pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] incomplete secondary structure

[h. a. s. <h.a...@gm...>]

Hi all,

When I open 3jav the backbone shows many helices, but Pymol doesn’t draw them as helices when showing the cartoon. Clearly there is something that is not perfect with the deposited cyro structure.

If I run the dss command, the cartoon structure isn’t fixed, and I get repeats of the following error for each residue from 1-2750 for each chain: 
 AssignSS-Warning: Ignoring incomplete residue /3jav//D/2750  …

Does anyone know how I can fix the secondary structure without having to manually assign it to each helix?

Thanks!


Adam

Re: [PyMOL] [EXTERNAL] Apply valence settings to an object

[Chris F. <fa...@gm...>]

Many thanks for your assistance, Blaine!

For the second point, I wanted to use the stick_ball setting on the ligand
only. I was able to modify your command as follows:
hide sticks; set stick_ball, on, ligand; show sticks

Best wishes,
Chris

On Fri, Apr 10, 2020 at 9:37 PM Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Chris,
>
> Here is a one compound setting command (copy and paste at the PyMOL command
> prompt above the viewport) that turns on valence for the ligand bonds
> in ligand RZS of the covid-19 protease structure PDB 5R82 while turning
> off the valence for the protein bonds.
>
> set valence, on, resn RZS; set valence, off, not resn RZs
>
>
> For your second question, set the the stick radius for a single bond by
> specifying the two atoms
>
> hide sticks; set_bond stick_radius, 0.05, /5r82/B/A/RZS`1001/C07,
> /5r82/B/A/RZS`1001/C08; show sticks
>
> https://pymolwiki.org/index.php/Stick_radius
>
> Recent versions of PyMOL show the ligand as sticks rather than lines when
> first loaded into PyMOL.
> You may have to turn off sticks, reset the set radius of interest, and
> then turn the sticks back on.
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> ________________________________________
> From: Chris Fage [fa...@gm...]
> Sent: Friday, April 10, 2020 2:00 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] Apply valence settings to an object
>
> Dear Pymol Fanatics,
>
> I would like to show the valence of ligand bonds only and not those of the
> surrounding amino acid residues. Is there any easy way to do this, aside
> from manually editing every bond? I’m also curious how one would set the
> stick_ball setting for a single object and not the rest of the protein.
> Many thanks in advance!
>
> Best,
> Chris
>

Re: [PyMOL] [EXTERNAL] Apply valence settings to an object

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

Hi Chris,

Here is a one compound setting command (copy and paste at the PyMOL command
prompt above the viewport) that turns on valence for the ligand bonds
in ligand RZS of the covid-19 protease structure PDB 5R82 while turning
off the valence for the protein bonds.

set valence, on, resn RZS; set valence, off, not resn RZs


For your second question, set the the stick radius for a single bond by specifying the two atoms  

hide sticks; set_bond stick_radius, 0.05, /5r82/B/A/RZS`1001/C07, /5r82/B/A/RZS`1001/C08; show sticks

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

Recent versions of PyMOL show the ligand as sticks rather than lines when first loaded into PyMOL.
You may have to turn off sticks, reset the set radius of interest, and then turn the sticks back on.
Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Chris Fage [fa...@gm...]
Sent: Friday, April 10, 2020 2:00 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Apply valence settings to an object

Dear Pymol Fanatics,

I would like to show the valence of ligand bonds only and not those of the surrounding amino acid residues. Is there any easy way to do this, aside from manually editing every bond? I’m also curious how one would set the stick_ball setting for a single object and not the rest of the protein. Many thanks in advance!

Best,
Chris

[PyMOL] Apply valence settings to an object

[Chris F. <fa...@gm...>]

Dear Pymol Fanatics,

I would like to show the valence of ligand bonds only and not those of the
surrounding amino acid residues. Is there any easy way to do this, aside
from manually editing every bond? I’m also curious how one would set the
stick_ball setting for a single object and not the rest of the protein.
Many thanks in advance!

