pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Unable to use NVIDIA as GL_Vendor

[PALLAV S. <s.p...@ii...>]

Dear users,
I have been using PyMOL quite some time and the NVIDIA cannot be used for rendering although I have all the required drivers installed yet during the startup, I have been encountering a message like this:

PyMOL(TM) Molecular Graphics System, Version 2.3.0.
Detected OpenGL version 3.1. Shaders available.
 Geometry shaders not available
 Detected GLSL version 1.40.
 OpenGL graphics engine:
  GL_VENDOR:   Mesa/X.org
  GL_RENDERER: llvmpipe (LLVM 12.0.0, 256 bits)
  GL_VERSION:  3.1 Mesa 21.2.6
 Detected 16 CPU cores.  Enabled multithreaded rendering.

This is the information of my graphics card:
*-display
       description: VGA compatible controller
       product: GP104GL [Quadro P4000]
       vendor: NVIDIA Corporation
       physical id: 0
       bus info: pci@0000:65:00.0
       version: a1
       width: 64 bits
       clock: 33MHz
       capabilities: pm msi pciexpress vga_controller bus_master cap_list rom
       configuration: driver=nvidia latency=0
       resources: irq:48 memory:d7000000-d7ffffff memory:c0000000-cfffffff memory:d0000000-d1ffffff ioport:b000(size=128) memory:c0000-dffff

This means that the PyMOL is unable to use NVIDIA as the GL_Vendor and also the Quadro P4000 as the GL_RENDERER. Is there any way during installation by which I can utilize the NVIDIA graphics acceleration such that I get better performance during rendering?

Pallav Sengupta,
Research Scholar,
Computational Biology Lab,
Department of Bioscience and Bioengineering(BSBE),
Indian Institute of Technology, Guwahati.
Guwahati, 781039.

[PyMOL] View of the ligand binding site

[Enrico M. <jms...@gm...>]

Dear Pymol users
I am looking for a possibility to automatize orientation of the camera
on the ligand binding cavity working with different protein-ligand
complexes. Is it possible to calculate centroid of the ligand and then
orient the view of it ?
Many thanks in advance
Cheers,
Enrico

Re: [PyMOL] pymol for educational purpose

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

Hello,

Our mailing server issue was fixed yesterday. Please re-register and/or
check spam folders if it doesn't arrive. Otherwise, contact
he...@sc...

Best,

Jarrett J

On Fri, Jul 22, 2022 at 6:41 AM LETIZIA PIZZORNI <
let...@un...> wrote:

> Goodmorning,
> I am a student of the University of Pavia and i need pymol; I tried to
> register on the site for getting it free but the confirmation email didn't
> arrive. How can i fix this?
>
> Have a good day.
> Letizia Pizzorni.
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] pymol for educational purpose

[LETIZIA P. <let...@un...>]

Goodmorning,
I am a student of the University of Pavia and i need pymol; I tried to
register on the site for getting it free but the confirmation email didn't
arrive. How can i fix this?

Have a good day.
Letizia Pizzorni.

Re: [PyMOL] Object name for each object in grid display mode

[Tomas M. <tom...@gm...>]

Hi Rintarou,

Your script works beautifully! Thanks a lot.

Best wishes,
Tomas

On Wed, Jul 20, 2022 at 3:50 AM Suzuki, Rintarou <rs...@af...> wrote:
>
> Hi Tomas,
>
> You can do it with the following script
>
>
> from pymol import cmd
>
> cmd.set('grid_mode', 1)
> ids = ("1A70", "1AG6", "1B9W", "1BJA", "1BM8", "1BMG", "1BOX", "1BTE",
> "1BXU", "1BXV", "1BYO", "1BYP")
>
> for i in ids:
>   cmd.fetch(i)
>   if i != "1A70":
>     cmd.cealign("1A70", i+" & c. A")
> cmd.zoom("all", "-20")
>
> for i in ids:
>   cmd.pseudoatom(i+"_info")
>   cmd.label(i+"_info", '"{}"'.format(i))
>   cmd.set('label_size', 16, i+"_info")
>   cmd.set('label_position', '0, 7, 10', i+"_info")
>   cmd.group(i+"_group", "{0} {0}_info".format(i))
>
> cmd.hide("everything", "r. hoh")
> cmd.hide("everything", "c. B")
> cmd.hide("nonbonded")
>
>
> Regards,
> Rintaro
>
>
> On 2022/07/20 1:48, Tomas Malinauskas wrote:
> > Dear All,
> >
> > Is it possible to show the object name for each object in grid display
> > mode? E.g. I have 12 PDBs loaded in grid mode and would like to show
> > their IDs (not in the side panel but in the main window) at the same
> > time.
> >
> > I thank you for your help.
> >
> > Best wishes,
> > Tomas
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Object name for each object in grid display mode

