pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Labeling residues for publication

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

Hi George,

Can you try downloading from the pymol.org website?

Best,

Jarrett J

On Thu, Oct 28, 2021 at 9:50 AM George Tzotzos <gtz...@me...> wrote:

> Thank you both for the suggestions.
>
> I tried to upgrade. I get “pymol” is already at the latest version
>
> All the best
>
> George
>
> On 28.10.2021, at 14:40, Jarrett Johnson <jar...@sc...>
> wrote:
>
> Hi George,
>
> This issue should've been addressed in PyMOL 2.5.1. I would consider
> upgrading if you can.
>
> Best,
> Jarrett J
>
> On Thu, Oct 28, 2021 at 9:31 AM George Tzotzos via PyMOL-users <
> pym...@li...> wrote:
>
>> Hi everybody,
>>
>> I’d be grateful for any suggestions regarding the editing of labels.
>>
>> I’ve labeled a few residues and I’m trying to give them a better placing
>> in the structure. I’m using mouse/2 button editing.  Clicking on control
>> and then moving the labels works, but alas as soon as I release the control
>> key pymol crashes.
>>
>> I’m using
>> PyMOL(TM) 2.5.0 - Incentive Product
>>
>> Thanks in advance
>>
>> George
>>
>> _______________________________________________
>> 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
> [image: Schrodinger Logo] <https://www.schrodinger.com/>
>
>
>

-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

Re: [PyMOL] Labeling residues for publication

[George T. <gtz...@me...>]

Thank you both for the suggestions.

I tried to upgrade. I get “pymol” is already at the latest version

All the best

George

> On 28.10.2021, at 14:40, Jarrett Johnson <jar...@sc...> wrote:
> 
> Hi George,
> 
> This issue should've been addressed in PyMOL 2.5.1. I would consider upgrading if you can.
> 
> Best,
> Jarrett J
> 
> On Thu, Oct 28, 2021 at 9:31 AM George Tzotzos via PyMOL-users <pym...@li... <mailto:pym...@li...>> wrote:
> Hi everybody,
> 
> I’d be grateful for any suggestions regarding the editing of labels.
> 
> I’ve labeled a few residues and I’m trying to give them a better placing in the structure. I’m using mouse/2 button editing.  Clicking on control and then moving the labels works, but alas as soon as I release the control key pymol crashes.
> 
> I’m using 
> PyMOL(TM) 2.5.0 - Incentive Product
> 
> Thanks in advance
> 
> George
> 
> _______________________________________________
> 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
>  <https://www.schrodinger.com/>

[PyMOL] Labeling residues for publication

[George T. <gtz...@me...>]

Hi everybody,

I’d be grateful for any suggestions regarding the editing of labels.

I’ve labeled a few residues and I’m trying to give them a better placing in the structure. I’m using mouse/2 button editing.  Clicking on control and then moving the labels works, but alas as soon as I release the control key pymol crashes.

I’m using 
PyMOL(TM) 2.5.0 - Incentive Product

Thanks in advance

George

Re: [PyMOL] [EXTERNAL] basic trouble viewing electron density maps

[criss.hartzell <cri...@gm...>]

That explains it! Thanks. I guess I need a tutorial on how to look at EM maps. 

Criss Hartzell


> On Oct 27, 2021, at 12:26 PM, Brown, Zuben <zb...@cu...> wrote:
> 
> 
> They are different types of maps.
> 
> 2F67 -- X-ray map
> 7B5C -- EM map
> 
> 7B5C is not a 2fofc map.
> 
> Best wishes,
> Zuben
> From: Criss Hartzell <cri...@gm...>
> Sent: Wednesday, October 27, 2021 2:51 PM
> To: Pymol User list <pym...@li...>
> Subject: [EXTERNAL] [PyMOL] basic trouble viewing electron density maps
>  
> I am having trouble viewing electron density maps. 
> Everything works fine if I use the protein 2F67. But with 7B5C, I am stumped.
> 
> fetch 7b5c, type=2fofc gives me an error: 
> Warning: failed to fetch from https://www.ebi.ac.uk/pdbe/coordinates/files/7b5c.ccp4
> 
>  Error-fetch: unable to load '7b5c'.
> If I go to EMDB and download the map file (EMD_12025) and load it manually:
> (set normalize_ccp4_maps, 0
> load H:/.../emd_12025.map, \emd_12025
> isomesh emd_12025_isomesh, emd_12025, 1.0)
> The screen is blank and changing levels, etc. does nothing.
> But it works in UCSF Chimera. What am I missing?
> Thanks.
> Criss
> 
> 

Re: [PyMOL] [EXTERNAL] basic trouble viewing electron density maps

[Brown, Z. <zb...@cu...>]

They are different types of maps.

