pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Jarret,

Since I don’t have a microphone on my computer, may we talk on the phone while we screen share come 9:30 this morning?

Ph: 562-360-7713

Get Outlook for iOS<" rel="nofollow">https://aka.ms/o0ukef>
________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: Monday, March 27, 2023 5:34:41 PM
To: Neena Susan Eappen <nee...@gm...>
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] Question on rmsd alignment

                EXTERNAL EMAIL : Exercise caution when responding, opening links, or opening attachments.


Hi Neena,

I wouldn't put too much stock into what you're observing in the first image with the red arrow. PyMOL doesn't make the determination of whether that structure is stable; but it can provide visual aid and secondary structure assignment/hinting from coordinates and residue/atomic information.

As for the second question, Not all 177 atoms were used in the alignment to calculate the RMSD. This depends on your alignment method and other parameters that you set. In your case, 144 atom pairs were used for the alignment.

Hope this helps,
Jarrett J.

On Tue, Mar 21, 2023 at 11:11 AM Neena Susan Eappen <nee...@gm...<mailto:nee...@gm...>> wrote:
Hello PyMOL users,

1. I see this unusual secondary structural element in the peptide structure shown below. It was generated from computations, so the unusual element arose from positive dihedral across lysine residue. My question is whether it is structurally possible or if it is a stable structure?
[image.png]
[image.png]

2. Also when using alignment tool on PyMOL for the below two structures, RMSD is displayed with a certain number of atoms in parentheses (144 atoms). However, there are 177 atoms in total. So does this RMSD mean that the total difference in RMSD between these two structures is 0.602 Angstroms and only 144 out of 177 atoms with very close alignment/ position?


RMSD =    0.602 (144 atoms)

[image.png]
Any insight would be appreciated!

Thank you so much for your help,
Neena



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--

Jarrett Johnson | Senior Developer, PyMOL

[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

Hi Neena,

I wouldn't put too much stock into what you're observing in the first image
with the red arrow. PyMOL doesn't make the determination of whether that
structure is stable; but it can provide visual aid and secondary structure
assignment/hinting from coordinates and residue/atomic information.

As for the second question, Not all 177 atoms were used in the alignment to
calculate the RMSD. This depends on your alignment method and other
parameters that you set. In your case, 144 atom pairs were used for the
alignment.

Hope this helps,
Jarrett J.

On Tue, Mar 21, 2023 at 11:11 AM Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> 1. I see this unusual secondary structural element in the peptide
> structure shown below. It was generated from computations, so the
> unusual element arose from positive dihedral across lysine residue. My
> question is whether it is structurally possible or if it is a stable
> structure?
> [image: image.png]
> [image: image.png]
>
> 2. Also when using alignment tool on PyMOL for the below two structures,
> RMSD is displayed with a certain number of atoms in parentheses (144
> atoms). However, there are 177 atoms in total. So does this RMSD mean that
> the total difference in RMSD between these two structures is 0.602
> Angstroms and only 144 out of 177 atoms with very close alignment/
> position?
>
> RMSD =    0.602 (144 atoms)
> [image: image.png]
> Any insight would be appreciated!
>
> Thank you so much for your help,
> Neena
>
>
>
> _______________________________________________
> 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

Hi Kyle,

The approach you listed looks about right to me. Using conda commands from
the PyMOL commandline in the bundles don't seem to be working in those
builds, but should be fine if you use another terminal. Either way, I will
reach out to you directly.

Best,
Jarrett J.

On Mon, Mar 27, 2023 at 3:46 PM Kyle Moorman via PyMOL-users <
pym...@li...> wrote:

> To whom it may concern,
>
>
>
> While I am a licensed user of PyMol, he...@sc... has still not
> responded to me. I have some very technical installation questions which
> upon trying to solve on my own is only making the problem worse.
>
>
>
> Below is all the information I have and what I’ve sent to
> he...@sc... This has truly been a huge impediment to my work and
> your help in this matter would be greatly appreciated. Currently conda is
> crashing every time I try to open it and the instructions I’ve found on
> pymolwiki as well as various other sites I’ve come across are not very
> clear at all. Below is the message I sent to he...@sc...  Could
> you help please? Thanks in advance:
>
>
>
> PyMOL 2.5.4
> Windows-10-10.0.19041-SP0
> ATI Technologies Inc.
> AMD Radeon(TM) HD8490
> 4.5.13399 Compatibility Profile Context 15.201.1151.1008
> PyMOL Invoice #49406
> 01-mar-2024
>
> Filename of downloaded installer: PyMOL-2.5.4_404-Win64-portable-py37
>
>
>
>
>
>
>
> I’m requesting help once more. An extension is not downloading for me.
> Please let me know if there is any other information I need to provide in
> order to receive installation help. This has thus far been a very
> unsatisfactory experience. Below is the email I sent before:
>
>
>
> To whom it may concern,
>
> I have used the following commands in attempt to download psico:
>
> I used this file path:
> "C:\Users\admin\PyMOL\condabin\conda.bat"
>
> In order to install this code:
>
> conda install -c schrodinger pymol
> conda install -c schrodinger pymol-psico
> conda install -c rdkit rdkit
> conda install -c speleo3 csb
>
> I am now having trouble using the commands in this code within the command
> line in PyMol. I believe that I need to use some sort of API in order to
> use the commands from psico. I am installing these packages specifically to
> use the 'mcsalign' function to calculate better rmsd's based off structural
> overlap of molecules I'm studying in school right now.
>
>
> I have version of 2.5.4 of PyMol and 2.7 version of Python. Could you
> please provide help as to how specifically download an API so I may employ
> the commands from psico? This function would be incredibly useful but I'm
> getting very caught up with the installation. If there is someone I can
> share my screen with so I can get this going, I'd really appreciate it. I'm
> really stuck and in need of help.
>
> Thanks so much in advance,
>
> Kyle
>
>
> _______________________________________________
> 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

Thank you SO MUCH. My computer is going into overdrive. I want to use another terminal, but I’ve spent all last night and all day today trying to figure it out.

My phone number is 562-360-7713.

I’m really doing whatever it takes to make this work. Thank you again.

Kyle

Get Outlook for iOS<" rel="nofollow">https://aka.ms/o0ukef>
________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: Monday, March 27, 2023 4:23:30 PM
To: Kyle Moorman <kmo...@fa...>
Cc: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] PLEASE HELP

                EXTERNAL EMAIL : Exercise caution when responding, opening links, or opening attachments.


Hi Kyle,

The approach you listed looks about right to me. Using conda commands from the PyMOL commandline in the bundles don't seem to be working in those builds, but should be fine if you use another terminal. Either way, I will reach out to you directly.

Best,
Jarrett J.

On Mon, Mar 27, 2023 at 3:46 PM Kyle Moorman via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:

To whom it may concern,



While I am a licensed user of PyMol, he...@sc...<mailto:he...@sc...> has still not responded to me. I have some very technical installation questions which upon trying to solve on my own is only making the problem worse.



Below is all the information I have and what I’ve sent to he...@sc...<mailto:he...@sc...> This has truly been a huge impediment to my work and your help in this matter would be greatly appreciated. Currently conda is crashing every time I try to open it and the instructions I’ve found on pymolwiki as well as various other sites I’ve come across are not very clear at all. Below is the message I sent to he...@sc...<mailto:he...@sc...>  Could you help please? Thanks in advance:



PyMOL 2.5.4
Windows-10-10.0.19041-SP0
ATI Technologies Inc.
AMD Radeon(TM) HD8490
4.5.13399 Compatibility Profile Context 15.201.1151.1008
PyMOL Invoice #49406
01-mar-2024

Filename of downloaded installer: PyMOL-2.5.4_404-Win64-portable-py37







I’m requesting help once more. An extension is not downloading for me. Please let me know if there is any other information I need to provide in order to receive installation help. This has thus far been a very unsatisfactory experience. Below is the email I sent before:



To whom it may concern,

I have used the following commands in attempt to download psico:

I used this file path:
"C:\Users\admin\PyMOL\condabin\conda.bat"

In order to install this code:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c rdkit rdkit
conda install -c speleo3 csb

I am now having trouble using the commands in this code within the command line in PyMol. I believe that I need to use some sort of API in order to use the commands from psico. I am installing these packages specifically to use the 'mcsalign' function to calculate better rmsd's based off structural overlap of molecules I'm studying in school right now.


I have version of 2.5.4 of PyMol and 2.7 version of Python. Could you please provide help as to how specifically download an API so I may employ the commands from psico? This function would be incredibly useful but I'm getting very caught up with the installation. If there is someone I can share my screen with so I can get this going, I'd really appreciate it. I'm really stuck and in need of help.

Thanks so much in advance,

Kyle



_______________________________________________
PyMOL-users mailing list
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--

Jarrett Johnson | Senior Developer, PyMOL

[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

To whom it may concern,

While I am a licensed user of PyMol, he...@sc...<mailto:he...@sc...> has still not responded to me. I have some very technical installation questions which upon trying to solve on my own is only making the problem worse.

