pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Problem Compiling PyMOL in WSL2/Debian Bullseye

[Stephen P. M. <s.m...@sb...>]

I have installed Debian Bullseye on my Windows 10 Laptop using WSL2 and 
have encountered a problem with PyMOL-2.6.a0a.

I compiled the source code using the instructions in the PyMOL Wiki.

Unfortunately, there were errors when I attempted running PyMOL:

Please wait...

Qt not available (pymol.Qt), using GLUT/Tk interface
Traceback (most recent call last):
   File "/home/comp/Apps/PyMOL-2.6.a0a/lib/python/pymol/__init__.py", 
line 73, in <module>
     sys.exit(pymol.launch(args))
   File "/home/comp/Apps/PyMOL-2.6.a0a/lib/python/pymol/__init__.py", 
line 429, in launch
     _cmd.runpymol(None, block_input_hook)
NotImplementedError: compile with --glut

 >>>> END OF COMMAND <<<<

The build commands and build log are attached.

I should mention that I have comp[iled PyMOL quite a few times in 
multiple Linux distros without this particular problem.

A solution will be appreciated.

Thanks in advance.

-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1

[PyMOL] drawing small organic molecules

[Janos D. <jan...@gm...>]

Dear All,

I am searching for some features in pymol, I hope these are implemented
features:
I would like to:
-add crosses on spheres like:
https://www.cylview.org/ewExternalFiles/CYLview_manual_revC.pdf (page 1.)
or
https://rb.gy/gru47s

-increase the stick diameter for H atoms from commandline like:

Setting: stick_h_scale set to 1.00000. (Settings/ lines and sticks /
hydrogen scale: 1)
-add and remove bonds from commandline
-add dashed bonds from commandline


Many thanks in advance!

Best,

Janos

Re: [PyMOL] PyMOL for M1 macs

[Florian N. <mai...@na...>]

Hi,

You can install the open source version 2.5 of PyMOL using homebrew and it will be M1 native (see https://brew.sh)

But frankly, the intel version is already so fast with rosetta2 on the M1 that it does not worth it except if you do really fancy stuff.

Florian

> On 6 Dec 2021, at 08:00, Chris Swain via PyMOL-users <pym...@li...> wrote:
> 
> Hi,
> 
> Thanks all will give it a try
> 
> Cheers,
> 
> Chris
> 
>> On 6 Dec 2021, at 06:08, Jarrett Johnson <jar...@sc... <mailto:jar...@sc...>> wrote:
>> 
>> IIRC when we tried with Rosetta2, PyMOL was still faster (about 2x I think) than the previous x86. Your mileage may vary.
>> 
>> Best,
>> Jarrett J
>> 
>> On Mon, Dec 6, 2021 at 12:46 AM Xin Yu <xin...@gm... <mailto:xin...@gm...>> wrote:
>> It looks like while you can’t run it natively on M1, maybe you can do it through rosetta2 translation via Conda install?
>> See here: https://pymol.org/2/support.html? <https://pymol.org/2/support.html?>
>> Supported platform states M1 with rosetta2. Perhaps with some penalty for efficiency though. Anyone tried?
>> 
>> Sent from my iPhone
>> 
>>> On Dec 5, 2021, at 10:27 PM, Jarrett Johnson <jar...@sc... <mailto:jar...@sc...>> wrote:
>>> 
>>> 
>>> Hi Chris,
>>> 
>>> We haven't released any official Incentive PyMOL builds yet for M1 ARM mac yet but it's on our radar to do so soon.
>>> 
>>> Best,
>>> 
>>> Jarrett J
>>> 
>>> On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users <pym...@li... <mailto:pym...@li...>> wrote:
>>> Hi,
>>> 
>>> Is there a build of PyMOL for M1 Macs yet?
>>> 
>>> Cheers,
>>> 
>>> Chris
>>> 
>>> 
>>> _______________________________________________
>>> 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>
>>> 
>>> 
>>> -- 
>>> Jarrett Johnson | Senior Developer, PyMOL
>>> 
>>> _______________________________________________
>>> 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>
>> 
>> -- 
>> Jarrett Johnson | Senior Developer, PyMOL
>> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Missing structure