2F67 -- X-ray map
7B5C -- EM map

7B5C is not a 2fofc map.

Best wishes,
Zuben
________________________________
From: Criss Hartzell <cri...@gm...>
Sent: Wednesday, October 27, 2021 2:51 PM
To: Pymol User list <pym...@li...>
Subject: [EXTERNAL] [PyMOL] basic trouble viewing electron density maps

I am having trouble viewing electron density maps.
Everything works fine if I use the protein 2F67. But with 7B5C, I am stumped.

fetch 7b5c, type=2fofc gives me an error:

Warning: failed to fetch from https://www.ebi.ac.uk/pdbe/coordinates/files/7b5c.ccp4<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ebi.ac.uk_pdbe_coordinates_files_7b5c.ccp4&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=gjXm-pi8KE6bTBC8di1Ue68XZy2E2aRL9MnN2J1bJLc&s=MUITh2JiB3m_JBC4jNMoDm8CR051F-3qt8WIJbFOHD4&e=>
 Error-fetch: unable to load '7b5c'.

If I go to EMDB and download the map file (EMD_12025) and load it manually:

(set normalize_ccp4_maps, 0

load H:/.../emd_12025.map, \emd_12025

isomesh emd_12025_isomesh, emd_12025, 1.0)

The screen is blank and changing levels, etc. does nothing.

But it works in UCSF Chimera. What am I missing?

Thanks.

Criss

[PyMOL] basic trouble viewing electron density maps

[Criss H. <cri...@gm...>]

I am having trouble viewing electron density maps.
Everything works fine if I use the protein 2F67. But with 7B5C, I am
stumped.

fetch 7b5c, type=2fofc gives me an error:

Warning: failed to fetch from
https://www.ebi.ac.uk/pdbe/coordinates/files/7b5c.ccp4
 Error-fetch: unable to load '7b5c'.

If I go to EMDB and download the map file (EMD_12025) and load it manually:

(set normalize_ccp4_maps, 0

load H:/.../emd_12025.map, \emd_12025

isomesh emd_12025_isomesh, emd_12025, 1.0)

The screen is blank and changing levels, etc. does nothing.

But it works in UCSF Chimera. What am I missing?

Thanks.

Criss

[PyMOL] APBS with ions

[Kamil S. <kam...@gm...>]

Hi,
How to include Ca/Zn ions when using APBS built into Pymol? I'm switching
to CHARMM in command line options; CHARMM has CAL and ZN2 atoms already
defined in the DAT file. But there's still no difference in electrostatics
maps with and without ions in the structure. Also, the default 'prepared01'
object lacks the ions.
Thanks for any clues,
Kamil

Re: [PyMOL] PyMOL-users Digest, Vol 185, Issue 11

[ahoneg <ann...@uz...>]

> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 24 Oct 2021 12:32:19 +0000
> From: Xiao Yin Lee <xia...@ku...>
> To: "pym...@li..."
> 	<pym...@li...>
> Subject: [PyMOL] show cartoon mode failed
> Message-ID: <163...@ku...>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> [cid:9f729fc7-e472-42fe-ac95-f7fff9d9bce2]Hi
> 
> 
> Dear,
> 
> 
> I would like to perform the show cartoon command. And everything seems to turn to no color as above. I have tried to change the colour to default but it doenst work. Could you please help?
> 
> Is that anyway to reset the color?
> 
> 
> Thank you?

By default, the cartoon takes its colours from the color of the C alpha atoms at the time when you generate the cartoon. You can change the atom colors later on without changing the cartoon color. 
You can also change the cartoon color with "set cartoon_color“  https://pymolwiki.org/index.php/Cartoon_color

Annemarie Honegger

[PyMOL] show cartoon mode failed

[Xiao Y. L. <xia...@ku...>]

[cid:9f729fc7-e472-42fe-ac95-f7fff9d9bce2]Hi


Dear,


I would like to perform the show cartoon command. And everything seems to turn to no color as above. I have tried to change the colour to default but it doenst work. Could you please help?

Is that anyway to reset the color?


Thank you?

Re: [PyMOL] Export aligned sequence

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

Please ignore my previous message!

File > Export alignment!

From: Joel Tyndall <joe...@ot...>
Sent: Tuesday, 19 October 2021 4:24 pm
To: pym...@li...
Subject: [PyMOL] Export aligned sequence

Hi folks,

I have two proteins aligned in PyMOL. Is there a way to export the resulting sequence alignment?

