pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Selecting the water within a protein channel

[Jason M. <par...@gm...>]

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
<https://signaldomn.online/click?redirect=https%3A%2F%2Fpastebin.com%2F1iBZ7rKi&dID=1616175096424&linkName=https://pastebin.com/1iBZ7rKi>

Best,
Jason M.

[PyMOL] Using pyvol plug in pymol

[ALBAYATI S. H. K. / U. <gs...@st...>]

Hi guys
May I know if anyone have experience in using pyvol plug in prosperity to
check the protein binding site volume.
Thanks
Samah Albayati

[PyMOL] Modify anisotropic temperature factors

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

Hello,
I now know it's possible to modify the isotropic B-values with

alter SELECTION, b=VALUE

but is there a way to change the anisotropic temperature covariance matrix?
I can read it for example with

cmd.get_model(SELECTION, 1).atom[0].u_aniso

But neither trying to change it with

cmd.get_model(SELECTION, 1).atom[0].u_aniso = [1, 2, 3, 4, 5, 6]


nor

alter SELECTION, u_aniso=[1, 2, 3, 4, 5, 6]

has any effect. The second says it changed the selected atoms, but reading the array back shows the old values.

Is it possible to change this array from within pymol?
Thanks
Stefan

Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

[Ali S. K. <aku...@un...>]

Hi Jeff, 

That would be cmd.disable("object name") # https://pymolwiki.org/index.php/Disable 

Cheers,

Ali

On 1/3/21, 9:05 pm, "Jeff Saxon" <jms...@gm...> wrote:

    Thank you very much, Ali!
    Yes, actually, I suppose I have set up vdw radii using those commands,
    considering specific selections,e.g this is part of my pymol script
    that I am using in bash.
    $pymol -c -d "
    from pymol import cmd

    cmd.load('${storage}/${syst_name}/all_clusters.pdb')
    cmd.split_states('all_clusters*')
    cmd.select('all_clusters*')
    cmd.show('spheres', 'sele')
    cmd.set('sphere_transparency', '0.2', 'sele')
    cmd.color('marine', 'sele' )
    cmd.alter('all_clusters*', 'vdw=0.75')
    cmd.select('all_clusters*')
    cmd.show( 'spheres', 'sele' )
    cmd.rebuild()
    cmd.bg_color('white')
    cmd.save('${syst}/${syst_name}.pse')
    cmd.png('${vizu}/${syst_name}.png',width=${image},height=${image},dpi=50,ray=0)
    "

    Eventually in my saved pml session everything looks fine BUT on the
    png image some of the spheres (notably located on the back plane in
    the space) are appeared to be smaller compared to the others (although
    in pymol all of them were identified using the same selection). So
    probably this is an issue of PNG command, which I used to make a
    screenshot.

    Also one question: as it can be seed from my script I used command
    split states for all_clusters object (which contain 100 conformations
    of the centre of mass) and then operate with the visualization of
    splited states. I noticed that the multi-model object is still exist
    along with its separate models, which command could be used to disable
    its visualization in GUI (like if I click on it in the context menu,
    while operating in gui)?

    Cheers,
    J.

    пт, 26 февр. 2021 г. в 12:29, Ali Saad Kusay <aku...@un...>:
    >
    > Hi Jeff,
    >
    > The sphere size is controlled by the vdw property, to change it:
    > alter *, vdw=1.0 # this will set the sphere size to be equal for all atom i.e. hydrogens atom would be same size as carbon
    >
    > you also need to use the "rebuild" command to implement the changes
    >
    > At this point, you can control the sphere sizes consistently using:
    > set sphere_scale, 1.5 # or what ever size you need
    >
    > Cheers,
    >
    > Ali
    >
    > Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
    > The University of Sydney School of Pharmacy | Faculty of Medicine and Health
    > 424, Brain and Mind Centre | The University of Sydney | NSW 2050
    >
    >
    > On 26/2/21, 2:15 am, "Jeff Saxon" <jms...@gm...> wrote:
    >
    >     Dear Pymol Users,
    >
    >     Working on the visualisation of protein-ligand interactions, notably
    >     focusing on the visualisation of sphres atoms covered protein surface,
    >     I noticed on the resulted PNG that some sphere objects (located on the
    >     backing plane) looks VERY small compared to the rest. For example as
    >     it could be seen while major spheres represent like spheres, some of
    >     them look like dots, while in the pml session everything looks
    >     correctly. How could I fix using some pymol settings ?
    >     Thank you in advance!
    >     J
    >

Re: [PyMOL] Ribbon width per residue

[Ali S. K. <aku...@un...>]

Hi Stefan,

As far as a I know cartoon width settings like "cartoon_oval_length" and "cartoon_oval_width" are object level settings meaning they cannot be implemented on a per residues basis (https://pymolwiki.org/index.php/Cartoon_Helix_Settings).