[Dr. K. M J. <kj...@st...>]

Looks like the nucleic acid sits on a 2-fold crystallographic symmetry axis. You can generate symmetry-related molecules using symexp:

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

Alternatively, from the rcsb page for the structure, click “Download Files > Biological Assembly” or fetch it in pymol with:
Fetch 1bg1, type=pdb1


From: JJ Oliveira <joa...@gm...>
Date: Wednesday, December 8, 2021 at 9:57 AM
To: PYMOLBB <PyM...@li...>
Subject: [PyMOL] Missing structure
Hi there

PyMol doesn't show the full PDB file 1BG1 (TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX) as shown in rcsb.org<http://rcsb.org> (2nd attached image).

How do I fix that?

Thank you!

[cid:image001.png@01D7EC1D.B053FD20]
[cid:image002.png@01D7EC1D.B053FD20]

Re: [PyMOL] Missing structure

[Jarrett J. <jar...@sc...>]

Hello,

The top image from the RCSB site is illustrating the entire biological
assembly. From what I see, the PDB file includes data for the
asymmetric unit.

To get the whole assembly:

`set assembly, 1`
`fetch 1bg1`

should get you what you want.


Best,
Jarrett J.

On Wed, Dec 8, 2021 at 12:56 PM JJ Oliveira <joa...@gm...> wrote:

> Hi there
>
> PyMol doesn't show the full PDB file 1BG1 (TRANSCRIPTION FACTOR STAT3B/DNA
> COMPLEX) as shown in rcsb.org (2nd attached image).
>
> How do I fix that?
>
> Thank you!
>
> [image: image.png]
> [image: image.png]
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] Missing structure

[CRAIG A B. <cab...@wi...>]

You need to download the biological assembly

[cid:image001.png@01D7EC2C.356AB220]

From: joa...@gm... <joa...@gm...>
Date: Wednesday, December 8, 2021 at 11:56 AM
To: PYMOLBB <PyM...@li...>
Subject: [PyMOL] Missing structure
Hi there

PyMol doesn't show the full PDB file 1BG1 (TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX) as shown in rcsb.org<http://rcsb.org> (2nd attached image).

How do I fix that?

Thank you!

[cid:image002.png@01D7EC2C.356AB220]
[cid:image003.png@01D7EC2C.356AB220]

Re: [PyMOL] Missing structure

[Marko H. <mh...@ca...>]

Looks like you have half a dimer in asymmetric unit which is what PDB depositions would have. You can either see if you can download the biological complex or, within PyMOL, you can find symmetry mates from Action menu for the object. After that you need to remove those that are not related to dimeric complex.

Best, Marko

----
Marko Hyvonen
Department of Biochemistry
University of Cambridge
https://hyvonen.bioc.cam.ac.uk
@HyvonenGroup
mh...@ca...
________________________________
From: JJ Oliveira <joa...@gm...>
Sent: Wednesday, December 8, 2021 2:54:31 PM
To: PYMOLBB <PyM...@li...>
Subject: [PyMOL] Missing structure

Hi there

PyMol doesn't show the full PDB file 1BG1 (TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX) as shown in rcsb.org<http://rcsb.org> (2nd attached image).

How do I fix that?

Thank you!

[image.png]
[image.png]

[PyMOL] Missing structure

[JJ O. <joa...@gm...>]

Hi there

PyMol doesn't show the full PDB file 1BG1 (TRANSCRIPTION FACTOR STAT3B/DNA
COMPLEX) as shown in rcsb.org (2nd attached image).

How do I fix that?

Thank you!