[Suzuki, R. <rs...@af...>]

Hi Tomas,

You can do it with the following script


from pymol import cmd

cmd.set('grid_mode', 1)
ids = ("1A70", "1AG6", "1B9W", "1BJA", "1BM8", "1BMG", "1BOX", "1BTE",
"1BXU", "1BXV", "1BYO", "1BYP")

for i in ids:
  cmd.fetch(i)
  if i != "1A70":
    cmd.cealign("1A70", i+" & c. A")
cmd.zoom("all", "-20")

for i in ids:
  cmd.pseudoatom(i+"_info")
  cmd.label(i+"_info", '"{}"'.format(i))
  cmd.set('label_size', 16, i+"_info")
  cmd.set('label_position', '0, 7, 10', i+"_info")
  cmd.group(i+"_group", "{0} {0}_info".format(i))

cmd.hide("everything", "r. hoh")
cmd.hide("everything", "c. B")
cmd.hide("nonbonded")


Regards,
Rintaro


On 2022/07/20 1:48, Tomas Malinauskas wrote:
> Dear All,
> 
> Is it possible to show the object name for each object in grid display
> mode? E.g. I have 12 PDBs loaded in grid mode and would like to show
> their IDs (not in the side panel but in the main window) at the same
> time.
> 
> I thank you for your help.
> 
> Best wishes,
> Tomas
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Object name for each object in grid display mode

[Tomas M. <tom...@gm...>]

Dear All,

Is it possible to show the object name for each object in grid display
mode? E.g. I have 12 PDBs loaded in grid mode and would like to show
their IDs (not in the side panel but in the main window) at the same
time.

I thank you for your help.

Best wishes,
Tomas

Re: [PyMOL] Portable Version of Python 3.8 with Portable PyMOL+RDKIt+Many More

[James P. (Staff) <J.P...@du...>]

Hi Vijay – this sounds interesting!  Does the project have a web presence yet ?  Since we added PyMOL support to Jalview (see https://discourse.jalview.org/t/jalview-2-11-2-0-now-available/), we’re interested in any solutions that make it easy for adding in additional tools.

Jim.

From: Dr. Vijay Masand <vij...@gm...>
Date: Monday, 18 July 2022 at 16:08
To: pymol-users <PyM...@li...>
Subject: [PyMOL] Portable Version of Python 3.8 with Portable PyMOL+RDKIt+Many More

CAUTION: This email originated from outside the University of Dundee. Do not click links or open attachments unless you recognise the sender's email address and know the content is safe.
Dear all
We have successfully developed a new portable version of Python 3.8 (64 bit only) for windows 7, 10 and 11. It contains fully functional and smoothly running portable versions of Open Source PyMOL 2.5, RDKit 2022.3.2.1, Jupyter Notebook, Matplotlib, Sci-Py, Numpy, PyQt5, Pip, Pandas, IPython, and many more.
No need to install above modules or even Python 3.8, the new portable version of Python 3.8 developed by us contains all required functionalities. Just copy and paste anywhere in your computer or in pendrive and use it without any issue. If interested, kindly contact (vij...@gm...<mailto:vij...@gm...>)
Cheers
Vijay

With Warm Regards
Dr. Vijay H. Masand
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

The University of Dundee is a registered Scottish Charity, No: SC015096

Re: [PyMOL] invalid namespace

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

Hello Criss,

I suggest doing this in two parts:

1)

run colorbyrmsd.py

At the bottom of that script, this function is extended to PyMOL. Thus
after importing the function, you should be able to run the function
natively in PyMOL's commandline:

2)
colorbyrmsd obj1, obj2

Hope this helps,
Jarrett J.