I have had a very brief look at structural alignment servers but PyMOL seems to give me what I want structurally....and sequence wise

J

Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | pharmacy.otago.ac.nz<https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpharmacy.otago.ac.nz%2F&data=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7Cf232d9f54d694d443e6f08d992b2d687%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637702120007832511%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=HW9FGLBC%2B0Ah5QHNNwGCylLKHgW3VTNQjo6w5pAOMxw%3D&reserved=0>

[PyMOL] Export aligned sequence

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

Hi folks,

I have two proteins aligned in PyMOL. Is there a way to export the resulting sequence alignment?

I have had a very brief look at structural alignment servers but PyMOL seems to give me what I want structurally....and sequence wise

J

Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | pharmacy.otago.ac.nz

Re: [PyMOL] [EXTERNAL] Superposition of native pdb to scripted pdb.

[George T. <gtz...@me...>]

Hi Zuben,

I think I “solved” the problem. Converting “closed.py” to “closed.pse” does the trick. 

Many thanks for your suggestions

George

> On 14 Oct 2021, at 22:26, Brown, Zuben <zb...@cu...> wrote:
> 
> Hi George, 
> 
> The image came through. 
> 
> I think the problem is that it is assigning the same chain ID to multiple chains. Can you give each protein (open, closed) unique chain IDs and see if the problem persists?
> 
> best,
> Zuben
> From: Brown, Zuben <zb...@cu...>
> Sent: Thursday, October 14, 2021 4:42 PM
> To: George Tzotzos <gtz...@me...>
> Cc: pym...@li... <pym...@li...>
> Subject: Re: [PyMOL] [EXTERNAL] Superposition of native pdb to scripted pdb.
>  
> Hi George, 
> 
> It seems that image can't be loaded, possibly due to security settings with my email.
> 
> Anyway, if the issue only occurs after running closed.py then that must be the issue.  I assume loading open.pdb and closed.pdb without that script shows no issue. 
> 
> Without knowing what closed.py is doing, it will be hard to troubleshoot.
> If it isn't a long script, then perhaps you could post it?
> 
> Best wishes,
> Zuben
> From: George Tzotzos <gtz...@me...>
> Sent: Thursday, October 14, 2021 2:29 PM
> To: Brown, Zuben <zb...@cu...>
> Cc: pym...@li... <pym...@li...>
> Subject: Re: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb.
>  
> Zuben, thank you for the prompt response.
> 
> Perhaps, I didn’t describe well the problem. I’m attaching a snapshot showing the loaded scripted structure (“closed.py". It shows anti-correlated movement of backbone atoms of my protein in “closed” conformation. The same protein also adopts an “open” conformation, say “open.pdb”. I know want to load open.pdb in the same pymol session with closed.py. Upon opening/loading open.pdb, the protein can be seen in the pymol window but it is total garbled. Somehow, it seems that the script of closed.py affects the appearance of open.pdb. That is before I even attempt to align the two conformations.
> 
> Once again, many thanks
> 
> George
> 
> <PastedGraphic-1.tiff> 
> 
> 
> 
>> On 14 Oct 2021, at 18:34, Brown, Zuben <zb...@cu... <mailto:zb...@cu...>> wrote:
>> 
>> Have a look here to see if this is what you want:
>> 
>> https://pymolwiki.org/index.php/Align <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Align&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=vRK3AvbEVUrswd78pyC5leKAJSWaMy8peponXB8jGzc&e=>
>> Align - PyMOLWiki <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Align&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=vRK3AvbEVUrswd78pyC5leKAJSWaMy8peponXB8jGzc&e=>
>> align performs a sequence alignment followed by a structural superposition, and then carries out zero or more cycles of refinement in order to reject structural outliers found during the fit.align does a good job on proteins with decent sequence similarity (identity >30%).For comparing proteins with lower sequence identity, the super and cealign commands perform better.
>> pymolwiki.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__pymolwiki.org_&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=G-DVox001clYfvlqDJi_SO3fjxMwUnWEXG1mDewzLoA&e=>
>> 
>> best wishes,
>> Zuben
>> From: George Tzotzos via PyMOL-users <pym...@li... <mailto:pym...@li...>>
>> Sent: Thursday, October 14, 2021 12:06 PM
>> To: pym...@li... <mailto:pym...@li...> <pym...@li... <mailto:pym...@li...>>
>> Subject: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb.
>>  
>> Apologies if this is trivial but I’m rather new to Pymol.
>> 
>> I’m loading a script (x.py) that allows me to visualise correlations in the atomic movements of my protein. I have no problems with this.
>> 
>> My next task is to load the native pdb file (e.g y.pdb) of the same protein but in a different conformation. Once I do this, y.pdb comes out garbled. My goal is to superimpose the y to x to check if the atomic correlations correspond to the conformation of y.
>> 
>> Many thanks in advance for any suggestions
>> 
>> George
>> 
>> 
>> 
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=V3QCdoTZnZUiJepLeIuFTYhGOyNdEmY0slebFRPGECw&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=V3QCdoTZnZUiJepLeIuFTYhGOyNdEmY0slebFRPGECw&e=> 
>> Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=FZ0aDkzSeZUxYs9UfM3YoG-Hj9tSNmJ-Zk8QG0Cq1Rc&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=FZ0aDkzSeZUxYs9UfM3YoG-Hj9tSNmJ-Zk8QG0Cq1Rc&e=>