Below is all the information I have and what I've sent to he...@sc...<mailto:he...@sc...> This has truly been a huge impediment to my work and your help in this matter would be greatly appreciated. Currently conda is crashing every time I try to open it and the instructions I've found on pymolwiki as well as various other sites I've come across are not very clear at all. Below is the message I sent to he...@sc...<mailto:he...@sc...>  Could you help please? Thanks in advance:


PyMOL 2.5.4
Windows-10-10.0.19041-SP0
ATI Technologies Inc.
AMD Radeon(TM) HD8490
4.5.13399 Compatibility Profile Context 15.201.1151.1008
PyMOL Invoice #49406
01-mar-2024

Filename of downloaded installer: PyMOL-2.5.4_404-Win64-portable-py37




I'm requesting help once more. An extension is not downloading for me. Please let me know if there is any other information I need to provide in order to receive installation help. This has thus far been a very unsatisfactory experience. Below is the email I sent before:

To whom it may concern,

I have used the following commands in attempt to download psico:

I used this file path:
"C:\Users\admin\PyMOL\condabin\conda.bat"

In order to install this code:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c rdkit rdkit
conda install -c speleo3 csb

I am now having trouble using the commands in this code within the command line in PyMol. I believe that I need to use some sort of API in order to use the commands from psico. I am installing these packages specifically to use the 'mcsalign' function to calculate better rmsd's based off structural overlap of molecules I'm studying in school right now.


I have version of 2.5.4 of PyMol and 2.7 version of Python. Could you please provide help as to how specifically download an API so I may employ the commands from psico? This function would be incredibly useful but I'm getting very caught up with the installation. If there is someone I can share my screen with so I can get this going, I'd really appreciate it. I'm really stuck and in need of help.

Thanks so much in advance,

Kyle

Hello PyMOL users,

1. I see this unusual secondary structural element in the peptide structure
shown below. It was generated from computations, so the unusual element
arose from positive dihedral across lysine residue. My question is whether
it is structurally possible or if it is a stable structure?
[image: image.png]
[image: image.png]

2. Also when using alignment tool on PyMOL for the below two structures,
RMSD is displayed with a certain number of atoms in parentheses (144
atoms). However, there are 177 atoms in total. So does this RMSD mean that
the total difference in RMSD between these two structures is 0.602
Angstroms and only 144 out of 177 atoms with very close alignment/
position?

RMSD =    0.602 (144 atoms)
[image: image.png]
Any insight would be appreciated!

Thank you so much for your help,
Neena

Dear PyMOL experts,

in GPCR crystal structures it is quite common to have fusions with 
lysozyme or BRIL in the third intracellular loop. The residue numbers of 
the inserted domains are often incremented by 1000. As a result, the two 
residues at the fusion point jump from for example 223 to 1002. As a 
result, gaps exist in the cartoon representation at the fusion points. 
Increasing cartoon_gap_cutoff does not help as PyMOL rather connects the 
C- and N-termini of the GPCR fold. In stick representation, the peptide 
bonds at the fusion points are represented fine. I could not find any 
options like "cartoon_use_peptide_bonds" or  "bond_cartoon selection, 
selection". A workaround would probably be to renumber the residues of 
the fusion protein and use insertion codes, I did not try this yet. An 
example is pdb id 4eiy.

Is there a better solution, have I overlooked an option?

Best regards,

Norbert

Are they still sending out Education licenses? I teach a research class where we/students need it for 1-2 semesters.



Dr. Ann Kimble-Hill, Ph.D.
Asst. Director DEI, IU Simon Comprehensive Cancer Center
IUPUI PREP Program Coordinator
Asst. Research Professor
Dept. Biochemistry & Mol. Biology
Indiana University School of Medicine
ank...@iu...
Pronouns: She/Her/Hers

“Ignorance is a cure for nothing. ” ― W. E. B. Dubois
________________________________
From: MILY BHATTACHARYA via PyMOL-users <pym...@li...>
Sent: Saturday, March 11, 2023 11:10:57 AM
To: pym...@li... <pym...@li...>
Subject: [External] [PyMOL] Unable to install PyTM plugin in PyMOL

You don't often get email from pym...@li.... Learn why this is important<" rel="nofollow">https://aka.ms/LearnAboutSenderIdentification>
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.

Hello PyMOL support team,

I am unable to install the post-translational modification (PyTM) plugin in my PyMOL. If I try to copy-paste the PyMOLwiki or the respective repository URL in the given box under the "Install new plugins" tab (Plugin manager), it shows some error (...sscl:504, 1407742e...etc.). I would appreciate it if you could kindly assist me in sorting this out. I am using the educational version of PyMOL on Windows.