On Mon, Jul 18, 2022 at 7:59 PM Criss Hartzell <cri...@gm...>
wrote:

> I am trying to compare two structures using the script colorbyrmsd.py.
> If I "run colorbyrmsd.py obj1, obj2" I get an error "invalid namespace
> 'obj02' ". I don't know what this means. Can anyone help? Thanks.
>
> --
> Criss Hartzell
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] invalid namespace

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

I am trying to compare two structures using the script colorbyrmsd.py.
If I "run colorbyrmsd.py obj1, obj2" I get an error "invalid namespace
'obj02' ". I don't know what this means. Can anyone help? Thanks.

-- 
Criss Hartzell

[PyMOL] Portable Version of Python 3.8 with Portable PyMOL+RDKIt+Many More

[Dr. V. M. <vij...@gm...>]

Dear all

We have successfully developed a new portable version of Python 3.8 (64 bit
only) for windows 7, 10 and 11. It contains fully functional and smoothly
running portable versions of Open Source PyMOL 2.5, RDKit 2022.3.2.1,
Jupyter Notebook, Matplotlib, Sci-Py, Numpy, PyQt5, Pip, Pandas, IPython,
and many more.

No need to install above modules or even Python 3.8, the new portable
version of Python 3.8 developed by us contains all required
functionalities. Just copy and paste anywhere in your computer or in
pendrive and use it without any issue. If interested, kindly contact (
vij...@gm...)

Cheers

Vijay


With Warm Regards
*Dr. Vijay H. Masand*
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

[PyMOL] PyMOL Announcements (Fellowship & Future of PyMOL)

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

Hello PyMOL Community,

After a three-year hiatus of the Warren L. Delano Memorial PyMOL
Fellowship, we are once again reopening applications to prospective fellows.

More information, including directions on completing the application
process, can be found on our website at pymol.org/fellowship .

Next, as many of you have noticed, it has been quite some time since we’ve
even released a maintenance patch. Going forward, we will work diligently
to get these updates in your hands at a much quicker cycle. Barring any
major unforeseen obstacles, we will upload maintenance releases onto the
PyMOL website and conda approximately once per month starting this week
with version 2.5.3.

As we are looking forward to the future of PyMOL, we have identified major
components that require either improvement in its appearance,
discoverability, and/or functionality. Thus, for the past several months,
we’ve been working hard to address those to ensure that PyMOL is software
that meets the needs and standards of the molecular visualization
community. We believe that the newest set of features offered are worthy of
a new chapter in PyMOL; therefore, expect 3.0 as the upcoming major version
for PyMOL. Stay tuned for more details on our website about PyMOL 3.0 and
our future roadmap later this year.

Best,

PyMOL Development Team
-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] Question about glm in pymol

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

Hi,

Your version of glm (default with Centos7 with yum) should now work. I
committed a change to fix this compiler error about twelve hours ago. You
just need to pull the latest changes.

Best,

Jarrett J.

On Tue, Jul 12, 2022 at 10:24 PM 张敏华 <mhz...@si...> wrote:

> Dear Jarrett Johnson：
>         In fact I encountered an error message when I am installing the
> latest version of pymol.  First I installed all the library that needed
> according the pymolwiki by yum.  Then during the installation process, an
> error message appeared:
>
>        “ layer0/TTT.cpp:87:27: error: no match for ‘operator=’ (operand
> types are ‘glm::vec3 {aka glm::tvec3<float, (glm::precision)0u>}’ and
> ‘glm::tmat4x4<float, (glm::precision)0u>::col_type {aka glm::tvec4<float,
> (glm::precision)0u>}’)
>
>    result.m_pretranslation = mult[3];
>
>          <other  outputs>
>
>         error:  command 'g++’failed with exit status 1”
>
>        So I guess there might be something wrong with glm, but I don't
> know how to solve it. Maybe the glm version installed by yum in CentOS7 is
> not the latest version? I searched the google and some threads suggests
> that should use the glm-0.9.9 instead yum installed glm-0.9.6. Then how to
> use the glm-0.9.9?
>
>
>
> ------------------------------
> Minhua Zhang, Ph.D., Assistant Professor
> Structural Biology Lab
> Institute of Plant Physiology and Ecology, Shanghai Institute of
> Biological Sciences
> Chinese Academy of Sciences
> 300 Fenglin Road, Shanghai, 20032, P.R.China
> Tel:  86 21 5492 4218
> Fax:  86 21 5492 4015
> Email: mh...@si...
>
>
> *From:* Jarrett Johnson <jar...@sc...>
> *Date:* 2022-07-13 00:33
> *To:* 张敏华 <mhz...@si...>
> *CC:* pymol-users <pym...@li...>
> *Subject:* Re: [PyMOL] Question about glm in pymol
> Hello,
>
> Through CentOS, you should be able to install glm with yum package manager.
>
> yum install glm-devel
>
> More info can be found here: https://pymolwiki.org/index.php/Linux_Install
> .
>
> Also take note that if you're using Centos 7, the default glm may not have
> a modern enough API for PyMOL code. I updated the codebase today which
> should make it compatible with this version of glm. Make sure to pull again
> if that's the case for you.
>
> Best,
> Jarrett J
>
> On Tue, Jul 12, 2022 at 12:26 PM 张敏华 <mhz...@si...> wrote:
>
>> Dear all:
>>         I want to comple open-source-pymol in CentOS. So I want to using
>> the latest glm. So how to install glm? or  I just put the glm folder into
>> the include folder in the open-sourde-pymol folder?
>>
>> ------------------------------
>> Minhua Zhang, Ph.D., Assistant Professor
>> Structural Biology Lab
>> Institute of Plant Physiology and Ecology, Shanghai Institute of
>> Biological Sciences
>> Chinese Academy of Sciences
>> 300 Fenglin Road, Shanghai, 20032, P.R.China
>> Tel:  86 21 5492 4218
>> Fax:  86 21 5492 4015
>> Email: mh...@si...
>> _______________________________________________
>> 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
>
>

