pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] representation of residue sidechain within a beta strand?

[Emilia C. A. (Emily) <ecg...@gm...>]

Thanks for the pointer to the cartoon_side_chain_helper function, Tomas.

Unfortunately setting this feature 'on' warps beta strands, making it look
curvy, which is an atypical representation. Unless there is another means
to connect side chains to secondary structure elements, I will have to see
on a case by case basis what is the most visually correct and
simultaneously appealing representation.

Emilia.

On Mon, Jan 18, 2021 at 12:34 AM Tomas Malinauskas <
tom...@gm...> wrote:

> Hi Emilia,
>
> You might try the following:
> set cartoon_side_chain_helper, on
>
> Hope that helps,
> Tomas
>
> On Mon, Jan 18, 2021 at 7:52 AM Emilia C. Arturo (Emily)
> <ecg...@gm...> wrote:
> >
> > Hi All,
> >
> > I'm wondering if anyone here knows how to represent an amino acid
> residue side chain that resides within a beta strand in stick
> representation such that the residue is linked in space with the backbone.
> This works fine when representing as sticks a residue that is within a loop
> or helix, but not within a strand; there it just sticks out into space,
> which looks awful if the figure is not turned 'just so' so that the viewer
> cannot see the space. I am using version 2.4.0 on my Mac.
> >
> > Regards,
> > Emilia.
> >
> > --
> > "Study as if you were going to live forever; live as if you were going
> to die tomorrow." - Maria Mitchell
> >
> > "I'm not afraid of storms for I'm learning to sail my ship."  - Louisa
> May Alcott
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May
Alcott

Re: [PyMOL] [EXTERNAL] Pucker calculations

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

Hi Isreal,

I converted the script with 2to3 using the command in a terminal:

2to3 pucker.py -w

The modified script ran as advertised on the Wiki in 
pymol 2.4.0 on both DNA and RNA fetched as cif (new default) or as pdb. 

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center

From: Israel Serrano [isr...@gm...]
Sent: Friday, February 12, 2021 3:54 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Pucker calculations

Hello PyMOL users,


I used to run the script https://urldefense.proofpoint.com/v2/url?u=http-3A__pucker.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=6MIjRV8jE5Xx0XTtn_34wRf6thWBe8MHvfmU7U9wCSE&s=oqRpFfO3IQkNfDPi0Q2w2tIOxTadxDYLOGY88h3JOtI&e=
(https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Pucker&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=6MIjRV8jE5Xx0XTtn_34wRf6thWBe8MHvfmU7U9wCSE&s=RPuMEUTeEl1SDk6fnvNjFrmWxHcAWeKBa9rst15Incs&e= ) in the old version of PyMOL.
It's a script to calculate the sugar pucker information of the nucleic
acid structures.

Unfortunately, it not working in PyMOL 2.4.1, I guess because is written
in Python 2. I have tried to run the 2to3 to update the script, but I
get some errors. Has anybody been able to run this script in PyMOL 2.4?


Thanks,

Israel



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[PyMOL] counting salt bridge pairs

[Chen, Q. <qi...@pi...>]

Hi, Pymol Users,

Would anyone help me how to count the salt bridges in all models?

After my script, I have the salt bridge list for each model. I would like to know all the possible salt bridges in all models, and their frequency of each salt bridge in all the models.

for example,
/A/ASP/446/OD2 to /A/LYS/239/NZ: 3.776 exist in both models, while A/GLU/328/OE1 to/A/ARG/322/NE: 2.377 exist in only one model.
I have total 50 models. I cannot image a manual way to isolate each salt bridge and count their frequency in 50 models.

My wild guess is that text processing might solve this issue.

Any suggestions?

Thanks!

The output of model00000 is as follows
    model00000/A/GLU/328/OE1 to model00000/A/ARG/322/NE: 2.377
    model00000/A/GLU/430/OE2 to model00000/A/ARG/368/NE: 3.883
    model00000/A/ASP/446/OD1 to model00000/A/LYS/239/NZ: 2.818
    model00000/A/ASP/446/OD2 to model00000/A/LYS/239/NZ: 3.877
    model00000/B/GLU/328/OE1 to model00000/B/ARG/322/NE: 2.376
    model00000/B/GLU/430/OE2 to model00000/B/ARG/368/NE: 3.884
    model00000/B/ASP/446/OD1 to model00000/B/LYS/239/NZ: 2.818
    model00000/B/ASP/446/OD2 to model00000/B/LYS/239/NZ: 3.877
    model00000/C/GLU/328/OE1 to model00000/C/ARG/322/NE: 2.377
    model00000/C/GLU/430/OE2 to model00000/C/ARG/368/NE: 3.883
    model00000/C/ASP/446/OD1 to model00000/C/LYS/239/NZ: 2.818
    model00000/C/ASP/446/OD2 to model00000/C/LYS/239/NZ: 3.876
    model00000/D/GLU/328/OE1 to model00000/D/ARG/322/NE: 2.377
    model00000/D/GLU/430/OE2 to model00000/D/ARG/368/NE: 3.883
    model00000/D/ASP/446/OD1 to model00000/D/LYS/239/NZ: 2.819
    model00000/D/ASP/446/OD2 to model00000/D/LYS/239/NZ: 3.876
    model00000/E/GLU/328/OE1 to model00000/E/ARG/322/NE: 2.378
    model00000/E/GLU/430/OE2 to model00000/E/ARG/368/NE: 3.883
    model00000/E/ASP/446/OD1 to model00000/E/LYS/239/NZ: 2.819
    model00000/E/ASP/446/OD2 to model00000/E/LYS/239/NZ: 3.877