[image: image.png]
[image: image.png]

Re: [PyMOL] PyMOL for M1 macs

[Chris S. <sw...@ma...>]

Hi,

Thanks all will give it a try

Cheers,

Chris

> On 6 Dec 2021, at 06:08, Jarrett Johnson <jar...@sc...> wrote:
> 
> IIRC when we tried with Rosetta2, PyMOL was still faster (about 2x I think) than the previous x86. Your mileage may vary.
> 
> Best,
> Jarrett J
> 
> On Mon, Dec 6, 2021 at 12:46 AM Xin Yu <xin...@gm... <mailto:xin...@gm...>> wrote:
> It looks like while you can’t run it natively on M1, maybe you can do it through rosetta2 translation via Conda install?
> See here: https://pymol.org/2/support.html? <https://pymol.org/2/support.html?>
> Supported platform states M1 with rosetta2. Perhaps with some penalty for efficiency though. Anyone tried?
> 
> Sent from my iPhone
> 
>> On Dec 5, 2021, at 10:27 PM, Jarrett Johnson <jar...@sc... <mailto:jar...@sc...>> wrote:
>> 
>> 
>> Hi Chris,
>> 
>> We haven't released any official Incentive PyMOL builds yet for M1 ARM mac yet but it's on our radar to do so soon.
>> 
>> Best,
>> 
>> Jarrett J
>> 
>> On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users <pym...@li... <mailto:pym...@li...>> wrote:
>> Hi,
>> 
>> Is there a build of PyMOL for M1 Macs yet?
>> 
>> Cheers,
>> 
>> Chris
>> 
>> 
>> _______________________________________________
>> 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>
>> 
>> 
>> -- 
>> Jarrett Johnson | Senior Developer, PyMOL
>> 
>> _______________________________________________
>> 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>
> 
> -- 
> Jarrett Johnson | Senior Developer, PyMOL
> 

Re: [PyMOL] PyMOL for M1 macs

[Jarrett J. <jar...@sc...>]

IIRC when we tried with Rosetta2, PyMOL was still faster (about 2x I think)
than the previous x86. Your mileage may vary.

Best,
Jarrett J

On Mon, Dec 6, 2021 at 12:46 AM Xin Yu <xin...@gm...> wrote:

> It looks like while you can’t run it natively on M1, maybe you can do it
> through rosetta2 translation via Conda install?
> See here: https://pymol.org/2/support.html?
> Supported platform states M1 with rosetta2. Perhaps with some penalty for
> efficiency though. Anyone tried?
>
> Sent from my iPhone
>
> On Dec 5, 2021, at 10:27 PM, Jarrett Johnson <
> jar...@sc...> wrote:
>
> 
> Hi Chris,
>
> We haven't released any official Incentive PyMOL builds yet for M1 ARM mac
> yet but it's on our radar to do so soon.
>
> Best,
>
> Jarrett J
>
> On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users <
> pym...@li...> wrote:
>
>> Hi,
>>
>> Is there a build of PyMOL for M1 Macs yet?
>>
>> Cheers,
>>
>> Chris
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] PyMOL for M1 macs

[Xin Yu <xin...@gm...>]

It looks like while you can’t run it natively on M1, maybe you can do it through rosetta2 translation via Conda install?
See here: https://pymol.org/2/support.html?
Supported platform states M1 with rosetta2. Perhaps with some penalty for efficiency though. Anyone tried?

Sent from my iPhone

> On Dec 5, 2021, at 10:27 PM, Jarrett Johnson <jar...@sc...> wrote:
> 
> 
> Hi Chris,
> 
> We haven't released any official Incentive PyMOL builds yet for M1 ARM mac yet but it's on our radar to do so soon.
> 
> Best,
> 
> Jarrett J
> 
>> On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users <pym...@li...> wrote:
>> Hi,
>> 
>> Is there a build of PyMOL for M1 Macs yet?
>> 
>> Cheers,
>> 
>> Chris
>> 
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> 
> -- 
> Jarrett Johnson | Senior Developer, PyMOL
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] PyMOL for M1 macs

[Jarrett J. <jar...@sc...>]

Hi Chris,

We haven't released any official Incentive PyMOL builds yet for M1 ARM mac
yet but it's on our radar to do so soon.

Best,

Jarrett J

On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users <
pym...@li...> wrote:

> Hi,
>
> Is there a build of PyMOL for M1 Macs yet?
>
> Cheers,
>
> Chris
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] PyMOL for M1 macs

[Chris S. <sw...@ma...>]

Hi,

Is there a build of PyMOL for M1 Macs yet?