-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] Question about glm in pymol

[张敏华 <mhz...@si...>]

Dear Jarrett Johnson：
        In fact I encountered an error message when I am installing the latest version of pymol.  First I installed all the library that needed according the pymolwiki by yum.  Then during the installation process, an error message appeared:
  
       “ layer0/TTT.cpp:87:27: error: no match for ‘operator=’ (operand types are ‘glm::vec3 {aka glm::tvec3<float, (glm::precision)0u>}’ and ‘glm::tmat4x4<float, (glm::precision)0u>::col_type {aka glm::tvec4<float, (glm::precision)0u>}’)
   result.m_pretranslation = mult[3];

         <other  outputs>

        error:  command 'g++’failed with exit status 1”

       So I guess there might be something wrong with glm, but I don't know how to solve it. Maybe the glm version installed by yum in CentOS7 is not the latest version? I searched the google and some threads suggests that should use the glm-0.9.9 instead yum installed glm-0.9.6. Then how to use the glm-0.9.9? 





Minhua Zhang, Ph.D., Assistant Professor
Structural Biology Lab
Institute of Plant Physiology and Ecology, Shanghai Institute of Biological Sciences
Chinese Academy of Sciences
300 Fenglin Road, Shanghai, 20032, P.R.China
Tel:  86 21 5492 4218
Fax:  86 21 5492 4015 
Email: mh...@si...
 
From: Jarrett Johnson
Date: 2022-07-13 00:33
To: 张敏华
CC: pymol-users
Subject: Re: [PyMOL] Question about glm in pymol
Hello,

Through CentOS, you should be able to install glm with yum package manager.

yum install glm-devel

More info can be found here: https://pymolwiki.org/index.php/Linux_Install .

Also take note that if you're using Centos 7, the default glm may not have a modern enough API for PyMOL code. I updated the codebase today which should make it compatible with this version of glm. Make sure to pull again if that's the case for you. 

Best,
Jarrett J

On Tue, Jul 12, 2022 at 12:26 PM 张敏华 <mhz...@si...> wrote:
Dear all:
        I want to comple open-source-pymol in CentOS. So I want to using the latest glm. So how to install glm? or  I just put the glm folder into the include folder in the open-sourde-pymol folder?



Minhua Zhang, Ph.D., Assistant Professor
Structural Biology Lab
Institute of Plant Physiology and Ecology, Shanghai Institute of Biological Sciences
Chinese Academy of Sciences
300 Fenglin Road, Shanghai, 20032, P.R.China
Tel:  86 21 5492 4218
Fax:  86 21 5492 4015 
Email: mh...@si...
_______________________________________________
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] Question about glm in pymol

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

Hello,

Through CentOS, you should be able to install glm with yum package manager.

yum install glm-devel

More info can be found here: https://pymolwiki.org/index.php/Linux_Install .

Also take note that if you're using Centos 7, the default glm may not have
a modern enough API for PyMOL code. I updated the codebase today which
should make it compatible with this version of glm. Make sure to pull again
if that's the case for you.