The output of model00001 is as follows
    model00001/A/ASP/429/OD1 to model00001/B/ARG/424/NE: 2.634
    model00001/A/ASP/429/OD2 to model00001/B/ARG/424/NE: 3.672
    model00001/A/GLU/437/OE2 to model00001/A/ARG/310/NE: 3.310
    model00001/A/ASP/446/OD2 to model00001/A/LYS/239/NZ: 3.776
    model00001/B/ASP/429/OD1 to model00001/C/ARG/424/NE: 2.600
    model00001/B/ASP/429/OD2 to model00001/C/ARG/424/NE: 3.629
    model00001/B/GLU/437/OE2 to model00001/B/ARG/310/NE: 3.311
    model00001/B/ASP/446/OD2 to model00001/B/LYS/239/NZ: 3.777
    model00001/C/ASP/429/OD1 to model00001/D/ARG/424/NE: 2.597
    model00001/C/ASP/429/OD2 to model00001/D/ARG/424/NE: 3.621
    model00001/C/GLU/437/OE2 to model00001/C/ARG/310/NE: 3.311
    model00001/C/ASP/446/OD2 to model00001/C/LYS/239/NZ: 3.776
    model00001/D/ASP/429/OD1 to model00001/E/ARG/424/NE: 2.574
    model00001/D/ASP/429/OD2 to model00001/E/ARG/424/NE: 3.604
    model00001/D/GLU/437/OE2 to model00001/D/ARG/310/NE: 3.310
    model00001/D/ASP/446/OD2 to model00001/D/LYS/239/NZ: 3.776
    model00001/E/ASP/429/OD1 to model00001/A/ARG/424/NE: 2.589
    model00001/E/ASP/429/OD2 to model00001/A/ARG/424/NE: 3.604
    model00001/E/GLU/437/OE2 to model00001/E/ARG/310/NE: 3.311
    model00001/E/ASP/446/OD2 to model00001/E/LYS/239/NZ: 3.776




Message: 3
Date: Fri, 12 Feb 2021 14:07:13 +0000
From: "Chen, Qiang" <qi...@pi...>
To: "pym...@li..."
        <pym...@li...>
Subject: Re: [PyMOL] PyMOL-users Digest, Vol 177, Issue 5
Message-ID:
        <BL0...@BL...>

Content-Type: text/plain; charset="us-ascii"

In case anyone has a similar problem, here is my solution

from pymol import cmd
from glob import glob
cmd.do("run list_hb.py")

for file in glob("model*.pdb"):
print(file)
cmd.load(file)
obj=cmd.get_object_list('all')
print(obj)
#hydrogen bonds
cmd.do("list_hb all, all, write_distances_file=hb_"+str(obj[0])+".txt")
#salt bridge
cmd.do("select negative, (resn ASP+GLU and name OD*+OE*)")
cmd.do("select positive, (resn Lys and name NZ) or (resn ARG and name NE + NH*)")
cmd.do("pairwise_dist negative, positive, 4, show=N, output="+str(obj[0]))

Re: [PyMOL] PyMOL-users Digest, Vol 177, Issue 5

[Chen, Q. <qi...@pi...>]

In case anyone has a similar problem, here is my solution

from pymol import cmd
from glob import glob
cmd.do("run list_hb.py")

for file in glob("model*.pdb"):
print(file)
cmd.load(file)
obj=cmd.get_object_list('all')
print(obj)
#hydrogen bonds
cmd.do("list_hb all, all, write_distances_file=hb_"+str(obj[0])+".txt")
#salt bridge
cmd.do("select negative, (resn ASP+GLU and name OD*+OE*)")
cmd.do("select positive, (resn Lys and name NZ) or (resn ARG and name NE + NH*)")
cmd.do("pairwise_dist negative, positive, 4, show=N, output="+str(obj[0]))
________________________________
From: pym...@li... <pym...@li...>
Sent: Thursday, February 11, 2021 7:02 AM
To: pym...@li... <pym...@li...>
Subject: PyMOL-users Digest, Vol 177, Issue 5

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Today's Topics:

   1. Salt bridges in same chains (Chen, Qiang)


----------------------------------------------------------------------

Message: 1
Date: Wed, 10 Feb 2021 15:09:28 +0000
From: "Chen, Qiang" <qi...@pi...>
To: "pym...@li..."
        <pym...@li...>
Subject: [PyMOL] Salt bridges in same chains
Message-ID:
        <DM6...@DM...>

Content-Type: text/plain; charset="iso-8859-1"

Hi, All,

I am writing a script to find all salt bridges in a pentameric proteins in 50 models.