Cheers,

Chris

Re: [PyMOL] Loading chempy objects into PyMOL 2.4.0

[R M. <rau...@us...>]

Dear Thomas,

Thanks! That solved the problem (I actually used load_coordset, so I could
keep my coordinates in their original order.

Cheers!

On Wed, Dec 1, 2021 at 6:44 PM Thomas Holder <th...@th...>
wrote:

> Hi Raul,
>
> I suggest to use cmd.load_coords() to add trajectory frames to your model.
>
> https://pymolwiki.org/index.php/Load_coords
>
> Cheers,
>   Thomas
>
>
> On Nov 30, 2021, at 21:49, R Mera <rau...@us...> wrote:
>
> Dear all,
>
> I am trying to implement a reader for a trajectory format.
> I use cmd.get_model to get the "reference" structure, and then iterate
> over the trajectory frames, everytime replacing the coordinates of my model
> with the ones from the trajectory, and then loading the modified model back
> into PyMOL with cmd.load_model, changing the state every time.
>
> The issue is, I can't get the sequence view to work correctly (i.e. to
> display the one-letter code of each residue). This happens even if I don't
> modify the coordinates at all, like here:
>
> #This doesn't display the sequence
> for i in range(9):
>    m=cmd.get_model("sele")
>    cmd.load_model(m,"sele2",state=i+1)
>
> On the other hand, if I load only one state for the object, the sequence
> is displayed correctly:
>
> #this DOES display the sequence
> for i in range(1):
>    m=cmd.get_model("sele")
>    cmd.load_model(m,"sele2",state=i+1)
>
>
>
> I have tried with the Wiki help and even looking at the cmd code, but I
> can't find any way of getting this to work. The options for load_model, for
> instance, have no effect. What I _can_ do is to use:
>
> cmd.set("seq_view_discrete_by_state",0)
>
> Which will show the sequence correctly (apparently, the first state always
> gets the sequence, the others don't).  It is not a good solution, though,
> as you can't use that sequence to select residues (it will only select them
> on the first state, _and_ it will take you back to that state).
>
> Is this possible at all to do? Is it an issue with my PyMOL version? (I am
> using PyMOL on Fedora [Linux], and it i the version from the Fedora 32
> repositories, by the way, although I don't think I am doing anything
> OS-dependent).
>
> Thanks!
>
> Raul
>
>
> --
>
> Prof. Dr. Raúl Mera Adasme
>
> Facultad de Química y Biología ,
> Universidad de Santiago de Chile (USACH).
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>

-- 

Prof. Dr. Raúl Mera Adasme

Facultad de Química y Biología ,
Universidad de Santiago de Chile (USACH).

Re: [PyMOL] Loading chempy objects into PyMOL 2.4.0

[Thomas H. <th...@th...>]

Hi Raul,

I suggest to use cmd.load_coords() to add trajectory frames to your model.

https://pymolwiki.org/index.php/Load_coords <https://pymolwiki.org/index.php/Load_coords>

Cheers,
  Thomas


> On Nov 30, 2021, at 21:49, R Mera <rau...@us...> wrote:
> 
> Dear all,
> 
> I am trying to implement a reader for a trajectory format.
> I use cmd.get_model to get the "reference" structure, and then iterate over the trajectory frames, everytime replacing the coordinates of my model with the ones from the trajectory, and then loading the modified model back into PyMOL with cmd.load_model, changing the state every time.
> 
> The issue is, I can't get the sequence view to work correctly (i.e. to display the one-letter code of each residue). This happens even if I don't modify the coordinates at all, like here:
> 
> #This doesn't display the sequence
> for i in range(9):
>    m=cmd.get_model("sele")
>    cmd.load_model(m,"sele2",state=i+1)
> 
> On the other hand, if I load only one state for the object, the sequence is displayed correctly:
> 
> #this DOES display the sequence
> for i in range(1):
>    m=cmd.get_model("sele")
>    cmd.load_model(m,"sele2",state=i+1)
> 
> 
> 
> I have tried with the Wiki help and even looking at the cmd code, but I can't find any way of getting this to work. The options for load_model, for instance, have no effect. What I _can_ do is to use:
> 
> cmd.set("seq_view_discrete_by_state",0)
> 
> Which will show the sequence correctly (apparently, the first state always gets the sequence, the others don't).  It is not a good solution, though, as you can't use that sequence to select residues (it will only select them on the first state, _and_ it will take you back to that state).
> 
> Is this possible at all to do? Is it an issue with my PyMOL version? (I am using PyMOL on Fedora [Linux], and it i the version from the Fedora 32 repositories, by the way, although I don't think I am doing anything OS-dependent). 
> 
> Thanks!
> 
> Raul
>  
> 
> -- 
> 
> Prof. Dr. Raúl Mera Adasme
> 
> Facultad de Química y Biología ,
> Universidad de Santiago de Chile (USACH).
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Blur text