Best,
Jarrett J

On Tue, Jul 12, 2022 at 12:26 PM 张敏华 <mhz...@si...> wrote:

> Dear all:
>         I want to comple open-source-pymol in CentOS. So I want to using
> the latest glm. So how to install glm? or  I just put the glm folder into
> the include folder in the open-sourde-pymol folder?
>
> ------------------------------
> Minhua Zhang, Ph.D., Assistant Professor
> Structural Biology Lab
> Institute of Plant Physiology and Ecology, Shanghai Institute of
> Biological Sciences
> Chinese Academy of Sciences
> 300 Fenglin Road, Shanghai, 20032, P.R.China
> Tel:  86 21 5492 4218
> Fax:  86 21 5492 4015
> Email: mh...@si...
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] Question about glm in pymol

[张敏华 <mhz...@si...>]

Dear all:
        I want to comple open-source-pymol in CentOS. So I want to using the latest glm. So how to install glm? or  I just put the glm folder into the include folder in the open-sourde-pymol folder?



Minhua Zhang, Ph.D., Assistant Professor
Structural Biology Lab
Institute of Plant Physiology and Ecology, Shanghai Institute of Biological Sciences
Chinese Academy of Sciences
300 Fenglin Road, Shanghai, 20032, P.R.China
Tel:  86 21 5492 4218
Fax:  86 21 5492 4015 
Email: mh...@si...

Re: [PyMOL] how to use cmd.label command

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

The second argument must be a string, so just put quotes around it:
cmd.label('CAs', '"%s%s" % (one_letter[resn],resi)')

This also works:
cmd.label('CAs', 'f"{oneletter}{resi}"')

Cheers,
  Thomas


On Fri, Jul 8, 2022 at 6:09 PM sunyeping via PyMOL-users
<pym...@li...> wrote:
>
> Dear all,
>
> I want to label residues with the resn+resi, and I tried the following command
>
> one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
> 'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',    \
> 'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',    \
> 'GLY':'G', 'PRO':'P', 'CYS':'C'}
>
> select CAs, obj & n. CAs
> label CAs, "%s%s" % (one_letter[resn],resi)
>
>
> These work find. However, when I write these in a script and the last two commands are written as:
>
>     cmd.select('CAs', 'obj & n. CAs')
>
>     cmd.label('CAs', "%s%s" % (one_letter[resn],resi))
>
> it gives the following error:
>
>     NameError: name 'resn' is not defined
>
>
> So could anyone tell me how to correctly use the cmd.label command?
>
> Thank you very much in advance
>
>
> _______________________________________________
> 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 use cmd.label command

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

Dear all, 

I want to label residues with the resn+resi, and I tried the following command

one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',    \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',    \
'GLY':'G', 'PRO':'P', 'CYS':'C'}

select CAs, obj & n. CAs
label CAs, "%s%s" % (one_letter[resn],resi)

These work find. However, when I write these in a script and the last two commands are written as:
    cmd.select('CAs', 'obj & n. CAs')
    cmd.label('CAs', "%s%s" % (one_letter[resn],resi))
it gives the following error:
 NameError: name 'resn' is not defined

So could anyone tell me how to correctly use the cmd.label command? 
Thank you very much in advance

[PyMOL] how to use cmd.label command

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

Dear all, 

I want to label residues with the resn+resi, and I tried the following command

one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',    \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',    \
'GLY':'G', 'PRO':'P', 'CYS':'C'}

select CAs, obj & n. CAs
label CAs, "%s%s" % (one_letter[resn],resi)

These work find. However, when I write these in a script and the last two commands are written as:
    cmd.select('CAs', 'obj & n. CAs')
    cmd.label('CAs', "%s%s" % (one_letter[resn],resi))
it gives the following error:
 NameError: name 'resn' is not defined

So could anyone tell me how to correctly use the cmd.label command? 
Thank you very much in advance

Re: [PyMOL] Nonsense mutagenesis

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

Hi Jevin -

Depending on how far the termination codon mutation is from the end, it may
work to just delete residues from 415 onward.  However, if this would
delete a substantial chunk of the protein, the real structure of the
truncated polypeptide may differ significantly from the crystal structure
of the full protein, so you should definitely proceed with caution when
interpreting any downstream results.