The issues are

  1.  There are no salt bridges found in the same chain. But I find some if I use this command.
>pairwise_dist /model00000//A/LYS+ARG/NZ+NE+NH*, /model00000//A/ASP+GLU/OD*+OE*, 4, show=N, output=P
My guess is that pairwise_dist does not take the same sel1, sel2 as a valid input. Any solutions/suggestions?
  2.  The script is apparently not optimized. Any suggestions?

Thanks!

Charles

Here are what I am using now.

from pymol import cmd
from glob import glob

for file in glob("model*.pdb"):
print(file)
cmd.load(file)
obj=cmd.get_object_list('all')
print(obj)
#salt bridge
cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_A")
cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_B")
cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_C")
cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_D")
cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_E")
cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_B")
cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_C")
cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_D")
cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_E")
cmd.do("pairwise_dist ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_C_C")
cmd.do("pairwise_dist ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_C_D")
cmd.do("pairwise_dist ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_C_E")
cmd.do("pairwise_dist ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_D_D")
cmd.do("pairwise_dist ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_D_E")
cmd.do("pairwise_dist ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_E_E")
cmd.delete("all")
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End of PyMOL-users Digest, Vol 177, Issue 5
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Re: [PyMOL] equals operator for q and b

[Ali S. K. <aku...@un...>]

Hi Benedikt, 

You can do a work around with '<' or '>':
Sele qm, q>0.9999999 and q<1.0000001

I checked that this works like this for my "obj" in PyMOL:
stored.q = []
iterate obj, stored.q.append(q)
q_arr = np.array(stored.q)
q_1 = q_arr[q_arr == 1] # only keep values of q that equal 1
print(len(q_1))

You can make actually use this numpy feature to slice the atom indices into an array (lets say atom_arr) then make a selection with it like this:
cmd.select("qm",f"index {'+',join(atom_arr)}") 

But '<' or '>' operators are quicker and seem safe

Kind regards,

Ali Kusay 

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
 

On 12/2/21, 11:34 pm, "Benedikt Floeser" <ben...@ce...> wrote:

    Dear fellow users,

    among other things I use pymol to edit PDB files so as to use them in
    an ORCA calculation. This entails changing the occupancy and B-factors
    to values of 0, 1 and 2.

    Changing these entries to the appropriate values but selecting, e.g.,
    all atoms with a q value of 1 or 1.00 with something like
    'select qm, q = 1' fails whereas it works with partial charges or
    formal charges. Is there any way to do this without resorting to
    workarounds with '<' or '>'?

    Best
    -- 
    Dr. Benedikt M. Flöser
    Max-Planck-Institute for Chemical Energy Conversion
    Stiftstraße 34-36
    45470 Mülheim a.d. Ruhr
    Germany

[PyMOL] equals operator for q and b

[Benedikt F. <ben...@ce...>]

Dear fellow users,

among other things I use pymol to edit PDB files so as to use them in
an ORCA calculation. This entails changing the occupancy and B-factors
to values of 0, 1 and 2.

Changing these entries to the appropriate values but selecting, e.g.,
all atoms with a q value of 1 or 1.00 with something like
'select qm, q = 1' fails whereas it works with partial charges or
formal charges. Is there any way to do this without resorting to
workarounds with '<' or '>'?

Best
-- 
Dr. Benedikt M. Flöser
Max-Planck-Institute for Chemical Energy Conversion
Stiftstraße 34-36
45470 Mülheim a.d. Ruhr
Germany

[PyMOL] Pucker calculations

[Israel S. <isr...@gm...>]

Hello PyMOL users,


I used to run the script pucker.py 
(https://pymolwiki.org/index.php/Pucker) in the old version of PyMOL. 
It's a script to calculate the sugar pucker information of the nucleic 
acid structures.

Unfortunately, it not working in PyMOL 2.4.1, I guess because is written 
in Python 2. I have tried to run the 2to3 to update the script, but I 
get some errors. Has anybody been able to run this script in PyMOL 2.4?


Thanks,

Israel

[PyMOL] Salt bridges in same chains

[Chen, Q. <qi...@pi...>]

Hi, All,

I am writing a script to find all salt bridges in a pentameric proteins in 50 models.

The issues are

  1.  There are no salt bridges found in the same chain. But I find some if I use this command.
>pairwise_dist /model00000//A/LYS+ARG/NZ+NE+NH*, /model00000//A/ASP+GLU/OD*+OE*, 4, show=N, output=P
My guess is that pairwise_dist does not take the same sel1, sel2 as a valid input. Any solutions/suggestions?
  2.  The script is apparently not optimized. Any suggestions?

Thanks!

Charles

Here are what I am using now.

from pymol import cmd
from glob import glob

for file in glob("model*.pdb"):
print(file)
cmd.load(file)
obj=cmd.get_object_list('all')
print(obj)
#salt bridge
cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_A")
cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_B")
cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_C")
cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_D")
cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_E")
cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_B")
cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_C")
cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_D")
cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_E")
cmd.do("pairwise_dist ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_C_C")
cmd.do("pairwise_dist ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_C_D")
cmd.do("pairwise_dist ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_C_E")
cmd.do("pairwise_dist ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_D_D")
cmd.do("pairwise_dist ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_D_E")
cmd.do("pairwise_dist ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_E_E")
cmd.delete("all")

Re: [PyMOL] Label charge sites, termini, check contrast

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

Hi Jared,

Thank you for teaching me that special feature on pymol; on my pymol
version set label_position worked (instead of set label_offset).