You can use the putty mode which sets width according to b-factors (https://www.pymolwiki.org/index.php/File:B_factor_putty.png)

You can set the residue b-factors to any desired per residue width

Another way is to use a colour spectrum instead of changing width

Let me know if you are interested in either of these approaches and I can help you

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050

On 2/3/21, 1:37 am, "achatz" <ac...@wz...> wrote:

    Hello,
    is it possible in Pymol to set the width of the ribbon representation per atom/residue like Chimera does with its ribscale command?
    Thanks Stefan



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[PyMOL] Ribbon width per residue

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

Hello,
is it possible in Pymol to set the width of the ribbon representation per atom/residue like Chimera does with its ribscale command?
Thanks Stefan

Re: [PyMOL] [EXTERNAL] Re: Question about visualisation of the spheres objects on PNG image

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

Hi Jeff,

In the png file that you posted last week, the smaller spheres
were a lot smaller. They reminded me of nb_spheres. 
Did you turn on the display of nb_spheres in your .pymolrc file?

Best regards,

Blaine

________________________________________
From: Jeff Saxon [jms...@gm...]
Sent: Monday, March 01, 2021 4:04 AM
To: Ali Saad Kusay
Cc: pymol-users
Subject: [EXTERNAL] Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

Thank you very much, Ali!
Yes, actually, I suppose I have set up vdw radii using those commands,
considering specific selections,e.g this is part of my pymol script
that I am using in bash.
$pymol -c -d "
from pymol import cmd

cmd.load('${storage}/${syst_name}/all_clusters.pdb')
cmd.split_states('all_clusters*')
cmd.select('all_clusters*')
cmd.show('spheres', 'sele')
cmd.set('sphere_transparency', '0.2', 'sele')
cmd.color('marine', 'sele' )
cmd.alter('all_clusters*', 'vdw=0.75')
cmd.select('all_clusters*')
cmd.show( 'spheres', 'sele' )
cmd.rebuild()
cmd.bg_color('white')
cmd.save('${syst}/${syst_name}.pse')
cmd.png('${vizu}/${syst_name}.png',width=${image},height=${image},dpi=50,ray=0)
"

Eventually in my saved pml session everything looks fine BUT on the
png image some of the spheres (notably located on the back plane in
the space) are appeared to be smaller compared to the others (although
in pymol all of them were identified using the same selection). So
probably this is an issue of PNG command, which I used to make a
screenshot.

Also one question: as it can be seed from my script I used command
split states for all_clusters object (which contain 100 conformations
of the centre of mass) and then operate with the visualization of
splited states. I noticed that the multi-model object is still exist
along with its separate models, which command could be used to disable
its visualization in GUI (like if I click on it in the context menu,
while operating in gui)?

Cheers,
J.

пт, 26 февр. 2021 г. в 12:29, Ali Saad Kusay <aku...@un...>:
>
> Hi Jeff,
>
> The sphere size is controlled by the vdw property, to change it:
> alter *, vdw=1.0 # this will set the sphere size to be equal for all atom i.e. hydrogens atom would be same size as carbon
>
> you also need to use the "rebuild" command to implement the changes
>
> At this point, you can control the sphere sizes consistently using:
> set sphere_scale, 1.5 # or what ever size you need
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
> On 26/2/21, 2:15 am, "Jeff Saxon" <jms...@gm...> wrote:
>
>     Dear Pymol Users,
>
>     Working on the visualisation of protein-ligand interactions, notably
>     focusing on the visualisation of sphres atoms covered protein surface,
>     I noticed on the resulted PNG that some sphere objects (located on the
>     backing plane) looks VERY small compared to the rest. For example as
>     it could be seen while major spheres represent like spheres, some of
>     them look like dots, while in the pml session everything looks
>     correctly. How could I fix using some pymol settings ?
>     Thank you in advance!
>     J
>


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Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

[Jeff S. <jms...@gm...>]

Thank you very much, Ali!
Yes, actually, I suppose I have set up vdw radii using those commands,
considering specific selections,e.g this is part of my pymol script
that I am using in bash.
$pymol -c -d "
from pymol import cmd

cmd.load('${storage}/${syst_name}/all_clusters.pdb')
cmd.split_states('all_clusters*')
cmd.select('all_clusters*')
cmd.show('spheres', 'sele')
cmd.set('sphere_transparency', '0.2', 'sele')
cmd.color('marine', 'sele' )
cmd.alter('all_clusters*', 'vdw=0.75')
cmd.select('all_clusters*')
cmd.show( 'spheres', 'sele' )
cmd.rebuild()
cmd.bg_color('white')
cmd.save('${syst}/${syst_name}.pse')
cmd.png('${vizu}/${syst_name}.png',width=${image},height=${image},dpi=50,ray=0)
"

Eventually in my saved pml session everything looks fine BUT on the
png image some of the spheres (notably located on the back plane in
the space) are appeared to be smaller compared to the others (although
in pymol all of them were identified using the same selection). So
probably this is an issue of PNG command, which I used to make a
screenshot.