Re: [PyMOL] [EXTERNAL] Superposition of native pdb to scripted pdb.

[Brown, Z. <zb...@cu...>]

Hi George,

The image came through.

I think the problem is that it is assigning the same chain ID to multiple chains. Can you give each protein (open, closed) unique chain IDs and see if the problem persists?

best,
Zuben
________________________________
From: Brown, Zuben <zb...@cu...>
Sent: Thursday, October 14, 2021 4:42 PM
To: George Tzotzos <gtz...@me...>
Cc: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] [EXTERNAL] Superposition of native pdb to scripted pdb.

Hi George,

It seems that image can't be loaded, possibly due to security settings with my email.

Anyway, if the issue only occurs after running closed.py then that must be the issue.  I assume loading open.pdb and closed.pdb without that script shows no issue.

Without knowing what closed.py is doing, it will be hard to troubleshoot.
If it isn't a long script, then perhaps you could post it?

Best wishes,
Zuben
________________________________
From: George Tzotzos <gtz...@me...>
Sent: Thursday, October 14, 2021 2:29 PM
To: Brown, Zuben <zb...@cu...>
Cc: pym...@li... <pym...@li...>
Subject: Re: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb.

Zuben, thank you for the prompt response.

Perhaps, I didn’t describe well the problem. I’m attaching a snapshot showing the loaded scripted structure (“closed.py". It shows anti-correlated movement of backbone atoms of my protein in “closed” conformation. The same protein also adopts an “open” conformation, say “open.pdb”. I know want to load open.pdb in the same pymol session with closed.py. Upon opening/loading open.pdb, the protein can be seen in the pymol window but it is total garbled. Somehow, it seems that the script of closed.py affects the appearance of open.pdb. That is before I even attempt to align the two conformations.

Once again, many thanks

George

[cid:D69B5C50-FFA0-4DFB-A640-6BE7833D0CA1]



On 14 Oct 2021, at 18:34, Brown, Zuben <zb...@cu...<mailto:zb...@cu...>> wrote:

Have a look here to see if this is what you want:

https://pymolwiki.org/index.php/Align<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Align&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=vRK3AvbEVUrswd78pyC5leKAJSWaMy8peponXB8jGzc&e=>
Align - PyMOLWiki<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Align&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=vRK3AvbEVUrswd78pyC5leKAJSWaMy8peponXB8jGzc&e=>
align performs a sequence alignment followed by a structural superposition, and then carries out zero or more cycles of refinement in order to reject structural outliers found during the fit.align does a good job on proteins with decent sequence similarity (identity >30%).For comparing proteins with lower sequence identity, the super and cealign commands perform better.
pymolwiki.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__pymolwiki.org_&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=G-DVox001clYfvlqDJi_SO3fjxMwUnWEXG1mDewzLoA&e=>


best wishes,
Zuben
________________________________
From: George Tzotzos via PyMOL-users <pym...@li...<mailto:pym...@li...>>
Sent: Thursday, October 14, 2021 12:06 PM
To: pym...@li...<mailto:pym...@li...> <pym...@li...<mailto:pym...@li...>>
Subject: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb.

Apologies if this is trivial but I’m rather new to Pymol.

I’m loading a script (x.py) that allows me to visualise correlations in the atomic movements of my protein. I have no problems with this.

My next task is to load the native pdb file (e.g y.pdb) of the same protein but in a different conformation. Once I do this, y.pdb comes out garbled. My goal is to superimpose the y to x to check if the atomic correlations correspond to the conformation of y.

