pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Problem with morphing RNA structures

[Mehmet G. <mg...@ku...>]

Dear Pymol Users,

I am having an issue while performing morph between two RNA structures. The
morphed structure loses the phosphate backbone and some parts of the side
chains (see attachment). Does anybody know why this problem occurs and how
to solve it if possible?
Thank you in advance.

Best regards,
Mehmet

Re: [PyMOL] Question on rmsd alignment

[Kyle M. <kmo...@fa...>]

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<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]

Re: [PyMOL] Question on rmsd alignment

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

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

Re: [PyMOL] PLEASE HELP

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

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

Re: [PyMOL] PLEASE HELP

[Kyle M. <kmo...@fa...>]

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<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



_______________________________________________
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--

Jarrett Johnson | Senior Developer, PyMOL

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

[PyMOL] PLEASE HELP

[Kyle M. <kmo...@fa...>]

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] Question on rmsd alignment

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

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] Gaps in cartoon representation due to non-continuous residue numbers

[Norbert S. <st...@bb...>]

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

[PyMOL] Education license

[Kimble-Hill, A. C. <ank...@iu...>]

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<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: 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: 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>

[PyMOL] Unable to install PyTM plugin in PyMOL

[MILY B. <mil...@th...>]

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

[PyMOL] Cartoon tube in no-backbone atoms

[Miguel G. <mga...@iq...>]

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

Re: [PyMOL] Align in PyMOL via Python script

[Irwin S. <irw...@po...>]

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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Re: [PyMOL] Align in PyMOL via Python script

[Tamas H. <bio...@gm...>]

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...
> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Align in PyMOL via Python script

[Irwin S. <irw...@po...>]

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] Connect to remote pymol instance.

[Petro <sub...@kh...>]

Hi.
I am curious if it is possible to run a local pymol and connect it to a
remote pymol.
 I use pymol to process data on the remote machine via SSH without X
forwarding using python and/or jupyter.
I would like to show images on the local computer.
Is it possible somehow without copying files to the local computer?
Thanks.
Petro.

[PyMOL] Can not open the .pse files by double clicking

[Gong, Z. <zg...@cu...>]

Dear Pymol users,

I am using the latest version of Pymol (version 2.5.4) and encountered this problem: I could open the .pse files ONLY through the “File” – “open…”, but NOT by double clicking on the .pse files. Could anyone please help what could be the problem and how to solve it? Many thanks in advance!

Best,
Zhen

[PyMOL] transform_selection not behaving like expected

[Olivia V. <oli...@gm...>]

Hi,

I am using pymol to generate surface meshes from pdb source files. I would like to have the vertices in the same reference frame as the original pdb coordinates. However, when I save the obj file the object is centered at [0,0,0].
I tried to use the following code snippet to transform the surface, but it didn't do anything to the coordinates.
What am I doing wrong, or is the command not behaving how supposed to?

pymol.load(pdb_file)
view = list(pymol.get_view())
M = view[0:3] + [-view[12]] + view[3:6] + [-view[13]] + view[6:9] + [-view[14]] + view[12:15] + [1.0]
pymol.transform_selection("(all)", M, 0, 0, 0, 1)
pymol.set_view([1, 0, 0, 0, 1, 0, 0, 0, 1] + view[9:])
Any help would be greatly appreciated. If there is a way to avoid the centering at the loading stage, that would be awesome too.
Thanks
Olivia

[PyMOL] Conference Announcement: 35th MMWS in Erlangen, Germany

[Harald L. <har...@fa...>]

