pymol


conda install -c schrodinger pymol

Jordan Willis, PhD

> On Jul 5, 2020, at 4:36 PM, Wink, Donald J <dw...@ui...> wrote:
> 
> I am a university (UIC) faculty member who is directing some entering college students in a structured research programs. Things are going pretty well for those with MacOS or Windows computers. But I have a couple of students with Chromebooks who are attempting to install and run the Linux version.
>  
> We’ve downloaded and extracted the tar files but encountered some library issues that are apparently blocking startup.
>  
> If there are users with experience in managing this environment, I’d love to pose some more detailed questions.
>  
> Thanks
> Donald Wink
>  
>  
> _______________________________________________
> 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] Running PyMol (Linux) on Chromebook

[Wink, D. J <dw...@ui...>]

I am a university (UIC) faculty member who is directing some entering college students in a structured research programs. Things are going pretty well for those with MacOS or Windows computers. But I have a couple of students with Chromebooks who are attempting to install and run the Linux version.

We've downloaded and extracted the tar files but encountered some library issues that are apparently blocking startup.

If there are users with experience in managing this environment, I'd love to pose some more detailed questions.

Thanks
Donald Wink

[PyMOL] Multi sequence edition simultaneously

[sepehr d. <dej...@gm...>]

Hi,

I have a question regarding adding peptide sequence to the original sequence in PyMOL. I have an original structure of a nanoparticle consisting of 420 monomers and I like to add a similar peptide sequence to each monomer. Is that any easy way to apply a sequence addition/ change to one monomer and apply it to the. whole structure rather than going and adding the sequence manually 420 times in PyMOL?

Sincerely,
Sepehr
Sent from my iPhone