Best,
Chris

[PyMOL] entering user input in Pymol script and defining sets in Python

[Luis G. A. <lga...@in...>]

Hello,
I have recently prepared a script for Pymol that works well in
evaluating RMSD values for a list of residues from proteins of interest
(targetted residues are generated by script embedded commands). However,
I wished to implement the script to allow the user to select what
residues to analyse. I have tried to use the INPUT function, but it
fails to work. Since the code is a bit long, I simplified progressively
the scripts to find out the problem. In that way, I ended up with the
following two scripts: 

"test.py":
```
import Bio.PDB
import numpy as
np
from pymol import cmd
import os,glob
from LFGA_functions import
user_entered

List_tot = user_entered()
print (List_tot)
```
which calls
the simple "user_entered" function that is inside the "My_function.py"
script, which generates the residue numbers for the same residue in a
hexameric protein:
```
def user_entered():
    List_res = []
   
List_tot = []
    a = input("Please indicate the number of residues to
analyze/per monomer:")
    numberRes =int(a)
    for i in
range(numberRes):
        Res = input("Please provide each residue
NUMBER and hit ENTER:")
        Res1 = int(Res)
        Res2 =
Res1+2000
        Res3 = Res1+3000
        Res4 = Res1+4000
        Res5
= Res1+5000
        Res6 = Res1+6000
        List_res =
(str(Res1),str(Res2),str(Res3),str(Res4),str(Res5),str(Res6))
       
List_tot.append(List_res)
    return List_tot
```
The script "test.py"
works well when directly executed by Python (3.7.5, which is installed
with Pymol 2.3.4,under Windows 7 Prof) from a windows command line. This
is an example of what I get: 

[first input "3" indicates that 3 cases
will be treated, followed by the identification number for each residue]


However, when the script is run from Pymol GUI, I get the following
error message:

INPUT():LOST SYS.STDIN

Here the error in more detail:


File "C:\Program Files\PyMOL\lib\site-packages\pymol\parsing.py", line
527, in execfile
    exec(co, global_ns, local_ns)
  File "C:/Program
Files/PyMOL/Lib/test.py", line 7, in <module>
    List_tot =
user_entered()
  File "C:\Program Files\PyMOL\lib\LFGA_functions.py",
line 18, in user_entered
    a = input("Please indicate the number of
residues to analyze/per monomer:")

Does anybody know what is the
problem. Please, take into account that I am a very basic Python user...


I profit also to ask something related to this problem... in the
original script that works well when run from Pymol (before trying to
implement the "input" option), I stored transiently some data (residue
name, type and chain) in the form of a Python "set". I need a set, and
not a list, because it removes automatically data repeatitions. However,
when I try to run the script from Python (with intention to overcome the
abovementioned problem with INPUT from Pymol), it stops with a message:


name 'close_to_A' not defined. 

This name corresponds to the set
name, which is defined as follows within the
script:
```
cmd.select("in_A", "Average and chain A near_to 5 of chain
B+C")
close_to_A =
set()
cmd.iterate("(around_A)","close_to_A.add((chain,resi,resn))")
```
How
shall I define a set in Python 3 ? Why does it work when run from Pymol
?

I would really appreciate if you could help me to solve these two
problems. Thank you in advance,

Best regards,

Luis 

  

Re: [PyMOL] Holes in dots

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

Hi Jason - 

This happens when there is an overlap with another atom's dots, for example where there is an H-bond or vdW contact.  One workaround would be to extract that residue you're showing in dots into a new object, so it doesn't have anything else in the object to interfere with it.

Hope that helps.

Cheers,
Jared



From: Jason Mosier <par...@gm...>
Reply: Jason Mosier <par...@gm...>
Date: April 8, 2020 at 3:07:37 PM
To: pym...@li... <pym...@li...>
Subject:  [PyMOL] Holes in dots  

Hi, I've been trying to figure out how to fix this and I just can't figure it out. I'm trying to make a nice render with dots and everything looks fine except for that the nitrogens and oxygens have these holes in them (see image: https://i.imgur.com/5G644br.png)
I know I could probably make an isomesh and all that, but if there's an easier way to fix this I'd rather do that.

Best,
Jason M.
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[PyMOL] Holes in dots

[Jason M. <par...@gm...>]

Hi, I've been trying to figure out how to fix this and I just can't figure
it out. I'm trying to make a nice render with dots and everything looks
fine except for that the nitrogens and oxygens have these holes in them
(see image: https://i.imgur.com/5G644br.png
<https://signtr.website/tracker/click?redirect=https%3A%2F%2Fi.imgur.com%2F5G644br.png&dID=1586372680751&linkName=https://i.imgur.com/5G644br.png>
)
I know I could probably make an isomesh and all that, but if there's an
easier way to fix this I'd rather do that.