<html>
  <head>
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
  </head>
  <body>
    Dear list subscribers,<br>
    <br>
    we are very delighted to announce this year’s<br>
    <br>
    “35th Molecular Modelling Workshop (MMWS)”<br>
    <a class="moz-txt-link-freetext" href="https://mmws2023.mgms-ds.de"
      moz-do-not-send="true">https://mmws2023.mgms-ds.de</a><br>
    <br>
    taking place on Monday 13th to Wednesday 15th March 2023<br>
    at the Friedrich-Alexander-Universität in Erlangen, Germany.<br>
    <br>
    The workshop, which is organised by the German Section of the
    Molecular<br>
    Graphics and Modelling Society (MGMS-DS e.V.), has a long history of<br>
    giving young scientists (especially graduate students) the
    opportunity<br>
    to present their work and dive into discussions with each other and
    the<br>
    "older experts" of the field to gain valuable feedback from
    academic, as<br>
    well as industrial colleagues. Oral and poster contributions are
    welcome<br>
    from all areas of molecular modelling – from the life sciences,<br>
    computational biology and chemistry, cheminformatics, to materials
    sciences.<br>
    <br>
    After the forced Corona break, this year's meeting, for the first
    time,<br>
    offers a special session focussing on high-performance computing
    (HPC)<br>
    aspects in molecular modelling.<br>
    <br>
    Starting with the scientific program on Monday after lunch should
    allow<br>
    to avoid travelling on weekend keeping the expenses at a minimum.
    Once<br>
    again the location changed - we are now guest at the new Chemikum of
    the<br>
    Erlangen University at Nikolaus-Fiebiger-Strasse 10 (see<br>
    <a class="moz-txt-link-freetext"
href="https://www.openstreetmap.de/karte/?zoom=17&amp;lat=49.5782&amp;lon=11.02864"
      moz-do-not-send="true">https://www.openstreetmap.de/karte/?zoom=17&amp;lat=49.5782&amp;lon=11.02864</a>).
    A<br>
    hearty workshop dinner and a traditional joint evening event
    complement<br>
    the scientific program.<br>
    <br>
    The website <a class="moz-txt-link-freetext"
      href="http://mmws2023.mgms-ds.de" moz-do-not-send="true">http://mmws2023.mgms-ds.de</a>
    provides all necessary<br>
    information about the meeting.<br>
    <br>
    ####### Plenary Speakers #######<br>
    We are very happy to announce that four outstanding researchers
    already<br>
    accepted our invitation to present a plenary lecture:<br>
    <br>
    Markus Reiher, ETH Zürich<br>
    “Prospects of Quantum Computing for Chemistry”<br>
    <br>
    Paolo Carloni, Forschungszentrum Jülich<br>
    "MiMiC: A new, highly scalable QM/MM interface for biophysical
    applications"<br>
    <br>
    Peter Hildebrand, Universität Leipzig<br>
    <br>
    Oliver Koch, Universität Münster<br>
    <br>
    ####### Poster and Lecture Awards #######<br>
    As in the past years, there will be two poster awards of EUR 100
    each<br>
    and three lecture awards for the best contributed oral
    presentations:<br>
    <br>
    1st winner: Travel bursary to attend the Young Modeller's Forum
    (YMF) in<br>
    London, UK, plus a recommendation for a speaker slot option at YMF<br>
    (travel expenses are reimbursed up to EUR 500)<br>
    2nd winner: EUR 200 travel expenses reimbursement<br>
    3rd winner: EUR 100 travel expenses reimbursement<br>
    <br>
    Only undergraduate and graduate research students qualify for the
    poster<br>
    and lecture awards.<br>
    <br>
    ####### Registration and poster/talk submission #######<br>
    Submit talk and/or poster titles via the registration form
    accessible on<br>
    the workshop website <a class="moz-txt-link-freetext"
      href="https://mmws2023.mgms-ds.de/index.php?m=register"
      moz-do-not-send="true">https://mmws2023.mgms-ds.de/index.php?m=register</a><br>
    The deadline for all submissions is February 26th, 2023.<br>
    <br>
    ####### NHR@FAU meeting #######<br>
    The Erlangen National High Performance Computing Center (NHR@FAU),
    which<br>
    is supporting our meeting, organizes it's first Colloquium and
    Results<br>
    Symposium. It will take place on Wednesday afternoon and Thursday,<br>
    directly after our event, at exactly the same venue. If you are<br>
    interested in Atomistic Simulations on High Performance Computing<br>
    clusters, consider to extend your stay in Erlangen and also attend
    the<br>
    NHR@FAU meeting for free! For further information have a look at<br>
    <a class="moz-txt-link-freetext" href="https://hpc.fau.de/"
      moz-do-not-send="true">https://hpc.fau.de/</a><br>
    <br>
    If you have any questions, do not hesitate to contact us via<br>
    <a class="moz-txt-link-abbreviated moz-txt-link-freetext"
      href="mailto:mm...@mg..." moz-do-not-send="true">mm...@mg...</a>
    .<br>
    We are looking forward to meeting you in Erlangen!<br>
    <br>
    On behalf of the workshop organising team<br>
    - Harald Lanig, Chairman of the MGMS-DS e.V. (<a
      class="moz-txt-link-freetext" href="http://www.mgms-ds.de"
      moz-do-not-send="true">http://www.mgms-ds.de</a>)<br>
    <br>
    <br>
    <pre class="moz-signature" cols="72">-- 
PD Dr. rer. nat. Harald Lanig (Dipl.-Chem.)
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Zentrum für Nationales Hochleistungsrechnen Erlangen (NHR@FAU)
NHR@FAU Geschäftsstelle am Regionalen Rechenzentrum Erlangen (RRZE)
Martensstrasse 1, 91058 Erlangen, Germany
<a class="moz-txt-link-abbreviated moz-txt-link-freetext" href="mailto:har...@fa..." moz-do-not-send="true">har...@fa...</a> - hpc.fau.de</pre>
  </body>
</html>