Also one question: as it can be seed from my script I used command
split states for all_clusters object (which contain 100 conformations
of the centre of mass) and then operate with the visualization of
splited states. I noticed that the multi-model object is still exist
along with its separate models, which command could be used to disable
its visualization in GUI (like if I click on it in the context menu,
while operating in gui)?

Cheers,
J.

пт, 26 февр. 2021 г. в 12:29, Ali Saad Kusay <aku...@un...>:
>
> Hi Jeff,
>
> The sphere size is controlled by the vdw property, to change it:
> alter *, vdw=1.0 # this will set the sphere size to be equal for all atom i.e. hydrogens atom would be same size as carbon
>
> you also need to use the "rebuild" command to implement the changes
>
> At this point, you can control the sphere sizes consistently using:
> set sphere_scale, 1.5 # or what ever size you need
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
> On 26/2/21, 2:15 am, "Jeff Saxon" <jms...@gm...> wrote:
>
>     Dear Pymol Users,
>
>     Working on the visualisation of protein-ligand interactions, notably
>     focusing on the visualisation of sphres atoms covered protein surface,
>     I noticed on the resulted PNG that some sphere objects (located on the
>     backing plane) looks VERY small compared to the rest. For example as
>     it could be seen while major spheres represent like spheres, some of
>     them look like dots, while in the pml session everything looks
>     correctly. How could I fix using some pymol settings ?
>     Thank you in advance!
>     J
>

[PyMOL] Question: Align object from group (and move rest of group with it)

[Jacek K. <jk...@ze...>]

Dear all,

I am trying to align (or pair fit) two structures and, at the same time,
move a density map belonging to the mobile structure with the alignment.
What would be the best way to achieve that?

I'd appreciate help or suggestions!

Thanks in advance!

Best,
Jacek

Re: [PyMOL] Calculating r.m.s.d values for ligands once proteins have been aligned

[Ali S. K. <aku...@un...>]

Hi Sacha,

You should be able to do this using the rms_curr command (https://pymolwiki.org/index.php/Rms_cur)

This will compute the rmsd without performing a superimposition

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050


From: "CHARLTON, SACHA (UG) via PyMOL-users" <pym...@li...>
Reply to: "CHARLTON, SACHA (UG)" <S.C...@wa...>
Date: Friday, 26 February 2021 at 9:31 pm
To: "pym...@li..." <pym...@li...>
Subject: [PyMOL] Calculating r.m.s.d values for ligands once proteins have been aligned

Dear all,

I hope you are keeping safe and well.

I am a new user to PyMOL and had a query that I hope someone can help me with. I have performed an alignment of two homologs with the super command on PyMOL, I have generated a rmsd value for this alignment using the C-alpha atoms as comparison. Both these proteins had ligands bound, and I would like to compare how closely these respective ligands match in space/binding pose. Would someone please be able to tell me how to calculate an rmsd value now for these ligands together once the proteins have been superimposed, without changing the coordinates of the ligands?

Thank you so much!

All the best,
Sacha

Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

[Ali S. K. <aku...@un...>]

Hi Jeff, 

The sphere size is controlled by the vdw property, to change it:
alter *, vdw=1.0 # this will set the sphere size to be equal for all atom i.e. hydrogens atom would be same size as carbon

you also need to use the "rebuild" command to implement the changes

At this point, you can control the sphere sizes consistently using:
set sphere_scale, 1.5 # or what ever size you need

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
 

On 26/2/21, 2:15 am, "Jeff Saxon" <jms...@gm...> wrote:

    Dear Pymol Users,

    Working on the visualisation of protein-ligand interactions, notably
    focusing on the visualisation of sphres atoms covered protein surface,
    I noticed on the resulted PNG that some sphere objects (located on the
    backing plane) looks VERY small compared to the rest. For example as
    it could be seen while major spheres represent like spheres, some of
    them look like dots, while in the pml session everything looks
    correctly. How could I fix using some pymol settings ?
    Thank you in advance!
    J

[PyMOL] Calculating r.m.s.d values for ligands once proteins have been aligned

[CHARLTON, S. (UG) <S.C...@wa...>]

Dear all,

I hope you are keeping safe and well.

