Re: [PyMOL] cmd.get_fastastr()

[Thomas Holder]

Hi Pedro,

cmd.get_fastastr() always returned a FASTA formatted string. What changed in 
PyMOL 2.2 is that it now creates a record for every chain, not just for every 
object. There is a new "key" argument, you get the old behavior with 
key="model".

print(cmd.get_fastastr(key="model"))

If you actually want the plain sequence and not the fasta formatted string, 
then I suggest you use a function like this:

def get_sequence(selection='all'):
return ''.join(L.strip() for L in cmd.get_fastastr(selection).splitlines()
   if not L.startswith('>'))


Cheers,
  Thomas


> On Jul 4, 2020, at 5:17 PM, Pedro Lacerda  wrote:
> 
> Hi,
> 
> The get_fastastr function changed. Before it returned the aminoacid sequence. 
> Now it returns a FASTA  formatted string.
> 
> How can I get the old behaviour (ie. get the aminoacid sequence)?
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] Running PyMol (Linux) on Chromebook

[Wink, Donald J]

Dr. Willis:

Thank you very much for the suggestion. I will proceed to share it with the 
students and we will gladly report back what happens.

As for the instruction line you mention: I assume this input on the (base) 
environment line indicated within the instalpython3.com/chromebook 
instructions. Or should we do it on the command line that appears *after* 
starting python?

Best wishes
Donald Wink

From: Jordan Willis 
Sent: Sunday, July 5, 2020 8:15 PM
To: Wink, Donald J 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Running PyMol (Linux) on Chromebook

Might I recommend a conda based solution.

https://installpython3.com/chromebook/

Install miniconda on your Chromebook using the attached link.

Then you can simply use conda to install pymol


conda install -c schrodinger pymol

Jordan Willis, PhD


On Jul 5, 2020, at 4:36 PM, Wink, Donald J 
mailto:dw...@uic.edu>> wrote:

I am a university (UIC) faculty member who is directing some entering college 
students in a structured research programs. Things are going pretty well for 
those with MacOS or Windows computers. But I have a couple of students with 
Chromebooks who are attempting to install and run the Linux version.

We’ve downloaded and extracted the tar files but encountered some library 
issues that are apparently blocking startup.

If there are users with experience in managing this environment, I’d love to 
pose some more detailed questions.

Thanks
Donald Wink


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Re: [PyMOL] Running PyMol (Linux) on Chromebook

[J.R. W]

> I assume this input on the (base) environment line indicated within the 
> instalpython3.com/chromebook  
> instructions.



This one. This is the command line terminal for instructions to send to the 
computer. Not to be confused with the Python Interpreter REPL (the >>> that 
comes up after typing “python”)

Jordan


> On Jul 5, 2020, at 8:28 PM, Wink, Donald J  wrote:
> 
> Dr. Willis:
> 
> Thank you very much for the suggestion. I will proceed to share it with the 
> students and we will gladly report back what happens.
>  
> As for the instruction line you mention:  Or should we do it on the command 
> line that appears *after* starting python?
>  
> Best wishes
> Donald Wink
>  
> From: Jordan Willis  
> Sent: Sunday, July 5, 2020 8:15 PM
> To: Wink, Donald J 
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Running PyMol (Linux) on Chromebook
>  
> Might I recommend a conda based solution. 
>  
> https://installpython3.com/chromebook/ 
> 
>  
> Install miniconda on your Chromebook using the attached link. 
>  
> Then you can simply use conda to install pymol
>  
>  
> conda install -c schrodinger pymol
>  
> Jordan Willis, PhD
> 
> 
> On Jul 5, 2020, at 4:36 PM, Wink, Donald J  > wrote:
>  
> I am a university (UIC) faculty member who is directing some entering college 
> students in a structured research programs. Things are going pretty well for 
> those with MacOS or Windows computers. But I have a couple of students with 
> Chromebooks who are attempting to install and run the Linux version.
>  
> We’ve downloaded and extracted the tar files but encountered some library 
> issues that are apparently blocking startup.
>  
> If there are users with experience in managing this environment, I’d love to 
> pose some more detailed questions.
>  
> Thanks
> Donald Wink
>  
>  
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> 
> Unsubscribe: 
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Re: [PyMOL] Running PyMol (Linux) on Chromebook

[Jordan Willis]

Might I recommend a conda based solution. 

https://installpython3.com/chromebook/ 

Install miniconda on your Chromebook using the attached link. 