[Yijie L. <yij...@br...>]

Hi!

I found all the text in PyMol interface became blur, could you help me to figure it out?

It happens after I set the GPU from the integrated video card to the external video card.

Thanks!

[cid:ec1ee628-a6d0-4b8c-90d7-8025edc0f138]

[PyMOL] Loading chempy objects into PyMOL 2.4.0

[R M. <rau...@us...>]

Dear all,

I am trying to implement a reader for a trajectory format.
I use cmd.get_model to get the "reference" structure, and then iterate over
the trajectory frames, everytime replacing the coordinates of my model with
the ones from the trajectory, and then loading the modified model back into
PyMOL with cmd.load_model, changing the state every time.

The issue is, I can't get the sequence view to work correctly (i.e. to
display the one-letter code of each residue). This happens even if I don't
modify the coordinates at all, like here:

#This doesn't display the sequence
for i in range(9):
   m=cmd.get_model("sele")
   cmd.load_model(m,"sele2",state=i+1)

On the other hand, if I load only one state for the object, the sequence is
displayed correctly:

#this DOES display the sequence
for i in range(1):
   m=cmd.get_model("sele")
   cmd.load_model(m,"sele2",state=i+1)



I have tried with the Wiki help and even looking at the cmd code, but I
can't find any way of getting this to work. The options for load_model, for
instance, have no effect. What I _can_ do is to use:

cmd.set("seq_view_discrete_by_state",0)

Which will show the sequence correctly (apparently, the first state always
gets the sequence, the others don't).  It is not a good solution, though,
as you can't use that sequence to select residues (it will only select them
on the first state, _and_ it will take you back to that state).

Is this possible at all to do? Is it an issue with my PyMOL version? (I am
using PyMOL on Fedora [Linux], and it i the version from the Fedora 32
repositories, by the way, although I don't think I am doing anything
OS-dependent).

Thanks!

Raul


-- 

Prof. Dr. Raúl Mera Adasme

Facultad de Química y Biología ,
Universidad de Santiago de Chile (USACH).

Re: [PyMOL] Complement or Inverse Selection in Pymol

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

Hi Gret,

No worries,

In regards to the selection: “resi 25 and object”

Its more so to ensure that you don’t accidently select “resi 25” from multiple chains or objects

Like if you load two pdb files into PyMOL (say obj01 and obj02) and both have a resi 25, then resi 25 from both objects will be selected if you don’t include the object in the selection.

On the other hand, If you:

select chA, resi 25 and obj01

Then the chA selection will only contain resi 25 from obj01 and ignore obj02.

Its more of a note about selections that you might already be familiar with

Cheers,

Ali

From: Gert Kruger <KR...@uk...>
Date: Saturday, 27 November 2021 at 5:05 pm
To: Ali Saad Kusay <aku...@un...>
Cc: "pym...@li..." <pym...@li...>
Subject: Re: [PyMOL] Complement or Inverse Selection in Pymol

Dear Ali,

Many thanks for your kind and very helpfull reply!  One question:

You wrote:  "Doing something like resi 25 and object is safer".