I am a new user to PyMOL and had a query that I hope someone can help me with. I have performed an alignment of two homologs with the super command on PyMOL, I have generated a rmsd value for this alignment using the C-alpha atoms as comparison. Both these proteins had ligands bound, and I would like to compare how closely these respective ligands match in space/binding pose. Would someone please be able to tell me how to calculate an rmsd value now for these ligands together once the proteins have been superimposed, without changing the coordinates of the ligands?

Thank you so much!

All the best,
Sacha

Re: [PyMOL] FW: Names of objects in GUI in pymol

[Jeff S. <jms...@gm...>]

It works, thank you Ali!!
Cheers,
J.

вт, 23 февр. 2021 г. в 07:26, Ali Saad Kusay <aku...@un...>:
>
> Resending since I forgot to copy the PyMOL mailing list
>
> On 23/2/21, 7:17 am, "Ali Saad Kusay" <aku...@un...> wrote:
>
>     Hi Jeff,
>
>     There is several ways you can do this with string function in python https://www.w3schools.com/python/python_ref_string.asp.
>     This is an easy one liner which replace "COG_" of "AA" with nothing if found
>     label sele, model.replace('COG_','').replace('AA_','')
>
>     Another way to do this is lets say you select an object beginning with COG_, you can slice away the first 4 characters to get rid of COG_
>     label sele, model[4:]
>
>     Cheers,
>
>     Ali
>
>     On 23/2/21, 1:32 am, "Jeff Saxon" <jms...@gm...> wrote:
>
>         pardon, just one additional question, which might be alitle bit custom
>         issue, however..
>
>         Imagine, that I have 2 groups of the pdbs objects loaded into same
>         pymol session: 2 pdbs with the prefix COG_*.pdb, and 2 pdbs with the
>         prefix AA_*.pdb. Would it be possible to subtract the both prefixes
>         from the labels produced using cmd.label('sele', 'model') ? Or
>         alternatively I ought to rename the both objects before their
>         labelling? What are the other possible solutions ?
>
>         пн, 22 февр. 2021 г. в 15:07, Jeff Saxon <jms...@gm...>:
>         >
>         > Right, this is what I was looking for!
>         > Thank you so much, Ali!
>         > Cheers,
>         > J.
>         >
>         > пн, 22 февр. 2021 г. в 14:59, Ali Saad Kusay <aku...@un...>:
>         > >
>         > > No worries Jeff,
>         > >
>         > > Use editing mode and you can move it with mouse. See around 3:30 in this video, https://protect-au.mimecast.com/s/_r_iCANpgjCwqAQMtGDPTv?domain=m.youtube.com.
>         > >
>         > > You can move all labels with this command:
>         > >
>         > > set label_position (x,y,z)
>         > >
>         > > This will move the labels as needed in the x, y and z directions
>         > >
>         > > Cheers,
>         > >
>         > > Ali
>         > >
>         > >
>         > > On 23 Feb 2021, at 12:51 am, Jeff Saxon <jms...@gm...> wrote:
>         > >
>         > > Thank you, Ali!
>         > > One question - is there any command which would allow to change
>         > > position of the text of the label produced by the label sele, model ?
>         > > In fact as I noticed, it produces correctly label text just above the
>         > > object, while I need to move it a litle bit in one of the directions
>         > > ...
>         > > Cheers,
>         > >
>         > > пн, 22 февр. 2021 г. в 14:14, Ali Saad Kusay <aku...@un...>:
>         > >
>         > >
>         > > Hi Jeff,
>         > >
>         > >
>         > > The name of an object is stored in the model attribute.
>         > >
>         > > Select an atom in the object and use this command:
>         > >
>         > > label sele, model
>         > >
>         > >
>         > > If you want to automate this over all your PyMOL objects, you can use this script, this will put a label at the centre of each object but it has to create a pseudoatom for each one. You can change coords.mean to coords.min or cords.max if you want the label to go at the corner of each object
>         > >
>         > > for i in cmd.get_object_list():
>         > >
>         > >    coords = cmd.get_coords(i)
>         > >
>         > >    mean_coords = coords.mean(axis=0).tolist()
>         > >
>         > >    cmd.pseudoatom(i+"_psu", pos=mean_coords)
>         > >
>         > >
>         > >    cmd.label(i+"_psu", "'{}'".format(i))
>         > >
>         > >
>         > > Cheers,
>         > >
>         > >
>         > > Ali
>         > >
>         > >
>         > > Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
>         > >
>         > > The University of Sydney School of Pharmacy | Faculty of Medicine and Health
>         > >
>         > > 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>         > >
>         > >
>         > > On 22/2/21, 10:47 pm, "Jeff Saxon" <jms...@gm...> wrote:
>         > >
>         > >
>         > >    Dear Pymol Users,
>         > >
>         > >
>         > >    I am looking for a possibility to display names of the objects in the
>         > >
>         > >    pymol session. For example I loaded 4 objects corresponded to 2
>         > >
>         > >    different positions of the same ligand as well as 2 positions of its
>         > >
>         > >    centres of masses. How would it be possible to display the names of
>         > >
>         > >    each of these loaded objects just near their visualisations in GUI in
>         > >
>         > >    order that I could understand who is who without operating with the
>         > >
>         > >    objects on the context menu?
>         > >
>         > >
>         > >
>         > >    _______________________________________________
>         > >
>         > >    PyMOL-users mailing list
>         > >
>         > >    Archives: https://protect-au.mimecast.com/s/1Qz7CBNqjlCw25G3t6a3Ug?domain=mail-archive.com
>         > >
>         > >    Unsubscribe: https://protect-au.mimecast.com/s/FesTCD1vlpTEGl9QfAQcf7?domain=sourceforge.net
>         > >
>         > >
>         > >
>         > >
>
>
>