To apply this naive version of the Gln415Ter nonsense mutation, assuming
the model is called "mystructure", the mutation is on chain A, and the
highest residue number on the chain is 999, you can do something like:

    remove mystructure and chain A and resi 415-999

Hope that helps.

Cheers,
Jared



On Thu, Jun 23, 2022 at 11:24 AM Jevin Parmar <jev...@pe...>
wrote:

> Hi there,
>
>
>
> I’m trying to conduct some mutagenesis on a protein, but I have found that
> PyMol only currently does mutagenesis from one amino acid to another. Is
> there a way to conduct mutagenesis for point mutations resulting in a
> termination codon (eg. p.Gln415Ter)?
>
>
>
> Addtionally, I am unsure how to do nucleotide mutagenesis on a PDB file
> that only had an AA sequence. Is there a way to change the amino acid
> sequence to a nucleotide sequence?
>
>
>
> Thank you in advance!
>
>
>
> Jevin Parmar
> _______________________________________________
> PyMOL-users mailing list
> Archives:
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Re: [PyMOL] How to show orientation axis in Pymol

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

Hi G.V. -

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

Hope that helps.

Cheers,
Jared

On Thu, Jun 23, 2022 at 8:03 PM Florian Nachon <mai...@na...>
wrote:

> Hi,
>
> Quite easy using CGO : https://pymolwiki.org/index.php/Cgo_arrow
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Cgo-5Farrow&d=DwMFAg&c=009klHSCxuh5AI1vNQzSO0KGjl4nbi2Q0M1QLJX9BeE&r=WvSdhOXcgk8Raz-627dE7KhFMSWU151EBdYq9Mqc8-Q&m=yk9ou6mOx-XPgl5E7uc65CzMfwSqSZtNUud6ITx5JAQx54rghUdkxhXdwv9aQYX3&s=h30tGj0PxrCUA1b5i2Sxo1b5Mj645mccwesww4KiuoQ&e=>
>
> Florian
>
> On 23 Jun 2022, at 14:40, Gundala Viswanath <gun...@gm...> wrote:
>
> Hi,
>
> Is there a way  to show the orientation axis in Pymol?
> VMD can do this:
>
>
> <Screen Shot 2022-06-23 at 21.37.30.png>
>
> G.V.
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
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>
>
>
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Re: [PyMOL] How to show orientation axis in Pymol

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

Hi,

Quite easy using CGO : https://pymolwiki.org/index.php/Cgo_arrow <https://pymolwiki.org/index.php/Cgo_arrow>

Florian

> On 23 Jun 2022, at 14:40, Gundala Viswanath <gun...@gm...> wrote:
> 
> Hi, 
> 
> Is there a way  to show the orientation axis in Pymol?
> VMD can do this:
> 
> 
> <Screen Shot 2022-06-23 at 21.37.30.png>
> 
> G.V.
> _______________________________________________
> 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 show orientation axis in Pymol

[Gundala V. <gun...@gm...>]

Hi,

Is there a way  to show the orientation axis in Pymol?
VMD can do this:


[image: Screen Shot 2022-06-23 at 21.37.30.png]

G.V.

[PyMOL] Capping the ends of peptides

[Peter K. <pk...@se...>]

Dear All,

I made a tripeptide of the form gly-X-gly using the Build function. The 
amino end has a single hydrogen on the nitrogen, and the carboxyl end 
has only one oxygen so that additional amino acids could be added to 
it.  How do I make the amino end into an -NH3with a plus charge and the 
carboxyl end into a COO with a minus charge?

Thanks,
Peter

-- 
Peter C. Kahn, Ph.D.
Professor of Biochemistry
Department of Biochemistry & Microbiology
Rutgers University
76 Lipman Drive
New Brunswick, NJ 08901

Telephone: 848-932-5618
Telefax:   732-932-8965
Email: pet...@ru...

[PyMOL] Nonsense mutagenesis

[Jevin P. <jev...@pe...>]

Hi there,

I’m trying to conduct some mutagenesis on a protein, but I have found that PyMol only currently does mutagenesis from one amino acid to another. Is there a way to conduct mutagenesis for point mutations resulting in a termination codon (eg. p.Gln415Ter)?

Addtionally, I am unsure how to do nucleotide mutagenesis on a PDB file that only had an AA sequence. Is there a way to change the amino acid sequence to a nucleotide sequence?

Thank you in advance!

Jevin Parmar