Neena

On Sun, 31 Jan 2021 at 20:17, Jared Sampson <jar...@co...>
wrote:

> Hi Neena -
>
> There is also a `label_offset` setting, which can be given an x,y,z vector
> in viewport coordinates. So if you want all labels to be in the foreground
> compared to their respective atom(s), you might set it via:
>
> set label_offset, [0,0,5]
>
> I believe this can also be done in an object-specific fashion, so you
> could also do:
>
> set label_offset, [0,0,5], myobject
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Sat, Jan 30, 2021 at 2:52 AM Neena Susan Eappen <
> nee...@gm...> wrote:
>
>> Hi Ali,
>>
>> Thank you for the brief and thorough explanation! All those commands gave
>> exactly what I was looking for!
>>
>> Many thanks,
>> Neena
>>
>> On Fri, 29 Jan 2021 at 18:36, Ali Saad Kusay <aku...@un...>
>> wrote:
>>
>>> Hi Neena,
>>>
>>> A simple way to label in PyMOL is to simply select the atom you want and
>>> enter the following command:
>>> label sele, "what you want to label"
>>>
>>> I.e. for the N:
>>> label sele, "N"
>>>
>>> PyMOL can render the special ⨁ you are using, through unicode:
>>> label sele, '\u2A01'
>>> Visit the wiki for more info:
>>> https://pymolwiki.org/index.php/Label_font_id
>>>
>>> The labels may be small, to change size,
>>> set label_size, 30
>>> Change the 30 to what size you need
>>>
>>> Finally, the labels will likely be off in position, the easiest way to
>>> change position is by using the editing mode:
>>> This helpful video shows this around 3:30 (
>>> https://www.youtube.com/watch?v=yBFzJ3ql4qU&ab_channel=MolecularMemory)
>>>
>>> Cheers,
>>>
>>> Ali
>>>
>>> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
>>> Supervised by A/Prof Thomas Balle
>>> The University of Sydney School of Pharmacy | Faculty of Medicine and
>>> Health
>>> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

[PyMOL] Plugin for beta- (and alpha-) peptide building

[András F. W. <wac...@tt...>]

Dear PyMOLers,

in case any of you is interested, we have developed a new plugin for 
peptide model building. Originally for beta-peptides, but works for 
natural ones as well. It can handle mono- and disubstituted beta-amino 
acids (and alpha ones) with arbitrary proteinogenic side-chains and 
arbitrary Calpha/Cbeta chirality, and features a library of secondary 
structures, thus entire sequences of peptides can be built with the 
secondary structure defined at a per-residue base.

More information can be found on the PyMOL Wiki page: 
https://pymolwiki.org/index.php/Pmlbeta and the links therein.

I hope this may help some of you.

Best regards,

Andras Wacha

-- 
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group (310)

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu

Re: [PyMOL] Label charge sites, termini, check contrast

[Jon R S. <j.r...@sh...>]

Or you can use "3 button edit mode" with a combination of Control (on a
Mac) and the left mouse button. It allows you to move the label in first
2Ds, release, rotate and do it again to position exactly where you want it,
e.g. in front, behind etc.

BW Jon

On Mon, 1 Feb 2021 at 21:23, Jared Sampson <jar...@co...>
wrote:

> Sorry, I replied from my phone earlier...the correct setting is
> `label_position`.  https://pymolwiki.org/index.php/Label_position
>
> Best,
> Jared
>
> On Sun, Jan 31, 2021 at 8:17 PM Jared Sampson <jar...@co...>
> wrote:
>
>> Hi Neena -
>>
>> There is also a `label_offset` setting, which can be given an x,y,z
>> vector in viewport coordinates. So if you want all labels to be in the
>> foreground compared to their respective atom(s), you might set it via:
>>
>> set label_offset, [0,0,5]
>>
>> I believe this can also be done in an object-specific fashion, so you
>> could also do:
>>
>> set label_offset, [0,0,5], myobject
>>
>> Hope that helps.
>>
>> Cheers,
>> Jared
>>
>>
>> On Sat, Jan 30, 2021 at 2:52 AM Neena Susan Eappen <
>> nee...@gm...> wrote:
>>
>>> Hi Ali,
>>>
>>> Thank you for the brief and thorough explanation! All those commands
>>> gave exactly what I was looking for!
>>>
>>> Many thanks,
>>> Neena
>>>
>>> On Fri, 29 Jan 2021 at 18:36, Ali Saad Kusay <aku...@un...>
>>> wrote:
>>>
>>>> Hi Neena,
>>>>
>>>> A simple way to label in PyMOL is to simply select the atom you want
>>>> and enter the following command:
>>>> label sele, "what you want to label"
>>>>
>>>> I.e. for the N:
>>>> label sele, "N"
>>>>
>>>> PyMOL can render the special ⨁ you are using, through unicode:
>>>> label sele, '\u2A01'
>>>> Visit the wiki for more info:
>>>> https://pymolwiki.org/index.php/Label_font_id
>>>>
>>>> The labels may be small, to change size,
>>>> set label_size, 30
>>>> Change the 30 to what size you need
>>>>
>>>> Finally, the labels will likely be off in position, the easiest way to
>>>> change position is by using the editing mode:
>>>> This helpful video shows this around 3:30 (
>>>> https://www.youtube.com/watch?v=yBFzJ3ql4qU&ab_channel=MolecularMemory)
>>>>
>>>> Cheers,
>>>>
>>>> Ali
>>>>
>>>> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
>>>> Supervised by A/Prof Thomas Balle
>>>> The University of Sydney School of Pharmacy | Faculty of Medicine and
>>>> Health
>>>> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>> 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