Best,
Jason M.

Re: [PyMOL] 13th CCP4/APS Crystallographic School in the US

[Xu, Q. <qx...@an...>]

Dear colleagues,



Due to the on-going pandemic, the 2020 CCP4/APS workshop (originally scheduled for June 15-22, 2020) is postponed. We will try to schedule the workshop at a later date. If no suitable date is found, the event will be cancelled. Further notice will be announced in the CCP4 bulletin board.  In the meantime, the registration site remains open. We are sorry for the inconvenience.





The CCP4/APS school organizers


From: Xu, Qingping <qx...@an...>
Sent: Monday, January 6, 2020 12:04 PM
To: CC...@JI...; phe...@ph...; pym...@li...
Subject: 13th CCP4/APS Crystallographic School in the US


Dear Colleagues,

We are pleased to announce the 13th annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on June 15-22, 2020 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2020/index.php.

Dates: June 15 through 22, 2020

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA

The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website.

Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.

Application: Application deadline is April 1st, 2020. To apply, visit https://www.ccp4.ac.uk/schools/APS-2020/application.php<https://www.ccp4.ac.uk/schools/APS-2019/application.php>.

Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for industrial researchers. A valid credit card is required for registration, however, it will be charged only for students selected to participate. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals).


We hope to see you at the school.


Charles, Garib and Qingping

Re: [PyMOL] Compare two structures with the same connectivity butdifferent stereochemistry?

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

Hi Peng - 

You probably want to use `pair_fit` here, to align on a conserved core of atom pairs between the two models.  However, two complicating issues here are 1) equivalent atoms are not listed in the same order in the .mol2 files, and 2) they don't have atom names, which makes selecting them difficult.

To get around this within PyMOL, you can perform atom selection with atom IDs.  You can view the atom IDs for a selection with the command `label <selection>, ID`, and then use `pair_fit` to align atom pairs from the two molecules.

If you save the following code block as a PyMOL script called e.g. "align_mol2.pml" in the same directory as your .mol2 files, launch PyMOL from that directory (or "File > Working Directory > Change" into it), then run the command `@align_mol2.pml` at the PyMOL command line, it should do the trick.  You can choose different atom pairs to align, just be sure to list them in the right order.

```
load MOL002088.mol2, m2088
load MOL002424.mol2, m2424

hide everything, elem H
label visible, ID

python

# Alternate collected atom IDs between models
models = ['MOL002088', 'MOL002424']

# Gather atom IDs from the conserved core
atom_ids = [
    # 5-membered ring
    20, 13,
    19, 12,
    8, 8,
    3, 7,
    9, 14,
    # adjoining 6-membered ring
    29, 42,
    26, 43,
    18, 9,
]

# Combine model names and atom IDs into tuples
from itertools import cycle
zipped_atoms = zip(cycle(models), atom_ids)

# Create a string from each tuple in the zipped atoms list
atoms_str = [f'{x[0]} and id {x[1]}' for x in zipped_atoms]

# Align the atom pai
cmd.pair_fit(*atoms_str)

python end

```

One further note: your molecule 2424 has quite a few chemically unrealistic bond lengths and angles, so I urge you to interpret these models with caution.

Hope that helps.

Cheers,
Jared



From: Peng Yu <pen...@gm...>
Reply: Peng Yu <pen...@gm...>
Date: March 25, 2020 at 10:52:00 AM
To: sujiaqi <su...@im...>
Cc: pymol-users <pym...@li...>
Subject:  Re: [PyMOL] Compare two structures with the same connectivity butdifferent stereochemistry?  

It still very hard to see the differences and similarities. They just
look like a mess. Is there a good way to reveal the differences and
similarities? Are the stereochemistry of all the carbons different? It
seems that the best way is just to show the different ones.