[PyMOL] Question about visualisation of the spheres objects on PNG image

[Jeff S. <jms...@gm...>]

Dear Pymol Users,

Working on the visualisation of protein-ligand interactions, notably
focusing on the visualisation of sphres atoms covered protein surface,
I noticed on the resulted PNG that some sphere objects (located on the
backing plane) looks VERY small compared to the rest. For example as
it could be seen while major spheres represent like spheres, some of
them look like dots, while in the pml session everything looks
correctly. How could I fix using some pymol settings ?
Thank you in advance!
J

Re: [PyMOL] How to read the alignment object

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

Hi Pedro,

Are you looking for cmd.get_raw_alignment()?

https://pymolwiki.org/index.php/Get_raw_alignment

Cheers,
  Thomas

On Tue, Feb 23, 2021 at 9:33 PM Pedro Lacerda <psl...@gm...> wrote:
>
> Hi,
>
> I aligned my structures with the align command and the object argument. So I got an alignment object.
>
> But how can I read this data structure?
>
> --
> 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
> _______________________________________________
> 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 read the alignment object

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

Hi,

I aligned my structures with the align command and the object argument. So
I got an alignment object.

But how can I read this data structure?

-- 
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

[PyMOL] How to add dynamic bonds

[Carlos B. <cb...@ua...>]

Hi

I've been playing around with some MD trajectory files (pdb). During the MD calculation, some bonds are broken and other ones are formed, including H-bonds. Is there an option to see the changes in bonding in trajectory files?

Best Regards,
Carlos

[PyMOL] FW: Names of objects in GUI in pymol

[Ali S. K. <aku...@un...>]

Resending since I forgot to copy the PyMOL mailing list

On 23/2/21, 7:17 am, "Ali Saad Kusay" <aku...@un...> wrote:

    Hi Jeff, 

    There is several ways you can do this with string function in python https://www.w3schools.com/python/python_ref_string.asp. 
    This is an easy one liner which replace "COG_" of "AA" with nothing if found
    label sele, model.replace('COG_','').replace('AA_','') 

    Another way to do this is lets say you select an object beginning with COG_, you can slice away the first 4 characters to get rid of COG_
    label sele, model[4:]

    Cheers, 

    Ali

    On 23/2/21, 1:32 am, "Jeff Saxon" <jms...@gm...> wrote:

        pardon, just one additional question, which might be alitle bit custom
        issue, however..

        Imagine, that I have 2 groups of the pdbs objects loaded into same
        pymol session: 2 pdbs with the prefix COG_*.pdb, and 2 pdbs with the
        prefix AA_*.pdb. Would it be possible to subtract the both prefixes
        from the labels produced using cmd.label('sele', 'model') ? Or
        alternatively I ought to rename the both objects before their
        labelling? What are the other possible solutions ?