Re: [PyMOL] [EXTERNAL] Question about formatting font size

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

Hi Chao,

Try issuing the following command at the PyMOL> prompt:

set display_scale_factor, 2

It enlarges the font of the sequence in the viewport and the text in the internal GUI.
It only takes whole numbers.
Try larger intergers; you can always return to 2 or 1.

It is useful when giving workshops and lectures about PyMOL.
It may not do all that you require.

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: Chao Chen <bio...@gm...>
Sent: Monday, February 6, 2023 12:41 PM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] Question about formatting font size

Dear Users,

I found in pymol layout somehow characters including protein sequence letters become very small. Not sure what I have done. Any ideas of changing to a bigger font? Thanks a lot in advance!

Kind regards,
Chao

[PyMOL] Question about formatting font size

[Chao C. <bio...@gm...>]

Dear Users,

I found in pymol layout somehow characters including protein sequence
letters become very small. Not sure what I have done. Any ideas of changing
to a bigger font? Thanks a lot in advance!

Kind regards,
Chao

Re: [PyMOL] [ccp4bb] 15th Annual CCP4/APS Crystallographic School (onsite)

[Qingping Xu <qx...@an...>]

This is reminder that the registration for the upcoming CCP4/APS school 
will close in two days (1/31/2023). If you plan to attend, please submit 
your application asap.

Thanks.

Charles, Andrey, Garib and Qingping


On 1/23/23 14:43, Qingping Xu wrote:
> This is a reminder for students interested in attending the upcoming 
> onsite CCP4/APS school, please submit your applications.
>
> Thanks
>
> Charles, Andrey, Garib and Qingping
>
>
> On 1/3/23 08:37, Qingping Xu wrote:
>> Dear colleagues,
>>
>> Happy new year!
>>
>> This is a reminder that the registration is open for the upcoming 
>> 2023 CCP4/APS school. Please note this year school is earlier than 
>> the usual summer date (before the APS upgrade starting in middle 
>> April). Please apply if you are interested in attending in person, or 
>> forward to students who may be interested.
>>
>> Thanks
>>
>>
>> Charles, Andrey, Garib and Qingping
>>
>>
>> On 10/20/22 12:13 PM, Qingping Xu wrote:
>>> Dear Colleagues,
>>>
>>> We are pleased to announce the 15th annual CCP4/APS crystallographic 
>>> school “From data collection to structure refinement and beyond” 
>>> will be held on March 27th to April 3rd, 2023 at the Advanced Photon 
>>> Source (APS), Argonne National Laboratory (ANL), near Chicago, 
>>> Illinois, USA. All details can be found at the school website: 
>>> http://www.ccp4.ac.uk/schools/APS-2023/index.php. This will be our 
>>> first post-COVID in person workshop, scheduled before the APS 
>>> upgrade shutdown.
>>>
>>>
>>> Dates: March 27 through April 3, 2023
>>> Location: Advanced Photon Source, Argonne National Laboratory, 
>>> Argonne (Near
>>> Chicago), Illinois, USA
>>>
>>> The school comprises two parts: data collection workshop and 
>>> crystallographic computing workshop. Data collection workshop 
>>> includes beamline training, data collection on GM/CA@APS beamlines 
>>> 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors 
>>> respectively, and data processing. For data collection, only the 
>>> participants' crystals will be used. Crystallographic computation 
>>> workshop will feature many modern crystallographic software packages 
>>> taught by authors and other experts. The daily schedule will be 
>>> organized in three sections – lectures, tutorials, and hands-on 
>>> (interactive trouble-shooting of the technical difficulties the 
>>> participants face in their projects). We have had considerable 
>>> success resolving these problems in past years, attested by 
>>> resulting publications (see 
>>> http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft 
>>> program can be found at the School website.
>>>
>>> Applicants: The workshop strongly encourages students who need 
>>> expert help with difficulties/challenges in their own projects. 
>>> Graduate students, postdoctoral researchers and early-career 
>>> faculty, along with commercial/industrial researchers are encouraged 
>>> to apply. Only about 20 applicants will be selected for participation.
>>>
>>> Application: Application deadline is Jan 31th, 2023. To apply, 
>>> visit  https://www.ccp4.ac.uk/schools/APS-2023/application.php
>>>
>>> Fees: There is a $500 participation fee for the selected academic 
>>> students and $1500 for industrial researchers. No credit card will 
>>> be required for registration, students who are selected to 
>>> participate will be contacted to pay. The students will be 
>>> responsible for their transportation and lodging. The workshop 
>>> organizers can assist in making lodging reservations at the Argonne 
>>> Guest House. The workshop will cover all other expenses (including 
>>> meals).
>>>
>>>
>>> We hope to see you at the school.
>>>
>>>
>>> Charles, Andrey, Garib and Qingping
>>>
>>> ######################################################################## 
>>>
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>
>>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a 
>>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
>>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>
>> ########################################################################
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a 
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
>> available at https://www.jiscmail.ac.uk/policyandsecurity/