Many thanks in advance for any suggestions

George




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Re: [PyMOL] [EXTERNAL] Superposition of native pdb to scripted pdb.

[Brown, Z. <zb...@cu...>]

Hi George,

It seems that image can't be loaded, possibly due to security settings with my email.

Anyway, if the issue only occurs after running closed.py then that must be the issue.  I assume loading open.pdb and closed.pdb without that script shows no issue.

Without knowing what closed.py is doing, it will be hard to troubleshoot.
If it isn't a long script, then perhaps you could post it?

Best wishes,
Zuben
________________________________
From: George Tzotzos <gtz...@me...>
Sent: Thursday, October 14, 2021 2:29 PM
To: Brown, Zuben <zb...@cu...>
Cc: pym...@li... <pym...@li...>
Subject: Re: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb.

Zuben, thank you for the prompt response.

Perhaps, I didn’t describe well the problem. I’m attaching a snapshot showing the loaded scripted structure (“closed.py". It shows anti-correlated movement of backbone atoms of my protein in “closed” conformation. The same protein also adopts an “open” conformation, say “open.pdb”. I know want to load open.pdb in the same pymol session with closed.py. Upon opening/loading open.pdb, the protein can be seen in the pymol window but it is total garbled. Somehow, it seems that the script of closed.py affects the appearance of open.pdb. That is before I even attempt to align the two conformations.

Once again, many thanks

George

[cid:D69B5C50-FFA0-4DFB-A640-6BE7833D0CA1]



On 14 Oct 2021, at 18:34, Brown, Zuben <zb...@cu...<mailto:zb...@cu...>> wrote:

Have a look here to see if this is what you want:

https://pymolwiki.org/index.php/Align<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Align&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=vRK3AvbEVUrswd78pyC5leKAJSWaMy8peponXB8jGzc&e=>
Align - PyMOLWiki<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Align&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=vRK3AvbEVUrswd78pyC5leKAJSWaMy8peponXB8jGzc&e=>
align performs a sequence alignment followed by a structural superposition, and then carries out zero or more cycles of refinement in order to reject structural outliers found during the fit.align does a good job on proteins with decent sequence similarity (identity >30%).For comparing proteins with lower sequence identity, the super and cealign commands perform better.
pymolwiki.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__pymolwiki.org_&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=G-DVox001clYfvlqDJi_SO3fjxMwUnWEXG1mDewzLoA&e=>


best wishes,
Zuben
________________________________
From: George Tzotzos via PyMOL-users <pym...@li...<mailto:pym...@li...>>
Sent: Thursday, October 14, 2021 12:06 PM
To: pym...@li...<mailto:pym...@li...> <pym...@li...<mailto:pym...@li...>>
Subject: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb.

Apologies if this is trivial but I’m rather new to Pymol.

I’m loading a script (x.py) that allows me to visualise correlations in the atomic movements of my protein. I have no problems with this.

My next task is to load the native pdb file (e.g y.pdb) of the same protein but in a different conformation. Once I do this, y.pdb comes out garbled. My goal is to superimpose the y to x to check if the atomic correlations correspond to the conformation of y.

Many thanks in advance for any suggestions

George




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Re: [PyMOL] [EXTERNAL] Superposition of native pdb to scripted pdb.

[George T. <gtz...@me...>]

Zuben, thank you for the prompt response.

Perhaps, I didn’t describe well the problem. I’m attaching a snapshot showing the loaded scripted structure (“closed.py". It shows anti-correlated movement of backbone atoms of my protein in “closed” conformation. The same protein also adopts an “open” conformation, say “open.pdb”. I know want to load open.pdb in the same pymol session with closed.py. Upon opening/loading open.pdb, the protein can be seen in the pymol window but it is total garbled. Somehow, it seems that the script of closed.py affects the appearance of open.pdb. That is before I even attempt to align the two conformations.

Once again, many thanks

George

 