        пн, 22 февр. 2021 г. в 15:07, Jeff Saxon <jms...@gm...>:
        >
        > Right, this is what I was looking for!
        > Thank you so much, Ali!
        > Cheers,
        > J.
        >
        > пн, 22 февр. 2021 г. в 14:59, Ali Saad Kusay <aku...@un...>:
        > >
        > > No worries Jeff,
        > >
        > > Use editing mode and you can move it with mouse. See around 3:30 in this video, https://protect-au.mimecast.com/s/_r_iCANpgjCwqAQMtGDPTv?domain=m.youtube.com.
        > >
        > > You can move all labels with this command:
        > >
        > > set label_position (x,y,z)
        > >
        > > This will move the labels as needed in the x, y and z directions
        > >
        > > Cheers,
        > >
        > > Ali
        > >
        > >
        > > On 23 Feb 2021, at 12:51 am, Jeff Saxon <jms...@gm...> wrote:
        > >
        > > Thank you, Ali!
        > > One question - is there any command which would allow to change
        > > position of the text of the label produced by the label sele, model ?
        > > In fact as I noticed, it produces correctly label text just above the
        > > object, while I need to move it a litle bit in one of the directions
        > > ...
        > > Cheers,
        > >
        > > пн, 22 февр. 2021 г. в 14:14, Ali Saad Kusay <aku...@un...>:
        > >
        > >
        > > Hi Jeff,
        > >
        > >
        > > The name of an object is stored in the model attribute.
        > >
        > > Select an atom in the object and use this command:
        > >
        > > label sele, model
        > >
        > >
        > > If you want to automate this over all your PyMOL objects, you can use this script, this will put a label at the centre of each object but it has to create a pseudoatom for each one. You can change coords.mean to coords.min or cords.max if you want the label to go at the corner of each object
        > >
        > > for i in cmd.get_object_list():
        > >
        > >    coords = cmd.get_coords(i)
        > >
        > >    mean_coords = coords.mean(axis=0).tolist()
        > >
        > >    cmd.pseudoatom(i+"_psu", pos=mean_coords)
        > >
        > >
        > >    cmd.label(i+"_psu", "'{}'".format(i))
        > >
        > >
        > > Cheers,
        > >
        > >
        > > Ali
        > >
        > >
        > > Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
        > >
        > > The University of Sydney School of Pharmacy | Faculty of Medicine and Health
        > >
        > > 424, Brain and Mind Centre | The University of Sydney | NSW 2050
        > >
        > >
        > > On 22/2/21, 10:47 pm, "Jeff Saxon" <jms...@gm...> wrote:
        > >
        > >
        > >    Dear Pymol Users,
        > >
        > >
        > >    I am looking for a possibility to display names of the objects in the
        > >
        > >    pymol session. For example I loaded 4 objects corresponded to 2
        > >
        > >    different positions of the same ligand as well as 2 positions of its
        > >
        > >    centres of masses. How would it be possible to display the names of
        > >
        > >    each of these loaded objects just near their visualisations in GUI in
        > >
        > >    order that I could understand who is who without operating with the
        > >
        > >    objects on the context menu?
        > >
        > >
        > >
        > >    _______________________________________________
        > >
        > >    PyMOL-users mailing list
        > >
        > >    Archives: https://protect-au.mimecast.com/s/1Qz7CBNqjlCw25G3t6a3Ug?domain=mail-archive.com
        > >
        > >    Unsubscribe: https://protect-au.mimecast.com/s/FesTCD1vlpTEGl9QfAQcf7?domain=sourceforge.net
        > >
        > >
        > >
        > >

[PyMOL] Virtual Annual CCP4/APS Crystallographic School (2021) in the US

[Xu, Q. <qx...@an...>]

Dear Colleagues,

We are pleased to announce the virtual annual CCP4/APS crystallographic school "From data collection to structure refinement and beyond" will be held on June 14-25, 2021 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2021/index.php.

Dates: June 14 through 25, 2021 (with a weekend break on June 19 and 20th)

Location: Virtual/Remote

The school comprises two parts: remote data collection workshop and virtual crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA at APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections - lectures, tutorials, and hands-on (interactive troubleshooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website.

Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.

Application: Application deadline is April 1st, 2021. To apply, visit https://www.ccp4.ac.uk/schools/APS-2021/application.php.

Fees: There is no fee for attending the virtual school for the chosen applicants.


We hope to see you at the school.


Charles, Garib and Qingping

Re: [PyMOL] Names of objects in GUI in pymol

[Jeff S. <jms...@gm...>]

pardon, just one additional question, which might be alitle bit custom
issue, however..

Imagine, that I have 2 groups of the pdbs objects loaded into same
pymol session: 2 pdbs with the prefix COG_*.pdb, and 2 pdbs with the
prefix AA_*.pdb. Would it be possible to subtract the both prefixes
from the labels produced using cmd.label('sele', 'model') ? Or
alternatively I ought to rename the both objects before their
labelling? What are the other possible solutions ?