-- 
Professor Jon R Sayers, FRSB
Department of Infection, Immunity & Cardiovascular Disease
University of Sheffield Medical School
Beech Hill Rd
Sheffield
S10 2RX
United Kingdom

Tel: +44 (0)114 215 9552
Fax: +44 (0)114 271 1863
Email: j.r...@sh...

https://www.sheffield.ac.uk/iicd/profiles/sayers
<http://www.sheffield.ac.uk/iicd/profiles/sayers>

Re: [PyMOL] Label charge sites, termini, check contrast

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

Sorry, I replied from my phone earlier...the correct setting is
`label_position`.  https://pymolwiki.org/index.php/Label_position

Best,
Jared

On Sun, Jan 31, 2021 at 8:17 PM Jared Sampson <jar...@co...>
wrote:

> Hi Neena -
>
> There is also a `label_offset` setting, which can be given an x,y,z vector
> in viewport coordinates. So if you want all labels to be in the foreground
> compared to their respective atom(s), you might set it via:
>
> set label_offset, [0,0,5]
>
> I believe this can also be done in an object-specific fashion, so you
> could also do:
>
> set label_offset, [0,0,5], myobject
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Sat, Jan 30, 2021 at 2:52 AM Neena Susan Eappen <
> nee...@gm...> wrote:
>
>> Hi Ali,
>>
>> Thank you for the brief and thorough explanation! All those commands gave
>> exactly what I was looking for!
>>
>> Many thanks,
>> Neena
>>
>> On Fri, 29 Jan 2021 at 18:36, Ali Saad Kusay <aku...@un...>
>> wrote:
>>
>>> Hi Neena,
>>>
>>> A simple way to label in PyMOL is to simply select the atom you want and
>>> enter the following command:
>>> label sele, "what you want to label"
>>>
>>> I.e. for the N:
>>> label sele, "N"
>>>
>>> PyMOL can render the special ⨁ you are using, through unicode:
>>> label sele, '\u2A01'
>>> Visit the wiki for more info:
>>> https://pymolwiki.org/index.php/Label_font_id
>>>
>>> The labels may be small, to change size,
>>> set label_size, 30
>>> Change the 30 to what size you need
>>>
>>> Finally, the labels will likely be off in position, the easiest way to
>>> change position is by using the editing mode:
>>> This helpful video shows this around 3:30 (
>>> https://www.youtube.com/watch?v=yBFzJ3ql4qU&ab_channel=MolecularMemory)
>>>
>>> Cheers,
>>>
>>> Ali
>>>
>>> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
>>> Supervised by A/Prof Thomas Balle
>>> The University of Sydney School of Pharmacy | Faculty of Medicine and
>>> Health
>>> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Label charge sites, termini, check contrast

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

Hi Neena -

There is also a `label_offset` setting, which can be given an x,y,z vector
in viewport coordinates. So if you want all labels to be in the foreground
compared to their respective atom(s), you might set it via:

set label_offset, [0,0,5]

I believe this can also be done in an object-specific fashion, so you could
also do:

set label_offset, [0,0,5], myobject

Hope that helps.

Cheers,
Jared


On Sat, Jan 30, 2021 at 2:52 AM Neena Susan Eappen <nee...@gm...>
wrote:

> Hi Ali,
>
> Thank you for the brief and thorough explanation! All those commands gave
> exactly what I was looking for!
>
> Many thanks,
> Neena
>
> On Fri, 29 Jan 2021 at 18:36, Ali Saad Kusay <aku...@un...>
> wrote:
>
>> Hi Neena,
>>
>> A simple way to label in PyMOL is to simply select the atom you want and
>> enter the following command:
>> label sele, "what you want to label"
>>
>> I.e. for the N:
>> label sele, "N"
>>
>> PyMOL can render the special ⨁ you are using, through unicode:
>> label sele, '\u2A01'
>> Visit the wiki for more info:
>> https://pymolwiki.org/index.php/Label_font_id
>>
>> The labels may be small, to change size,
>> set label_size, 30
>> Change the 30 to what size you need
>>
>> Finally, the labels will likely be off in position, the easiest way to
>> change position is by using the editing mode:
>> This helpful video shows this around 3:30 (
>> https://www.youtube.com/watch?v=yBFzJ3ql4qU&ab_channel=MolecularMemory)
>>
>> Cheers,
>>
>> Ali
>>
>> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
>> Supervised by A/Prof Thomas Balle
>> The University of Sydney School of Pharmacy | Faculty of Medicine and
>> Health
>> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Mac Installation Question

[Justine W. <jus...@uw...>]

Dear Users,

Thank you very much for the suggestions! I was able to connect to a computer remotely to try them out. In case anyone else has issues with this in the future: homebrew does indeed work nicely with open source PyMOL and Rdkit. It turns out there was an issue with the Python pathways since Anaconda was already installed and therefore by default the Anaconda Python was being referenced. Once I made sure to specify the Python pathway that corresponded to homebrew, additional dependencies I needed (such as matplotlib) could be installed with pip.