> On 14 Oct 2021, at 18:34, Brown, Zuben <zb...@cu...> wrote:
> 
> Have a look here to see if this is what you want:
> 
> https://pymolwiki.org/index.php/Align <https://pymolwiki.org/index.php/Align>
> Align - PyMOLWiki <https://pymolwiki.org/index.php/Align>
> align performs a sequence alignment followed by a structural superposition, and then carries out zero or more cycles of refinement in order to reject structural outliers found during the fit.align does a good job on proteins with decent sequence similarity (identity >30%).For comparing proteins with lower sequence identity, the super and cealign commands perform better.
> pymolwiki.org <http://pymolwiki.org/>
> 
> best wishes,
> Zuben
> From: George Tzotzos via PyMOL-users <pym...@li... <mailto:pym...@li...>>
> Sent: Thursday, October 14, 2021 12:06 PM
> To: pym...@li... <mailto:pym...@li...> <pym...@li... <mailto:pym...@li...>>
> Subject: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb.
>  
> Apologies if this is trivial but I’m rather new to Pymol.
> 
> I’m loading a script (x.py) that allows me to visualise correlations in the atomic movements of my protein. I have no problems with this.
> 
> My next task is to load the native pdb file (e.g y.pdb) of the same protein but in a different conformation. Once I do this, y.pdb comes out garbled. My goal is to superimpose the y to x to check if the atomic correlations correspond to the conformation of y.
> 
> Many thanks in advance for any suggestions
> 
> George
> 
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=V3QCdoTZnZUiJepLeIuFTYhGOyNdEmY0slebFRPGECw&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=V3QCdoTZnZUiJepLeIuFTYhGOyNdEmY0slebFRPGECw&e=> 
> Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=FZ0aDkzSeZUxYs9UfM3YoG-Hj9tSNmJ-Zk8QG0Cq1Rc&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=FZ0aDkzSeZUxYs9UfM3YoG-Hj9tSNmJ-Zk8QG0Cq1Rc&e=>

[PyMOL] Superposition of native pdb to scripted pdb.

[George T. <gtz...@me...>]

Apologies if this is trivial but I’m rather new to Pymol.

I’m loading a script (x.py) that allows me to visualise correlations in the atomic movements of my protein. I have no problems with this.

My next task is to load the native pdb file (e.g y.pdb) of the same protein but in a different conformation. Once I do this, y.pdb comes out garbled. My goal is to superimpose the y to x to check if the atomic correlations correspond to the conformation of y.

Many thanks in advance for any suggestions

George

Re: [PyMOL] Capping of multiple pdb file using python script in pymol

[shivani s. <shi...@gm...>]

Hi Thomas,

Thanks for your reply. I am currently using:
















*import __main____main__.pymol_argv = ['pymol','-qc']from pymol import cmd,
editorpymol.finish_launching()import globimport ospath =
os.path.dirname(pymol.__script__)pdb_files = glob.glob(os.path.join(path,
'*.pdb'))cmd.delete('all')for pdb in pdb_files:    cmd.load(pdb)
editor.attach_amino_acid("resi 10 and name N", 'ace')
editor.attach_amino_acid("resi 11 and name C", 'nme')    cmd.save(pdb)
cmd.delete('all')*

This seems to be working fine for me.

Shivani

On Thu, 14 Oct 2021 at 00:22, Thomas Holder <th...@th...> wrote:

> Hi Shivani,
>
> Your selection needs to be object-specific, e.g. like this:
>
> for filename in glob("*.pdb"):
>    cmd.load(filename)
>    obj = filename[:-4]
>    editor.attach_amino_acid(obj + " and resi 10 and name N", 'ace')
>
> Hope that helps.
>
> Cheers,
>  Thomas
>
>
> > On Oct 9, 2021, at 21:18, shivani sharma <shi...@gm...> wrote:
> >
> > Hi everyone,
> >
> > I am trying to cap (with ace and nme) various *.pdbs. I made a folder,
> where I have placed *.py file and *.pdb files. When I load the run
> following script:
> >
> > from pymol import cmd, editor
> > from glob import glob
> > for filename in glob("*.pdb"):
> >    cmd.load(filename)
> >    editor.attach_amino_acid("resi 10 and name N", 'ace')
> >    editor.attach_amino_acid("resi 11 and name C", 'nme')
> >
> > It is opening all files but capping only one of the files and giving me
> back an error:
> > Traceback (most recent call last):
> >  File "pyformol.py", line 6, in <module>
> >    editor.attach_amino_acid("resi 10 and name N", 'ace')
> >  File
> "C:\Users\Shivani\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\pymol\editor.py",
> line 129, in attach_amino_acid
> >    raise pymol.CmdException("invalid connection point: must be one atom,
> name N or C.")
> > pymol.CmdException:  Error: invalid connection point: must be one atom,
> name N or C.
> >
> > This seems like a looping error. I haven't been able to find much about
> "glob". Could someone suggest an easy way out? I want to create a loop
> where ace and nme should be added to all the dipeptides and save them as
> separate pdb files.
> >
> > Shivani
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Capping of multiple pdb file using python script in pymol

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

Hi Shivani,

Your selection needs to be object-specific, e.g. like this:

for filename in glob("*.pdb"):
   cmd.load(filename)
   obj = filename[:-4]
   editor.attach_amino_acid(obj + " and resi 10 and name N", 'ace')

Hope that helps.