пн, 22 февр. 2021 г. в 15:07, Jeff Saxon <jms...@gm...>:
>
> Right, this is what I was looking for!
> Thank you so much, Ali!
> Cheers,
> J.
>
> пн, 22 февр. 2021 г. в 14:59, Ali Saad Kusay <aku...@un...>:
> >
> > No worries Jeff,
> >
> > Use editing mode and you can move it with mouse. See around 3:30 in this video, https://m.youtube.com/watch?v=yBFzJ3ql4qU&ab_channel=MolecularMemory.
> >
> > You can move all labels with this command:
> >
> > set label_position (x,y,z)
> >
> > This will move the labels as needed in the x, y and z directions
> >
> > Cheers,
> >
> > Ali
> >
> >
> > On 23 Feb 2021, at 12:51 am, Jeff Saxon <jms...@gm...> wrote:
> >
> > Thank you, Ali!
> > One question - is there any command which would allow to change
> > position of the text of the label produced by the label sele, model ?
> > In fact as I noticed, it produces correctly label text just above the
> > object, while I need to move it a litle bit in one of the directions
> > ...
> > Cheers,
> >
> > пн, 22 февр. 2021 г. в 14:14, Ali Saad Kusay <aku...@un...>:
> >
> >
> > Hi Jeff,
> >
> >
> > The name of an object is stored in the model attribute.
> >
> > Select an atom in the object and use this command:
> >
> > label sele, model
> >
> >
> > If you want to automate this over all your PyMOL objects, you can use this script, this will put a label at the centre of each object but it has to create a pseudoatom for each one. You can change coords.mean to coords.min or cords.max if you want the label to go at the corner of each object
> >
> > for i in cmd.get_object_list():
> >
> >    coords = cmd.get_coords(i)
> >
> >    mean_coords = coords.mean(axis=0).tolist()
> >
> >    cmd.pseudoatom(i+"_psu", pos=mean_coords)
> >
> >
> >    cmd.label(i+"_psu", "'{}'".format(i))
> >
> >
> > Cheers,
> >
> >
> > Ali
> >
> >
> > Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> >
> > The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> >
> > 424, Brain and Mind Centre | The University of Sydney | NSW 2050
> >
> >
> > On 22/2/21, 10:47 pm, "Jeff Saxon" <jms...@gm...> wrote:
> >
> >
> >    Dear Pymol Users,
> >
> >
> >    I am looking for a possibility to display names of the objects in the
> >
> >    pymol session. For example I loaded 4 objects corresponded to 2
> >
> >    different positions of the same ligand as well as 2 positions of its
> >
> >    centres of masses. How would it be possible to display the names of
> >
> >    each of these loaded objects just near their visualisations in GUI in
> >
> >    order that I could understand who is who without operating with the
> >
> >    objects on the context menu?
> >
> >
> >
> >    _______________________________________________
> >
> >    PyMOL-users mailing list
> >
> >    Archives: https://protect-au.mimecast.com/s/I4YSC2xMQziByPypTnzh0G?domain=mail-archive.com
> >
> >    Unsubscribe: https://protect-au.mimecast.com/s/hFDYC3QNPBiyN6NpCqFgvq?domain=sourceforge.net
> >
> >
> >
> >

Re: [PyMOL] Names of objects in GUI in pymol

[Ali S. K. <aku...@un...>]

No worries Jeff,

Use editing mode and you can move it with mouse. See around 3:30 in this video, https://m.youtube.com/watch?v=yBFzJ3ql4qU&ab_channel=MolecularMemory.

You can move all labels with this command:

set label_position (x,y,z)

This will move the labels as needed in the x, y and z directions

Cheers,

Ali


On 23 Feb 2021, at 12:51 am, Jeff Saxon <jms...@gm...> wrote:

Thank you, Ali!
One question - is there any command which would allow to change
position of the text of the label produced by the label sele, model ?
In fact as I noticed, it produces correctly label text just above the
object, while I need to move it a litle bit in one of the directions
...
Cheers,

пн, 22 февр. 2021 г. в 14:14, Ali Saad Kusay <aku...@un...>:

Hi Jeff,

The name of an object is stored in the model attribute.
Select an atom in the object and use this command:
label sele, model

If you want to automate this over all your PyMOL objects, you can use this script, this will put a label at the centre of each object but it has to create a pseudoatom for each one. You can change coords.mean to coords.min or cords.max if you want the label to go at the corner of each object
for i in cmd.get_object_list():
   coords = cmd.get_coords(i)
   mean_coords = coords.mean(axis=0).tolist()
   cmd.pseudoatom(i+"_psu", pos=mean_coords)

   cmd.label(i+"_psu", "'{}'".format(i))

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050

On 22/2/21, 10:47 pm, "Jeff Saxon" <jms...@gm...> wrote:

   Dear Pymol Users,

   I am looking for a possibility to display names of the objects in the
   pymol session. For example I loaded 4 objects corresponded to 2
   different positions of the same ligand as well as 2 positions of its
   centres of masses. How would it be possible to display the names of
   each of these loaded objects just near their visualisations in GUI in
   order that I could understand who is who without operating with the
   objects on the context menu?