Justine

________________________________
From: Thomas Holder <tho...@sc...>
Sent: Wednesday, January 27, 2021 2:54 AM
To: Justine Williams <jus...@uw...>
Cc: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] Mac Installation Question

Hi Justine,

Have you tried with the official schrodinger::pymol package? If the user who wants to use your plugin has a PyMOL license, that should be the best option for him.

conda create -n pymol -c conda-forge python=3.7 rdkit=2020.03.3.0 matplotlib seaborn pip numpy schrodinger::pymol schrodinger::tk scikit-learn git

You can also test this without a license, PyMOL will run in evaluation mode but your plugin should be fully functional.

Cheers,
  Thomas


> On Jan 27, 2021, at 1:46 AM, Justine Williams <jus...@uw...> wrote:
>
> Dear users,
>
> Could someone please help me with installing open source pymol on MacOS? I created a plugin, but to allow it to be more easily available to users with different OS, I need to include installation instructions for installing open source pymol on each. I prepared some installation instructions for creating a conda environment that works with Windows and Linux, but am having some issues getting the installation to work consistently for the MacOS case. As a note, I am not a Mac user myself, and have been trying to troubleshoot remotely with the help of colleagues who own Macs.
>
> I need to have the rdkit package usable to pymol, which is why I was creating the conda environment. The general conda steps that worked for Windows/Linux were to install and activate Anaconda3 (https://docs.anaconda.com/anaconda/install/mac-os/). Next, to open a terminal in the Anaconda3 directory named "envs." Then to use the following command to create an environment named pymol with the packages necessary:
>
> conda create -n pymol python=3.7 rdkit=2020.03.3.0 matplotlib seaborn pip numpy conda-forge::pmw tpeulen::pymol-open-source scikit-learn git
>
> Finally, to activate the environment:
>
> conda activate pymol
>
> The error that is generated for this approach is "ImportError: dlopen(/Users/FarFar/anaconda3/envs/pymol/lib/python3.7/site-packages/pymol/_cmd.cpython-37m-darwin.so, 2): Symbol not found: _glAccum"
>
> I would really appreciate any assistance with installation for Mac cases, or if anyone knows of known issues with this. As of now, it seems like using homebrew to install open source pymol and rdkit might be the best approach to take, but I have not been able to get that working. If there are other strategies for installing open source pymol and rdkit I would really appreciate the help.
>
> Thank you,
>
> Justine
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Label charge sites, termini, check contrast

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

Hi Ali,

Thank you for the brief and thorough explanation! All those commands gave
exactly what I was looking for!

Many thanks,
Neena

On Fri, 29 Jan 2021 at 18:36, Ali Saad Kusay <aku...@un...>
wrote:

> Hi Neena,
>
> A simple way to label in PyMOL is to simply select the atom you want and
> enter the following command:
> label sele, "what you want to label"
>
> I.e. for the N:
> label sele, "N"
>
> PyMOL can render the special ⨁ you are using, through unicode:
> label sele, '\u2A01'
> Visit the wiki for more info:
> https://pymolwiki.org/index.php/Label_font_id
>
> The labels may be small, to change size,
> set label_size, 30
> Change the 30 to what size you need
>
> Finally, the labels will likely be off in position, the easiest way to
> change position is by using the editing mode:
> This helpful video shows this around 3:30 (
> https://www.youtube.com/watch?v=yBFzJ3ql4qU&ab_channel=MolecularMemory)
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> Supervised by A/Prof Thomas Balle
> The University of Sydney School of Pharmacy | Faculty of Medicine and
> Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
>
>
>
>
>
>
>

Re: [PyMOL] Label charge sites, termini, check contrast

[Ali S. K. <aku...@un...>]

Hi Neena, 

A simple way to label in PyMOL is to simply select the atom you want and enter the following command:
label sele, "what you want to label"

I.e. for the N:
label sele, "N"

PyMOL can render the special ⨁ you are using, through unicode:
label sele, '\u2A01'
Visit the wiki for more info: https://pymolwiki.org/index.php/Label_font_id

The labels may be small, to change size, 
set label_size, 30
Change the 30 to what size you need

Finally, the labels will likely be off in position, the easiest way to change position is by using the editing mode:
This helpful video shows this around 3:30 (https://www.youtube.com/watch?v=yBFzJ3ql4qU&ab_channel=MolecularMemory)

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
Supervised by A/Prof Thomas Balle
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
 
 

[PyMOL] Label charge sites, termini, check contrast

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

Hello PyMOL users,

Is there a way to label charge sites and termini on PyMOL as I have shown
in the below figure instead of using Paint?
In addition, is there a way to check color contrast for this peptide
structure for making it more accessible to the readers?
[image: image.png]
Many thanks,
Neena

Re: [PyMOL] representation of residue sidechain within a beta strand?