Cheers,
 Thomas


> On Oct 9, 2021, at 21:18, shivani sharma <shi...@gm...> wrote:
> 
> Hi everyone, 
> 
> I am trying to cap (with ace and nme) various *.pdbs. I made a folder, where I have placed *.py file and *.pdb files. When I load the run following script:
> 
> from pymol import cmd, editor
> from glob import glob
> for filename in glob("*.pdb"):
>    cmd.load(filename)
>    editor.attach_amino_acid("resi 10 and name N", 'ace')
>    editor.attach_amino_acid("resi 11 and name C", 'nme')
> 
> It is opening all files but capping only one of the files and giving me back an error:
> Traceback (most recent call last):
>  File "pyformol.py", line 6, in <module>
>    editor.attach_amino_acid("resi 10 and name N", 'ace')
>  File "C:\Users\Shivani\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\pymol\editor.py", line 129, in attach_amino_acid
>    raise pymol.CmdException("invalid connection point: must be one atom, name N or C.")
> pymol.CmdException:  Error: invalid connection point: must be one atom, name N or C.
> 
> This seems like a looping error. I haven't been able to find much about "glob". Could someone suggest an easy way out? I want to create a loop where ace and nme should be added to all the dipeptides and save them as separate pdb files.
> 
> Shivani
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] How to label on surface

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

Hi Yeping,

Try something like this, it moves the label 6 angstrom towards the front:

set label_position, [0,0,6]

See also
https://pymolwiki.org/index.php/label_position

Cheers,
  Thomas

> On Oct 11, 2021, at 05:52, sunyeping via PyMOL-users <pym...@li...> wrote:
> 
> Dear Pymol users,
> 
> I wish to label the one-letter residue names for a bunch of selected resides on surface representation of a protein, but I found the labels cannot be seen on the image. It seems that these labels can been seen on cartoon representation when the surface is hide.
> Could you tell to how to show the labels on the surface?
> I will appreciate any help!
> 
> Best regards
> _______________________________________________
> 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 label on surface

[sunyeping <sun...@al...>]

Dear Pymol users,

I wish to label the one-letter residue names for a bunch of selected resides on surface representation of a protein, but I found the labels cannot be seen on the image. It seems that these labels can been seen on cartoon representation when the surface is hide.
Could you tell to how to show the labels on the surface?
I will appreciate any help!

Best regards

[PyMOL] Capping of multiple pdb file using python script in pymol

[shivani s. <shi...@gm...>]

Hi everyone,

I am trying to cap (with ace and nme) various *.pdbs. I made a folder,
where I have placed *.py file and *.pdb files. When I load the run
following script:

from pymol import cmd, editor
from glob import glob
for filename in glob("*.pdb"):
    cmd.load(filename)
    editor.attach_amino_acid("resi 10 and name N", 'ace')
    editor.attach_amino_acid("resi 11 and name C", 'nme')

It is opening all files but capping only one of the files and giving me
back an error:

Traceback (most recent call last):
  File "pyformol.py", line 6, in <module>
    editor.attach_amino_acid("resi 10 and name N", 'ace')
  File "C:\Users\Shivani\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\pymol\editor.py",
line 129, in attach_amino_acid
    raise pymol.CmdException("invalid connection point: must be one
atom, name N or C.")
pymol.CmdException:  Error: invalid connection point: must be one
atom, name N or C.


This seems like a looping error. I haven't been able to find much about
"glob". Could someone suggest an easy way out? I want to create a loop
where ace and nme should be added to all the dipeptides and save them as
separate pdb files.


Shivani

Re: [PyMOL] how to find the distance between carbon carbon bonds of two molecules with in 5 angstrom

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

Hi,

You can specify carbon elements within a selection expression by adding `&
elem C`. Therefore your new command would look like:

dist Hydrophobic, alphaCD & elem C, carvacrol_out_ligand_01 & elem C, 5

[image: image.png]

Hope this helps,

Jarrett J

On Fri, Oct 1, 2021 at 2:49 AM chakkaravarthi saravanan <
cha...@gm...> wrote:

> What is the PYMOL common prompt to find all the carbon -carbon bonds
> within 5 Angstrom distance between the enclosed receptor and ligand
> molecules.
>
> I have used the following command However, It provides not only CC bonds
> it also provides C-OH bonds.
>
> dist Hydrophobic, alphaCD, carvacrol_out_ligand_01, 5
>
> How to specify the Carbon - Carbon bond between molecules.
>
>
> What is the command to calculate the number of those carbon-carbon bonds.
>
> Looking forward your reply
>
> Regards
>
> [image: image.png]
> --
> *Dr. S. Chakkaravarthi, Ph. D.,*
> Assistant Professor(Biochemistry)
> National Institute of Food Tech. Entrepreneurship & Management (NIFTEM)
> (Under MoFPI, Govt. of India)
> Plot No. 97, Sector 56, HSIIDC Industrial Estate
> Kundli, District- Sonipat, Haryana - 131 028
> Mobile:91-9466000676
> _______________________________________________
> 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
[image: Schrodinger Logo] <https://www.schrodinger.com/>

[PyMOL] how to find the distance between carbon carbon bonds of two molecules with in 5 angstrom

[chakkaravarthi s. <cha...@gm...>]

What is the PYMOL common prompt to find all the carbon -carbon bonds within
5 Angstrom distance between the enclosed receptor and ligand molecules.

I have used the following command However, It provides not only CC bonds it
also provides C-OH bonds.

dist Hydrophobic, alphaCD, carvacrol_out_ligand_01, 5

How to specify the Carbon - Carbon bond between molecules.


What is the command to calculate the number of those carbon-carbon bonds.

Looking forward your reply

Regards

[image: image.png]
-- 
*Dr. S. Chakkaravarthi, Ph. D.,*
Assistant Professor(Biochemistry)
National Institute of Food Tech. Entrepreneurship & Management (NIFTEM)
(Under MoFPI, Govt. of India)
Plot No. 97, Sector 56, HSIIDC Industrial Estate
Kundli, District- Sonipat, Haryana - 131 028
Mobile:91-9466000676

[PyMOL] extend electron density map/ align map to pdb

[Finton, K. <kf...@fr...>]

Hello,

I have generated a Polder/omit map in Phenix and am trying to visualize in Pymol to make a figure for publication. The issue is that the feature I want to see is cut in half because it is on the edge of the unit cell. Is there a way to solve this? I am wondering if you can generate maps to symmetry mates which, when combined, would show the complete feature?

Another issue is that the maps generated in Phenix (or CCP4 or Coot) do not align with the pdb in Pymol. I have been generating enough symmetry mates in Pymol to expand into the map area and then deleting all unwanted molecules. This normally isn't a big deal, but I am working with 36 complexes in the ASU and far distances between the map and the pdb positions, and it's really bogging down my computer. I'd love to figure out a way to have the map align with the pdb.

Thank you



Kathryn Finton, PhD
kf...@fh...<mailto:kf...@fh...>
206.667.2801 (Desk)
206.667.5588 (Lab)


[https://ci6.googleusercontent.com/proxy/wJKoE0y9yp3v5Q-EruldC9J-xStNHXG75wWe9a0yZ0TmX0wxV_164sCCwXN1pxeGRVvn2CMg1D-ciTorD_5h4FrequL3xYICSYjSnx4BNJ2wUdSGSnVkyl_1VmTcWCBDF6miGKM=s0-d-e1-ft#http://www.fredhutch.org/content/dam/public/email-signatures/2/fred_hutch_logo.png]<http://www.fredhutch.org/>
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
Weintraub bldg, B3-183
Seattle, WA 98109
fredhutch.org<http://www.fredhutch.org/>

Re: [PyMOL] [EXTERNAL] How to import anaconda packages in Pymol?

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

Hi Sunyeping,

Enter on the upper command line in PyMOL, "conda install pandas" to gain access to the pandas from PyMOL.

Alternatively, you can install pymol in an anaconda env, activate that env, and then install pandas in that env.

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

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: sunyeping via PyMOL-users [pym...@li...]
Sent: Wednesday, September 29, 2021 10:54 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] How to import anaconda packages in Pymol?

Dear all,

I installed Pymol in CentOS from source following the guide in "https://pymolwiki.org/index.php/Linux_Install<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Linux-5FInstall&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=4XDBZ4622O10xA5XUfZJ6zzsdZojw2K5JrAD2yjDdPM&s=TZs4hlwxHiDIAIki3LnjGsNjyzNEKHO4Vqpjtrox4mA&e=>". I compiled Pymol with the Python from anaconda, but I found that I cannot import anaconda packages (such as pandas, numpy, etc.) in Pymol.
The "import pandas" command will return "no such module named pandas" error. Could yuo tell me how to let pymol use the anaconda packages? I will appreciate any help.

Best regards