   _______________________________________________
   PyMOL-users mailing list
   Archives: https://protect-au.mimecast.com/s/I4YSC2xMQziByPypTnzh0G?domain=mail-archive.com
   Unsubscribe: https://protect-au.mimecast.com/s/hFDYC3QNPBiyN6NpCqFgvq?domain=sourceforge.net

Re: [PyMOL] Names of objects in GUI in pymol

[Jeff S. <jms...@gm...>]

Thank you, Ali!
One question - is there any command which would allow to change
position of the text of the label produced by the label sele, model ?
In fact as I noticed, it produces correctly label text just above the
object, while I need to move it a litle bit in one of the directions
...
Cheers,

пн, 22 февр. 2021 г. в 14:14, Ali Saad Kusay <aku...@un...>:
>
> Hi Jeff,
>
> The name of an object is stored in the model attribute.
> Select an atom in the object and use this command:
> label sele, model
>
> If you want to automate this over all your PyMOL objects, you can use this script, this will put a label at the centre of each object but it has to create a pseudoatom for each one. You can change coords.mean to coords.min or cords.max if you want the label to go at the corner of each object
> for i in cmd.get_object_list():
>     coords = cmd.get_coords(i)
>     mean_coords = coords.mean(axis=0).tolist()
>     cmd.pseudoatom(i+"_psu", pos=mean_coords)
>
>     cmd.label(i+"_psu", "'{}'".format(i))
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
> On 22/2/21, 10:47 pm, "Jeff Saxon" <jms...@gm...> wrote:
>
>     Dear Pymol Users,
>
>     I am looking for a possibility to display names of the objects in the
>     pymol session. For example I loaded 4 objects corresponded to 2
>     different positions of the same ligand as well as 2 positions of its
>     centres of masses. How would it be possible to display the names of
>     each of these loaded objects just near their visualisations in GUI in
>     order that I could understand who is who without operating with the
>     objects on the context menu?
>
>
>     _______________________________________________
>     PyMOL-users mailing list
>     Archives: https://protect-au.mimecast.com/s/YdVUCVARKgCWQ4kOsG8z8B?domain=mail-archive.com
>     Unsubscribe: https://protect-au.mimecast.com/s/u68CCWLVXkUMopXluxT1mn?domain=sourceforge.net
>
>

Re: [PyMOL] Names of objects in GUI in pymol

[Ali S. K. <aku...@un...>]

Hi Jeff, 

The name of an object is stored in the model attribute. 
Select an atom in the object and use this command:
label sele, model 

If you want to automate this over all your PyMOL objects, you can use this script, this will put a label at the centre of each object but it has to create a pseudoatom for each one. You can change coords.mean to coords.min or cords.max if you want the label to go at the corner of each object 
for i in cmd.get_object_list():
    coords = cmd.get_coords(i)
    mean_coords = coords.mean(axis=0).tolist()
    cmd.pseudoatom(i+"_psu", pos=mean_coords)

    cmd.label(i+"_psu", "'{}'".format(i))

Cheers, 

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050

On 22/2/21, 10:47 pm, "Jeff Saxon" <jms...@gm...> wrote:

    Dear Pymol Users,

    I am looking for a possibility to display names of the objects in the
    pymol session. For example I loaded 4 objects corresponded to 2
    different positions of the same ligand as well as 2 positions of its
    centres of masses. How would it be possible to display the names of
    each of these loaded objects just near their visualisations in GUI in
    order that I could understand who is who without operating with the
    objects on the context menu?


    _______________________________________________
    PyMOL-users mailing list
    Archives: https://protect-au.mimecast.com/s/YdVUCVARKgCWQ4kOsG8z8B?domain=mail-archive.com
    Unsubscribe: https://protect-au.mimecast.com/s/u68CCWLVXkUMopXluxT1mn?domain=sourceforge.net

[PyMOL] Names of objects in GUI in pymol

[Jeff S. <jms...@gm...>]

Dear Pymol Users,

I am looking for a possibility to display names of the objects in the
pymol session. For example I loaded 4 objects corresponded to 2
different positions of the same ligand as well as 2 positions of its
centres of masses. How would it be possible to display the names of
each of these loaded objects just near their visualisations in GUI in
order that I could understand who is who without operating with the
objects on the context menu?

[PyMOL] Custom text in openGL window

[Milosz G. <M.G...@sy...>]

Hi All,
Is there a way (via scripting) to display text in the renderer window.
I know that one is able to generate object using CGO and print a text like with "Hello World"
But I am after that is not coordinates bound and always displayed in same place like the green text at the bottom.
The utility is to provide some additional information from sdf files I am loading, like logD etc.
Cheers,
Milosz
[cid:7925e66a-deb0-4cfe-a7f6-89e8e85a672f]

 Milosz Grabski

Senior Scientist 2

Address: Discovery Building | Biocity | Pennyfoot Street | Nottingham | NG1 1GR | United Kingdom
Office:  +44 (0)115 941 5401 | Email: m.g...@sy... |
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