[Thomas H. <tho...@sc...>]

Hi Yufeng,

The "Properties" panel can show you which settings got changed with the preset. The "pretty" preset indeed sets "cartoon_side_chain_helper" to "off" for the object. The easiest way to clear this setting is to use the "unset_deep" command.

unset_deep cartoon_side_chain_helper
set cartoon_side_chain_helper

https://pymolwiki.org/index.php/Unset_deep
https://pymolwiki.org/index.php/Properties_Inspector

Cheers,
  Thomas


> On Jan 29, 2021, at 6:26 AM, Yufeng Tong <yuf...@gm...> wrote:
> 
> Hi Tomas,
> 
> I noticed this setting is not working when
> preset.pretty(selection='all') has been invoked, that is, whether
> cartoon_side_chain_helper is set to on or off, the side chain is
> disconnected. Do you know what is changed when preset.pretty() is
> called?
> 
> The reason I want to call preset.pretty() is that if this is not
> called, the sticks representation of an isopeptide cannot be properly
> displayed (no sticks shown for the isopeptide bond), a bit of a
> dilemma.
> 
> Thanks,
> 
> Yufeng
> 
> 
> On Mon, Jan 18, 2021 at 3:35 AM Tomas Malinauskas
> <tom...@gm...> wrote:
>> 
>> Hi Emilia,
>> 
>> You might try the following:
>> set cartoon_side_chain_helper, on
>> 
>> Hope that helps,
>> Tomas
>> 
>> On Mon, Jan 18, 2021 at 7:52 AM Emilia C. Arturo (Emily)
>> <ecg...@gm...> wrote:
>>> 
>>> Hi All,
>>> 
>>> I'm wondering if anyone here knows how to represent an amino acid residue side chain that resides within a beta strand in stick representation such that the residue is linked in space with the backbone. This works fine when representing as sticks a residue that is within a loop or helix, but not within a strand; there it just sticks out into space, which looks awful if the figure is not turned 'just so' so that the viewer cannot see the space. I am using version 2.4.0 on my Mac.
>>> 
>>> Regards,
>>> Emilia.
>>> 
>>> --
>>> "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell
>>> 
>>> "I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May Alcott
>>> 
>>> _______________________________________________
>>> 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
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] representation of residue sidechain within a beta strand?

[Yufeng T. <yuf...@gm...>]

Hi Tomas,

I noticed this setting is not working when
preset.pretty(selection='all') has been invoked, that is, whether
cartoon_side_chain_helper is set to on or off, the side chain is
disconnected. Do you know what is changed when preset.pretty() is
called?

The reason I want to call preset.pretty() is that if this is not
called, the sticks representation of an isopeptide cannot be properly
displayed (no sticks shown for the isopeptide bond), a bit of a
dilemma.

Thanks,

Yufeng


On Mon, Jan 18, 2021 at 3:35 AM Tomas Malinauskas
<tom...@gm...> wrote:
>
> Hi Emilia,
>
> You might try the following:
> set cartoon_side_chain_helper, on
>
> Hope that helps,
> Tomas
>
> On Mon, Jan 18, 2021 at 7:52 AM Emilia C. Arturo (Emily)
> <ecg...@gm...> wrote:
> >
> > Hi All,
> >
> > I'm wondering if anyone here knows how to represent an amino acid residue side chain that resides within a beta strand in stick representation such that the residue is linked in space with the backbone. This works fine when representing as sticks a residue that is within a loop or helix, but not within a strand; there it just sticks out into space, which looks awful if the figure is not turned 'just so' so that the viewer cannot see the space. I am using version 2.4.0 on my Mac.
> >
> > Regards,
> > Emilia.
> >
> > --
> > "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell
> >
> > "I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May Alcott
> >
> > _______________________________________________
> > 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
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Re: [PyMOL] Iterate over residue index

[Thomas H. <tho...@sc...>]

Hi Ioannis,

You could make a mapping of rank to residue selection and then sort that by rank. Something like this:

from pymol import cmd, stored
stored.mydict = {}
cmd.iterate("guide", "stored.mydict[rank] = f'///{chain}/{resi}'")
for rank, sele in sorted(stored.mydict.items()):
    cmd.iterate(sele, "print(chain, resi, resn, name)")


Cheers,
  Thomas


> On Jan 13, 2021, at 10:38 AM, Ioannis G. Riziotis <riz...@eb...> wrote:
> 
> Hello,
> 
> Is there any way to iterate over residues by index in the PDB file (not resi, but the absolute order of the residues in the pdb). Something like the equivalent of ‘rank’ for atoms, but in residue level.
> 
> Best,
> Ioannis
> 
> 
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Mac Installation Question

[Thomas H. <tho...@sc...>]

Hi Justine,

Have you tried with the official schrodinger::pymol package? If the user who wants to use your plugin has a PyMOL license, that should be the best option for him.

conda create -n pymol -c conda-forge python=3.7 rdkit=2020.03.3.0 matplotlib seaborn pip numpy schrodinger::pymol schrodinger::tk scikit-learn git

You can also test this without a license, PyMOL will run in evaluation mode but your plugin should be fully functional.