Do you mean: select chA, resi 25

And will that reflect as follows in my requirement:

select other_waters, br. (resn WAT beyond 5 of chA, resi 25)

Best wishes
Gert Kruger

On Fri, 2021-11-26 at 15:09 +0000, Ali Saad Kusay wrote:
Hi Gert,

These selection commands will generate a selection object called "other_waters "

See https://pymolwiki.org/index.php/Selection_Algebra<https://protect-au.mimecast.com/s/h0hkCQnMBZfkPgpznSPf8vp?domain=protect-za.mimecast.com>

You can do:
select other_waters, br. (resn WAT and not sele) # after you make the selection in your email
or
select other_waters, br. (resn WAT beyond 5 of resi 25)

A few notes:
1) you need to select by residue otherwise your selection will yield incomplete water molecules i.e. waters with 1-2 atoms in the selection as opposed to all 3 atoms. To do this use "br."
2) Be careful of selections like resi 25 since if you have multiple chains or objects with "resi 25", all will be included in the selection. Doing something like resi 25 and object is safer, object is the name in the object list in PyMOL

To remove the unwanted water atoms, do:

remove other_waters

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 27/11/21, 1:57 am, "Gert Kruger" <KR...@uk...> wrote:

Dear All,

Apologies for my ignorance. I need to know which solvent molecules are
in the active site of an enzyme (HIV-PR). I use "tleap" in Amber to
create a solvent waterbox in and around the enzyme.

I found the following command that seems to find the Water molecules in
the active site:

> sele resn WAT within 5 sele resi 25

(ASP25 is in the active site).

Now I want to remove ALL other water/solvent molecules (those that are
not selected).

Is there a method to achieve a complement or inverse selection (to
hightlight ALL other watermolecules that are not currently selected?)

I am able save the selection, but that is a bit more tedious.

Question: Is there an easy way in Pymol to achieve a "complement" or
"inverse" selection of waters in a solvent box?
Thanks alot and best wishes
Gert Kruger

UKZN email disclaimer:
The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University.

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Re: [PyMOL] Complement or Inverse Selection in Pymol

[Gert K. <KR...@uk...>]

Dear Ali,

Many thanks for your kind and very helpfull reply!  One question:

You wrote:  "Doing something like resi 25 and object is safer".

Do you mean: select chA, resi 25

And will that reflect as follows in my requirement:

select other_waters, br. (resn WAT beyond 5 of chA, resi 25)

Best wishes
Gert Kruger

On Fri, 2021-11-26 at 15:09 +0000, Ali Saad Kusay wrote:
Hi Gert,

These selection commands will generate a selection object called "other_waters "

See https://pymolwiki.org/index.php/Selection_Algebra<https://protect-za.mimecast.com/s/zlwlCX6Vp3CG2Y35ukvxhi?domain=pymolwiki.org>

You can do:
select other_waters, br. (resn WAT and not sele) # after you make the selection in your email
or
select other_waters, br. (resn WAT beyond 5 of resi 25)

A few notes:
1) you need to select by residue otherwise your selection will yield incomplete water molecules i.e. waters with 1-2 atoms in the selection as opposed to all 3 atoms. To do this use "br."
2) Be careful of selections like resi 25 since if you have multiple chains or objects with "resi 25", all will be included in the selection. Doing something like resi 25 and object is safer, object is the name in the object list in PyMOL

To remove the unwanted water atoms, do:

remove other_waters

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 27/11/21, 1:57 am, "Gert Kruger" <KR...@uk...> wrote:

Dear All,

Apologies for my ignorance. I need to know which solvent molecules are
in the active site of an enzyme (HIV-PR). I use "tleap" in Amber to
create a solvent waterbox in and around the enzyme.

I found the following command that seems to find the Water molecules in
the active site:

> sele resn WAT within 5 sele resi 25

(ASP25 is in the active site).

Now I want to remove ALL other water/solvent molecules (those that are
not selected).

Is there a method to achieve a complement or inverse selection (to
hightlight ALL other watermolecules that are not currently selected?)

I am able save the selection, but that is a bit more tedious.

Question: Is there an easy way in Pymol to achieve a "complement" or
"inverse" selection of waters in a solvent box?
Thanks alot and best wishes
Gert Kruger

UKZN email disclaimer:
The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University.