Re: [PyMOL] [ccp4bb] 15th Annual CCP4/APS Crystallographic School (onsite)

[Qingping Xu <qx...@an...>]

This is a reminder for students interested in attending the upcoming 
onsite CCP4/APS school, please submit your applications.

Thanks

Charles, Andrey, Garib and Qingping


On 1/3/23 08:37, Qingping Xu wrote:
> Dear colleagues,
>
> Happy new year!
>
> This is a reminder that the registration is open for the upcoming 2023 
> CCP4/APS school. Please note this year school is earlier than the 
> usual summer date (before the APS upgrade starting in middle April). 
> Please apply if you are interested in attending in person, or forward 
> to students who may be interested.
>
> Thanks
>
>
> Charles, Andrey, Garib and Qingping
>
>
> On 10/20/22 12:13 PM, Qingping Xu wrote:
>> Dear Colleagues,
>>
>> We are pleased to announce the 15th annual CCP4/APS crystallographic 
>> school “From data collection to structure refinement and beyond” will 
>> be held on March 27th to April 3rd, 2023 at the Advanced Photon 
>> Source (APS), Argonne National Laboratory (ANL), near Chicago, 
>> Illinois, USA. All details can be found at the school website: 
>> http://www.ccp4.ac.uk/schools/APS-2023/index.php. This will be our 
>> first post-COVID in person workshop, scheduled before the APS upgrade 
>> shutdown.
>>
>>
>> Dates: March 27 through April 3, 2023
>> Location: Advanced Photon Source, Argonne National Laboratory, 
>> Argonne (Near
>> Chicago), Illinois, USA
>>
>> The school comprises two parts: data collection workshop and 
>> crystallographic computing workshop. Data collection workshop 
>> includes beamline training, data collection on GM/CA@APS beamlines 
>> 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors 
>> respectively, and data processing. For data collection, only the 
>> participants' crystals will be used. Crystallographic computation 
>> workshop will feature many modern crystallographic software packages 
>> taught by authors and other experts. The daily schedule will be 
>> organized in three sections – lectures, tutorials, and hands-on 
>> (interactive trouble-shooting of the technical difficulties the 
>> participants face in their projects). We have had considerable 
>> success resolving these problems in past years, attested by resulting 
>> publications (see 
>> http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft 
>> program can be found at the School website.
>>
>> Applicants: The workshop strongly encourages students who need expert 
>> help with difficulties/challenges in their own projects. Graduate 
>> students, postdoctoral researchers and early-career faculty, along 
>> with commercial/industrial researchers are encouraged to apply. Only 
>> about 20 applicants will be selected for participation.
>>
>> Application: Application deadline is Jan 31th, 2023. To apply, visit  
>> https://www.ccp4.ac.uk/schools/APS-2023/application.php
>>
>> Fees: There is a $500 participation fee for the selected academic 
>> students and $1500 for industrial researchers. No credit card will be 
>> required for registration, students who are selected to participate 
>> will be contacted to pay. The students will be responsible for their 
>> transportation and lodging. The workshop organizers can assist in 
>> making lodging reservations at the Argonne Guest House. The workshop 
>> will cover all other expenses (including meals).
>>
>>
>> We hope to see you at the school.
>>
>>
>> Charles, Andrey, Garib and Qingping
>>
>> ########################################################################
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a 
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> ########################################################################
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a 
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
> available at https://www.jiscmail.ac.uk/policyandsecurity/

