Re: [PyMOL] Farewell

[David Gae via PyMOL-users]

Dear Thomas Holder, 

Thank you for helping out PyMOL users like myself. Also putting up user 
friendly advise for the over the years who use PyMOL. 
I tend to read your email correspondence with other users, since they seem to 
be more thought through than my few emails I asked in these forums. 
I hope a lot more experts can do the same for people who are teaching molecular 
modeling or learning PyMOL. 

Sincerely,
David Gae

> On Apr 30, 2021, at 7:14 AM, Thomas Holder  
> wrote:
> 
> Dear PyMOL community -
> 
> The time has come for me to hand over my PyMOL development
> responsibilities at Schrödinger. It's been an incredible journey for
> me to get involved with the PyMOL community, to become a PyMOL fellow
> in 2011 and to start working full time for the project in 2012. I'm
> extremely grateful to all the people at Schrödinger who made this
> possible, and of course to all of you - the user community - who've
> shown me every day that my work is meaningful.
> 
> PyMOL has a unique place within Schrödinger, and a highly motivated
> and skilled team of developers and scientists stand behind it. They
> have some great plans and I'm excited to watch how they will take
> PyMOL to the next level.
> 
> I don't think that my PyMOL journey is over yet. But for the next
> chapter in my career, I'll "just" be a user and a member of the
> community. See you around.
> 
> Cheers,
>  Thomas
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
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Re: [PyMOL] Help ASPB

[David Gae via PyMOL-users]


Dear Clarisa, 


> On Sep 10, 2020, at 2:56 AM, Clarisa Alvarez  
> wrote:
> 
> Dear David
> Thank you very much!you do not know how much you helped me!!Thanks!
> I have two questions:



> - with you sent I only saw lateral chains, how could I see backbone?

You want to click on “H” button and hide all.
Then click on “S” ribbons to see backbone atoms.

> - I might have missed the amino acid grouping, I do not understand.

The group refer to acid and base and non-charge groups that play factor in 
generating the electrostatic potential. 
I am just curious have you tried this type of simple model: q1q2/4*Pier^2


Best Regards,
David 


> Thank you again!
> Have a good day.
> Clarisa.
> 
> El mié., 9 sept. 2020 a las 19:11, David Gae ( <mailto:dd...@ucdavis.edu>>) escribió:
> 
> select pos,(resn arg+lys+his)
> show sticks, (pos and !name c+n+o)
> color marine,pos
> disable pos
> select neg,(resn glu+asp)
> show sticks, (neg and !name c+n+o)
> color red,neg
> disable neg
> select neutral, (resn 
> gly+ala+val+ile+leu+met+ser+cys+trp+phe+tyr+pro+gln+asn+phe)
> show sticks, (neutral and !name c+n+o)
> color yellow, neutral
> 
> I might have missed the amino acid grouping, I hope you check it before you 
> use it.  
> Hope this helps,
> 
> 
> 
>> On Sep 9, 2020, at 4:28 AM, Clarisa Alvarez > <mailto:clarisae.alva...@gmail.com>> wrote:
>> 
>> GenScript
>> Dear all, Thanks in advance.
>> I have this problem, I have two pockets with electrostatic potential made by 
>> APSB, does anyone know how I could tell which residue contributes to each 
>> potential in each protein?
>> Thanks in advance.
>> Regards,
>> Clarisa.
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Re: [PyMOL] Help ASPB

[David Gae via PyMOL-users]

select pos,(resn arg+lys+his)
show sticks, (pos and !name c+n+o)
color marine,pos
disable pos
select neg,(resn glu+asp)
show sticks, (neg and !name c+n+o)
color red,neg
disable neg
select neutral, (resn 
gly+ala+val+ile+leu+met+ser+cys+trp+phe+tyr+pro+gln+asn+phe)
show sticks, (neutral and !name c+n+o)
color yellow, neutral

I might have missed the amino acid grouping, I hope you check it before you use 
it.  
Hope this helps,



> On Sep 9, 2020, at 4:28 AM, Clarisa Alvarez  
> wrote:
> 
> GenScript
> Dear all, Thanks in advance.
> I have this problem, I have two pockets with electrostatic potential made by 
> APSB, does anyone know how I could tell which residue contributes to each 
> potential in each protein?
> Thanks in advance.
> Regards,
> Clarisa.
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Re: [PyMOL] monitor same protein conformational change with multiple trajectory files

[David Gae]

Dear  Yu,

Try this  bash script and then run "pymol all.pdb” in your PDB directory. this 
might help you view your files as a trajectory. 


for i in {1..3000}
do
# change frame_$i.pdb to your file name. for example mine is frame_1.pdb
[ -f "frame_$i.pdb" ] 
z=frame_$i.pdb  
sed  's/END/ENDMDL/g' $z > $z.r 
{ echo 'MODEL'; cat $z.r; } >$z.new

rm $z.r 
done

cat *.new > all.pdb
rm *.new
-

I am sure there are many ways to do this inside pymol as well. you might want 
to look up https://pymolwiki.org/index.php/Main_Page

hope this helps,
David

> On Apr 30, 2019, at 5:57 PM, Yu Qi  wrote:
> 
> Some background: I'm an undergraduate student and am doing research with my 
> professor about modeling protein conformational changes. I am new to this 
> field and and am actively learning how to use command lines, python and other 
> relative tools. I have simulated how the protein will walk with CAMPARI and 
> have gotten back 3000 trajectory (pdb) files, my question is: how do I use 
> PyMOL to make a movie by using those trajectory files? Basically, I want to 
> know how to visualize how the protein moved from the first pdb file to the 
> second, then to the third, etc.
> 
> I tried morphing two pdb files with one step from file_1.pdb to file_2.pdb, I 
> aligned them first, then morphed them. I'm not sure how to go from there 
> because I had a result file with 2 states and 2 frames, then when I tried to 
> morph the result file with file_3.pdb, it did not work as I expected.
> 
> please let me know if you have questions, and I really appreciate the help.
> 
> Thank you for the help,
> Yu
> 
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Re: [PyMOL] Combining views of different Pymol sessions in one single file ?

[david gae]

Dear Maria, 

I don’t think there is a direct way to connect two sessions together. One 
thought I had is that you could save coordinates from one session and then same 
coordinates from the other session.

lastly, open an another session and do the following:

load state1.pdb 
load state2.pdb, state1

cheers,
David 

 
> On Dec 28, 2017, at 10:16 AM, COSTA Maria  
> wrote:
> 
>  
> Dear PyMOL users,
>  
> I would like to do a movie showing a conformational change of my molecule. I 
> guess that for that purpose I need to store the views of the two states but 
> the problem is that my two states are in two different pymol sessions. Is 
> there a way to combine the two views in the same pymol file ? or I need to 
> redo the views in the same pymol session from the beginning ?
> I hope I’m being clear enough….
>  
> Thank you so much for any help !
>  
> Maria Costa
>  
> I2BC – UMR9198
> 91198 Gif-sur-Yvette cedex
> France  
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