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Re: [PyMOL] Complement or Inverse Selection in Pymol

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

Hi Gert, 

These selection commands will generate a selection object called "other_waters "

See https://pymolwiki.org/index.php/Selection_Algebra

You can do:
select other_waters, br. (resn WAT and not sele) # after you make the selection in your email
or
select other_waters, br. (resn WAT beyond 5 of resi 25)

A few notes:
1) you need to select by residue otherwise your selection will yield incomplete water molecules i.e. waters with 1-2 atoms in the selection as opposed to all 3 atoms. To do this use "br."
2) Be careful of selections like resi 25 since if you have multiple chains or objects with "resi 25", all will be included in the selection. Doing something like resi 25 and object is safer, object is the name in the object list in PyMOL

To remove the unwanted water atoms, do:

remove other_waters

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 27/11/21, 1:57 am, "Gert Kruger" <KR...@uk...> wrote:

    Dear All,

    Apologies for my ignorance.  I need to know which solvent molecules are
    in the active site of an enzyme (HIV-PR).  I use "tleap" in Amber to
    create a solvent waterbox in and around the enzyme.

    I found the following command that seems to find the Water molecules in
    the active site:

    > sele resn WAT within 5 sele resi 25

    (ASP25 is in the active site).

    Now I want to remove ALL other water/solvent molecules (those that are
    not selected).

    Is there a method to achieve a complement or inverse selection (to
    hightlight ALL other watermolecules that are not currently selected?)

    I am able save the selection, but that is a bit more tedious.

    Question:  Is there an easy way in Pymol to achieve a "complement" or
    "inverse" selection of waters in a solvent box?
    Thanks alot and best wishes
    Gert Kruger

    UKZN email disclaimer:
    The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University.

    _______________________________________________
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    Archives: https://protect-au.mimecast.com/s/G7JzCXLW2mUXKGn89c6nIX_?domain=mail-archive.com
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[PyMOL] Complement or Inverse Selection in Pymol

[Gert K. <KR...@uk...>]

Dear All,

Apologies for my ignorance.  I need to know which solvent molecules are
in the active site of an enzyme (HIV-PR).  I use "tleap" in Amber to
create a solvent waterbox in and around the enzyme.

I found the following command that seems to find the Water molecules in
the active site:

> sele resn WAT within 5 sele resi 25

(ASP25 is in the active site).

Now I want to remove ALL other water/solvent molecules (those that are
not selected).

Is there a method to achieve a complement or inverse selection (to
hightlight ALL other watermolecules that are not currently selected?)

I am able save the selection, but that is a bit more tedious.

Question:  Is there an easy way in Pymol to achieve a "complement" or
"inverse" selection of waters in a solvent box?
Thanks alot and best wishes
Gert Kruger

UKZN email disclaimer:
The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University.

Re: [PyMOL] fusing structures

[Joel T. <joe...@ot...>]

Have you tried superimposing the loop (or the main chain of the terminal fragments? You could then export the moved loop and edit the pdb

J

From: zeinab masoomi <zei...@gm...>
Sent: Monday, 22 November 2021 9:52 PM
To: pym...@li...
Subject: [PyMOL] fusing structures

Hi
I want to fuse a modeled loop into a protein structure, is this possible? how can I merge two structures into one file to put them close enough and fuse them?
structures are attached below
thank you.

[PyMOL] fusing structures

[zeinab m. <zei...@gm...>]

Hi
I want to fuse a modeled loop into a protein structure, is this possible?
how can I merge two structures into one file to put them close enough and
fuse them?
structures are attached below
thank you.

[PyMOL] fusing structures

[zeinab m. <zei...@gm...>]

Hi
I want to fuse a modeled loop into a protein structure, is this possible?
how can I merge two structures into one file to put them close enough and
fuse them?
thank you.