Re: [PyMOL] Get/edit molecule title?

[Jared S. <jar...@co...>]

Hi Petro -

This is the object's "title" attribute, and can be accessed using the
Properties
Inspector <https://pymolwiki.org/index.php/Properties_Inspector> in the top
right part of the GUI, as well as read or edited via the `get_title
<https://pymolwiki.org/index.php/Get_Title>` or `set_title
<https://pymolwiki.org/index.php/Set_title>` commands, respectively (e.g.
`get_title group1-out, 1`).

Hope that helps.

Cheers,
Jared

On Thu, Jan 19, 2023 at 5:09 AM Petro <sub...@kh...> wrote:

> Hi again.
> I got a proposal to use the action menu, but it is a bit different.
> https://photos.app.goo.gl/GkCyr67JfWSDKUU57
> Please take a look at this photo.
> I am interested in reading and editing the information in green.
> Thanks.
> Petro.
>
>
> On Wed, 18 Jan 2023 at 13:44, Petro <sub...@kh...> wrote:
>
>> Hi, list.
>> When I load the mol2 file, the title of the molecule is shown near the
>> object name in green in the internal GUI. Is there a way to read it? Maybe
>> even edit it?
>> Thanks.
>> Petro.
>>
>> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Get/edit molecule title?

[Petro <sub...@kh...>]

Hi Jared.
Have not tried yet, but it looks like you have solved the problem for me.
Thanks.
Petro.

On Thu, 19 Jan 2023, 8:13 pm Jared Sampson, <jar...@co...>
wrote:

> Hi Petro -
>
> This is the object's "title" attribute, and can be accessed using the Properties
> Inspector <https://pymolwiki.org/index.php/Properties_Inspector> in the
> top right part of the GUI, as well as read or edited via the `get_title
> <https://pymolwiki.org/index.php/Get_Title>` or `set_title
> <https://pymolwiki.org/index.php/Set_title>` commands, respectively (e.g.
> `get_title group1-out, 1`).
>
> Hope that helps.
>
> Cheers,
> Jared
>
> On Thu, Jan 19, 2023 at 5:09 AM Petro <sub...@kh...> wrote:
>
>> Hi again.
>> I got a proposal to use the action menu, but it is a bit different.
>> https://photos.app.goo.gl/GkCyr67JfWSDKUU57
>> Please take a look at this photo.
>> I am interested in reading and editing the information in green.
>> Thanks.
>> Petro.
>>
>>
>> On Wed, 18 Jan 2023 at 13:44, Petro <sub...@kh...> wrote:
>>
>>> Hi, list.
>>> When I load the mol2 file, the title of the molecule is shown near the
>>> object name in green in the internal GUI. Is there a way to read it? Maybe
>>> even edit it?
>>> Thanks.
>>> Petro.
>>>
>>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Get/edit molecule title?

[Petro <sub...@kh...>]

Hi again.
I got a proposal to use the action menu, but it is a bit different.
https://photos.app.goo.gl/GkCyr67JfWSDKUU57
Please take a look at this photo.
I am interested in reading and editing the information in green.
Thanks.
Petro.


On Wed, 18 Jan 2023 at 13:44, Petro <sub...@kh...> wrote:

> Hi, list.
> When I load the mol2 file, the title of the molecule is shown near the
> object name in green in the internal GUI. Is there a way to read it? Maybe
> even edit it?
> Thanks.
> Petro.
>
>