Then you can simply use conda to install pymol


conda install -c schrodinger pymol

Jordan Willis, PhD

> On Jul 5, 2020, at 4:36 PM, Wink, Donald J  wrote:
> 
> I am a university (UIC) faculty member who is directing some entering college 
> students in a structured research programs. Things are going pretty well for 
> those with MacOS or Windows computers. But I have a couple of students with 
> Chromebooks who are attempting to install and run the Linux version.
>  
> We’ve downloaded and extracted the tar files but encountered some library 
> issues that are apparently blocking startup.
>  
> If there are users with experience in managing this environment, I’d love to 
> pose some more detailed questions.
>  
> Thanks
> Donald Wink
>  
>  
> ___
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> 
> Unsubscribe: 
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[PyMOL] Running PyMol (Linux) on Chromebook

[Wink, Donald J]

I am a university (UIC) faculty member who is directing some entering college 
students in a structured research programs. Things are going pretty well for 
those with MacOS or Windows computers. But I have a couple of students with 
Chromebooks who are attempting to install and run the Linux version.

We've downloaded and extracted the tar files but encountered some library 
issues that are apparently blocking startup.

If there are users with experience in managing this environment, I'd love to 
pose some more detailed questions.

Thanks
Donald Wink


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[PyMOL] Multi sequence edition simultaneously

[sepehr dejdar]

Hi,

I have a question regarding adding peptide sequence to the original sequence in 
PyMOL. I have an original structure of a nanoparticle consisting of 420 
monomers and I like to add a similar peptide sequence to each monomer. Is that 
any easy way to apply a sequence addition/ change to one monomer and apply it 
to the. whole structure rather than going and adding the sequence manually 420 
times in PyMOL?

Sincerely,
Sepehr
Sent from my iPhone

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Re: [PyMOL] Radius of gyration of a trimer

[Pedro Lacerda]

Correction: gyradius is the name.

Em dom., 5 de jul. de 2020 às 06:42, Pedro Lacerda 
escreveu:

> It can be accomplished with the following command (gyration on psico
> library):
>
> https://pymolwiki.org/index.php/Radius_of_gyration
>
>
> Em dom., 5 de jul. de 2020 às 04:15, Dr. Subramanian, Senthil Kumar <
> senth...@hu-berlin.de> escreveu:
>
>> Hello,
>>
>> I would like to measure radius of gyration for a protein (1JB0). The PDB
>> structure is only a monomer. But, I would like to find the RoG for the
>> trimer. Could any one please help me? Bytheway, I failed massively even to
>> get RoG for monomer and it says 'RoG is not defined'. I would appreciate
>> your time and effort.
>>
>> Thank you.
>>
>> Best regards,
>>
>> Senthil
>> ___
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>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
>


-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907
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Re: [PyMOL] Radius of gyration of a trimer

[Pedro Lacerda]

It can be accomplished with the following command (gyration on psico
library):

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


Em dom., 5 de jul. de 2020 às 04:15, Dr. Subramanian, Senthil Kumar <
senth...@hu-berlin.de> escreveu:

> Hello,
>
> I would like to measure radius of gyration for a protein (1JB0). The PDB
> structure is only a monomer. But, I would like to find the RoG for the
> trimer. Could any one please help me? Bytheway, I failed massively even to
> get RoG for monomer and it says 'RoG is not defined'. I would appreciate
> your time and effort.
>
> Thank you.
>
> Best regards,
>
> Senthil
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-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907
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[PyMOL] Radius of gyration of a trimer

[Dr. Subramanian, Senthil Kumar]

Hello, 


I would like to measure radius of gyration for a protein (1JB0). The PDB
structure is only a monomer. But, I would like to find the RoG for the
trimer. Could any one please help me? Bytheway, I failed massively even
to get RoG for monomer and it says 'RoG is not defined'. I would
appreciate your time and effort. 

Thank you. 

Best regards, 


Senthil___
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