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[Xiang-Jun Lu <3d...@gm...>]

On Fri, Nov 12, 2021 at 11:15 AM amirhossein taghavi <
tag...@gm...> wrote:

> Hi Xiang-Jun,
>
> Sorry to bother. I meant if I can do the same thing you have done with
> DSSR pro with free version of x3dna-dssr, as I am getting some error
> messages:
>

No, as made clear in my previous response to Blaine: "The duplicated model
was generated with following DSSR Pro commands:"

Best regards,

Xiang-Jun


> x3dna-dssr -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
> Processing file 'model.pdb'
> total number of nucleotides: 26
> [e] no matched residue for option --frame
>
> Thanks for your help.
>
> Best,
> Amir
>
>
> On Fri, Nov 12, 2021 at 11:00 AM Xiang-Jun Lu <3d...@gm...> wrote:
>
>> Hi Amir,
>>
>> Please have a look at the announcement "No more grant funding for
>> 3DNA/DSSR" (
>> http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/)
>> on the 3DNA Forum. DSSR results are reproduced, period.
>>
>> Best wishes,
>>
>> Xiang-Jun
>>
>> --
>> Xiang-Jun Lu (Ph.D.)
>> Email: xia...@x3...
>> Web: http://x3dna.org/
>> Forum: http://forum.x3dna.org/
>>
>>
>> On Fri, Nov 12, 2021 at 10:51 AM amirhossein taghavi <
>> tag...@gm...> wrote:
>>
>>> Hello Dr. Xiang-Jun Lu,
>>>
>>> Thanks a lot for your help. The model you have duplicated is exactly
>>> what I am looking for (checked it with VMD). Unfortunately I do not have
>>> access to DSSR-Pro. Is there any way that I can reproduce your procedure
>>> with x3dna-dssr?
>>> I need to create different numbers of duplicates (2,4,6,5,8) for
>>> different systems and this will be very helpful.
>>>
>>> Thanks in advance.
>>>
>>> Best regards,
>>> Amir
>>>
>>> On Fri, Nov 12, 2021 at 10:33 AM Xiang-Jun Lu <3d...@gm...> wrote:
>>>
>>>> Dear Blaine,
>>>>
>>>> On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
>>>> Bla...@ou...> wrote:
>>>>
>>>>> Hi Xiang-Jun Lu,
>>>>>
>>>>> Thanks for proving me wrong. Congratulations on your duplicated model!
>>>>> Please share the commands that you used with DSSR to generate the
>>>>> duplicated helix.
>>>>>
>>>>
>>>> The duplicated model was generated with following DSSR Pro commands:
>>>>
>>>> ```
>>>> x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
>>>>
>>>> x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
>>>> x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair
>>>> -o=ref-conn.pdb
>>>>
>>>> x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb'
>>>> -o=temp1.pdb
>>>>
>>>> x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair
>>>> -o=temp2.pdb
>>>> x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb
>>>>
>>>> x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb'
>>>> -o=duplicate-model.pdb
>>>> ```
>>>>
>>>> It takes seconds to run. Moreover, by replacing `--seq=GG` with
>>>> `--seq=GA10G` for example, one can easily get a linker with 10 adenines.
>>>> The 'GG` is just a space-holder, and can be replaced with any other bases.
>>>> The linker sequence could be any bases: eg. A5T3G6, AAATTGG, etc. Users who
>>>> want to know more about DSSR can watch the overview video
>>>> http://docs.x3dna.org/dssr-overview/ (20m).
>>>>
>>>>
>>>>> PyMOL does not generate the cartoon representation for the backbones
>>>>> of your duplicate helix.
>>>>> Do you know why?
>>>>>
>>>>
>>>> I noticed the phenomenon but I really do not know why. I used 'as
>>>> lines' in PyMOL to verify the duplicated model.
>>>>
>>>> Best regards,
>>>>
>>>> Xiang-Jun
>>>>
>>>> Best regards,
>>>>>
>>>>> Blaine
>>>>>
>>>>> Blaine Mooers, Ph.D.
>>>>> Associate Professor
>>>>> Department of Biochemistry and Molecular Biology, College of Medicine
>>>>> Director of the Laboratory of Biomolecular Structure and Function
>>>>> Academic Director, Biomolecular Structure Core, COBRE in Structural
>>>>> Biology
>>>>> Full Member, Cancer Biology Program, Stephenson Cancer Center
>>>>> University of Oklahoma Health Sciences Center
>>>>>
>>>>> Mailing Address:
>>>>> 975 NE 10th Street, BRC 466
>>>>> Oklahoma City, OK 73104-5419
>>>>> Office: 405-271-8300 Lab: 405-271-8312
>>>>>
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>> Unsubscribe:
>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>
>>>