Thank you in advance.

Sincerely,
Mily.

======================================================
Dr. Mily Bhattacharya, Ph.D.

Assistant Professor
School of Chemistry and Biochemistry,

Thapar Institute of Engineering & Technology (Deemed to be University),

Thapar Technology Campus, Post Box No. 32, Bhadson Road.
Patiala - 147004, Punjab, India.

Email: mil...@th...<mailto:mil...@th...> and mi...@gm...<mailto:mi...@gm...>
Homepage: " rel="nofollow">https://sites.google.com/site/milybhattacharyamohali/home<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fsite%2Fmilybhattacharyamohali%2Fhome&data=05%7C01%7Cankimble%40iu.edu%7C92c3d96303ef40eefc7008db224f4db1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C638141496224819199%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=a%2BxjF2YjdU%2FccMmSHdFQozOWrQuYz5r%2FuayLYvDeORs%3D&reserved=0>
ORCID: " rel="nofollow">http://orcid.org/0000-0003-2670-6709<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Forcid.org%2F0000-0003-2670-6709&data=05%7C01%7Cankimble%40iu.edu%7C92c3d96303ef40eefc7008db224f4db1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C638141496224819199%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=q9TGrmN83DAepm3%2BVq63et8rUIKR6E2VNi7xJqVEKOA%3D&reserved=0>

Hello PyMOL support team,

I am unable to install the post-translational modification (PyTM) plugin in
my PyMOL. If I try to copy-paste the PyMOLwiki or the respective repository
URL in the given box under the "Install new plugins" tab (Plugin manager),
it shows some error (...sscl:504, 1407742e...etc.). I would appreciate it
if you could kindly assist me in sorting this out. I am using the
educational version of PyMOL on Windows.

Thank you in advance.

Sincerely,
Mily.

======================================================
Dr. Mily Bhattacharya, Ph.D.

Assistant Professor
School of Chemistry and Biochemistry,

Thapar Institute of Engineering & Technology (Deemed to be University),
Thapar Technology Campus, Post Box No. 32, Bhadson Road.
Patiala - 147004, Punjab, India.

Email: mil...@th... and mi...@gm...
Homepage: https://sites.google.com/site/milybhattacharyamohali/home
ORCID: http://orcid.org/0000-0003-2670-6709

Dear All,

I have a pdb structure of a triple helix having a non-nucleotide residue conjugated between two residues of one of the strands. I would like to represent the backbone of all the three strands as a continuous tube. However, the tube of the modified strand gets interrupted right before and after the conjugate. I assume that pymol is not recognizing the atoms linking the non-nucleotidic modification to both ends of the strands as backbone atoms. The backbone in nucleic acids is P(i)-O5’(i)-C5’(i)-C4’(i)-C3’(i+1)-O3’(i+1)-P(i+1), in the case of my molecule the linkage is P(i)-O5’(i)-C5’(i)-C3’(i+1)-O3’(i+1). So the C4’ (and no other sugar atoms are present in the “modified” residue that is conjugate between the flanking nucleotides.

Is there any way to make Pymol consider some atoms as atoms of the backbone or to represent certain atoms like a “tube” or cartoon-like backbone?

Thank you very much for you help.

All the best,

Miguel

Hi,

Thanks, that's sorted it.

A follow up question is that when printing the results of the align command, I've noticed that the number of cycles seems to max out at 1 regardless of what I set it to - is that because it's reaching convergence after the first cycle?

All the best,

Irwin
________________________________
From: Tamas Hegedus <bio...@gm...>
Sent: Thursday, March 2, 2023 8:24 AM
To: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] Align in PyMOL via Python script


Hi,


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


cmd: align x, y

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


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


Bests, Tamas


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

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

All the best,

Irwin







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Hi,


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


cmd: align x, y

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


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


Bests, Tamas


On 2023. 03. 02. 8:54, Irwin Selvam wrote:
> Hi,
>
> I would like to run the Align Python script found on the Align page of 
> the PyMOLwiki (https://pymolwiki.org/index.php/Align). I've tweaked it 
> slightly for my uses and it seems to run fine on PyMOL 2.5.0 but 
> according to the wiki it should output a list of results (RMSD etc) in 
> the internal feedback (or command prompt?), but it doesn't in my case. 
> Does anyone know why? It does seem like there some missing lines to 
> the script in order to achieve this. Apologies for the basic question!
>
> All the best,
>
> Irwin
>
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:http://www.mail-archive.com/pym...@li...
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Hi,

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

All the best,

Irwin