Cheers,
  Thomas


> On Jan 27, 2021, at 1:46 AM, Justine Williams <jus...@uw...> wrote:
> 
> Dear users,
>  
> Could someone please help me with installing open source pymol on MacOS? I created a plugin, but to allow it to be more easily available to users with different OS, I need to include installation instructions for installing open source pymol on each. I prepared some installation instructions for creating a conda environment that works with Windows and Linux, but am having some issues getting the installation to work consistently for the MacOS case. As a note, I am not a Mac user myself, and have been trying to troubleshoot remotely with the help of colleagues who own Macs.
>  
> I need to have the rdkit package usable to pymol, which is why I was creating the conda environment. The general conda steps that worked for Windows/Linux were to install and activate Anaconda3 (https://docs.anaconda.com/anaconda/install/mac-os/). Next, to open a terminal in the Anaconda3 directory named "envs." Then to use the following command to create an environment named pymol with the packages necessary:
>  
> conda create -n pymol python=3.7 rdkit=2020.03.3.0 matplotlib seaborn pip numpy conda-forge::pmw tpeulen::pymol-open-source scikit-learn git
>  
> Finally, to activate the environment:
>  
> conda activate pymol                     
>  
> The error that is generated for this approach is “ImportError: dlopen(/Users/FarFar/anaconda3/envs/pymol/lib/python3.7/site-packages/pymol/_cmd.cpython-37m-darwin.so, 2): Symbol not found: _glAccum”
>  
> I would really appreciate any assistance with installation for Mac cases, or if anyone knows of known issues with this. As of now, it seems like using homebrew to install open source pymol and rdkit might be the best approach to take, but I have not been able to get that working. If there are other strategies for installing open source pymol and rdkit I would really appreciate the help.
>  
> Thank you,
>  
> Justine                                                                                                                                                                                
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Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Mac Installation Question

[Justine W. <jus...@uw...>]

Dear users,

Could someone please help me with installing open source pymol on MacOS? I created a plugin, but to allow it to be more easily available to users with different OS, I need to include installation instructions for installing open source pymol on each. I prepared some installation instructions for creating a conda environment that works with Windows and Linux, but am having some issues getting the installation to work consistently for the MacOS case. As a note, I am not a Mac user myself, and have been trying to troubleshoot remotely with the help of colleagues who own Macs.

I need to have the rdkit package usable to pymol, which is why I was creating the conda environment. The general conda steps that worked for Windows/Linux were to install and activate Anaconda3 (https://docs.anaconda.com/anaconda/install/mac-os/). Next, to open a terminal in the Anaconda3 directory named "envs." Then to use the following command to create an environment named pymol with the packages necessary:

conda create -n pymol python=3.7 rdkit=2020.03.3.0 matplotlib seaborn pip numpy conda-forge::pmw tpeulen::pymol-open-source scikit-learn git

Finally, to activate the environment:

conda activate pymol

The error that is generated for this approach is "ImportError: dlopen(/Users/FarFar/anaconda3/envs/pymol/lib/python3.7/site-packages/pymol/_cmd.cpython-37m-darwin.so, 2): Symbol not found: _glAccum"

I would really appreciate any assistance with installation for Mac cases, or if anyone knows of known issues with this. As of now, it seems like using homebrew to install open source pymol and rdkit might be the best approach to take, but I have not been able to get that working. If there are other strategies for installing open source pymol and rdkit I would really appreciate the help.

Thank you,

Justine

Re: [PyMOL] representation of residue sidechain within a beta strand?

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

Hi Emilia,

You might try the following:
set cartoon_side_chain_helper, on

Hope that helps,
Tomas

On Mon, Jan 18, 2021 at 7:52 AM Emilia C. Arturo (Emily)
<ecg...@gm...> wrote:
>
> Hi All,
>
> I'm wondering if anyone here knows how to represent an amino acid residue side chain that resides within a beta strand in stick representation such that the residue is linked in space with the backbone. This works fine when representing as sticks a residue that is within a loop or helix, but not within a strand; there it just sticks out into space, which looks awful if the figure is not turned 'just so' so that the viewer cannot see the space. I am using version 2.4.0 on my Mac.
>
> Regards,
> Emilia.
>
> --
> "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell
>
> "I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May Alcott
>
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[PyMOL] representation of residue sidechain within a beta strand?

[Emilia C. A. (Emily) <ecg...@gm...>]

Hi All,

I'm wondering if anyone here knows how to represent an amino acid residue
side chain that resides within a beta strand in stick representation such
that the residue is linked in space with the backbone. This works fine when
representing as sticks a residue that is within a loop or helix, but not
within a strand; there it just sticks out into space, which looks awful if
the figure is not turned 'just so' so that the viewer cannot see the space.
I am using version 2.4.0 on my Mac.

Regards,
Emilia.

-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May
Alcott

[PyMOL] Iterate over residue index

[Ioannis G. R. <riz...@eb...>]

Hello,

Is there any way to iterate over residues by index in the PDB file (not 
resi, but the absolute order of the residues in the pdb). Something like 
the equivalent of ‘rank’ for atoms, but in residue level.

Best,
Ioannis