On 3/24/20, sujiaqi <su...@im...> wrote:
> You can just input this command to deal with the problem.
>
> PyMOL>align MOL002088, MOL002424
> Match: read scoring matrix.
> Match: assigning 1 x 1 pairwise scores.
> MatchAlign: aligning residues (1 vs 1)...
> MatchAlign: score 5.000
> ExecutiveAlign: 93 atoms aligned.
> ExecutiveRMS: 2 atoms rejected during cycle 1 (RMSD=5.48).
> Executive: RMSD = 5.238 (91 to 91 atoms)
>
> From: Peng Yu
> Sent: 2020年3月25日 6:28
> To: pym...@li...
> Subject: [PyMOL] Compare two structures with the same connectivity
> butdifferent stereochemistry?
>
> I'd like to compare the difference between the two structures which
> have the same connectivity but different stereochemistry. Could
> anybody show me if there is a way to do so in pymol? Thanks.
>
> http://tcmspw.com/tcmspmol/MOL002088.mol2
> http://tcmspw.com/tcmspmol/MOL002424.mol2
>
> --
> Regards,
> Peng
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>


--  
Regards,
Peng


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Re: [PyMOL] Compare two structures with the same connectivity butdifferent stereochemistry?

[Peng Yu <pen...@gm...>]

It still very hard to see the differences and similarities. They just
look like a mess. Is there a good way to reveal the differences and
similarities? Are the stereochemistry of all the carbons different? It
seems that the best way is just to show the different ones.

On 3/24/20, sujiaqi <su...@im...> wrote:
> You can just input this command to deal with the problem.
>
> PyMOL>align MOL002088, MOL002424
>  Match: read scoring matrix.
>  Match: assigning 1 x 1 pairwise scores.
>  MatchAlign: aligning residues (1 vs 1)...
>  MatchAlign: score 5.000
>  ExecutiveAlign: 93 atoms aligned.
>  ExecutiveRMS: 2 atoms rejected during cycle 1 (RMSD=5.48).
>  Executive: RMSD =    5.238 (91 to 91 atoms)
>
> From: Peng Yu
> Sent: 2020年3月25日 6:28
> To: pym...@li...
> Subject: [PyMOL] Compare two structures with the same connectivity
> butdifferent stereochemistry?
>
> I'd like to compare the difference between the two structures which
> have the same connectivity but different stereochemistry. Could
> anybody show me if there is a way to do so in pymol? Thanks.
>
> http://tcmspw.com/tcmspmol/MOL002088.mol2
> http://tcmspw.com/tcmspmol/MOL002424.mol2
>
> --
> Regards,
> Peng
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>


-- 
Regards,
Peng

[PyMOL] Compare two structures with the same connectivity but different stereochemistry?

[Peng Yu <pen...@gm...>]

I'd like to compare the difference between the two structures which
have the same connectivity but different stereochemistry. Could
anybody show me if there is a way to do so in pymol? Thanks.

http://tcmspw.com/tcmspmol/MOL002088.mol2
http://tcmspw.com/tcmspmol/MOL002424.mol2

-- 
Regards,
Peng

Re: [PyMOL] [EXTERNAL] Re: broken DNA cartoon

[h. a. s. <h.a...@gm...>]

Well, thank you very much Blaine! That worked great!

> On Mar 22, 2020, at 10:01 AM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:
> 
> Hi Adam,
> 
> On my first attempt with Jared's commands, I pasted both for loops at the top PyMOL prompt with a semicolon between the commands.
> This failed because I created a Python syntax error. 
> 
> When I issued Jared's commands one at a time, they worked.
> 
> Alternatively, rewrite Jared's for loops as list comprehensions.
> Now you can paste the two list comprehensions separated by a semicolon at the PyMOL prompt.
> 
> [cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P") for i in range(1, 80)]; [cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P") for i in range(81, 160)]
> 
> This worked for me. I am using PyMOL 2.3.4, the incentive product, but it should work for older versions, even PyMOL 0.99.
> 
> You can issue many commands on one line if they are separated by semicolons. There are some restrictions and limitations.
> For more details, https://github.com/MooersLab/EasyPyMOL and https://www.ncbi.nlm.nih.gov/pubmed/27488983
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: h. adam steinberg [h.a...@gm...]
> Sent: Sunday, March 22, 2020 8:16 AM
> To: Jared Sampson
> Cc: pymol-users
> Subject: [EXTERNAL] Re: [PyMOL] broken DNA cartoon
> 
> Thank you Jared!
> 
> The commands didn’t work, but at least I now know why, and how to manually fix this.
> 
> On Mar 20, 2020, at 10:37 PM, Jared Sampson <jar...@co...<mailto:jar...@co...>> wrote:
> 
> Hi Adam -
> 
> That's a fun one.  It appears that most of these O3' atoms are not bonded to the P atom of the following nucleotide, which you can see if you show the DNA chains as sticks.  Creating a bond via `bond atom1, atom2` results in a normal cartoon.  Fortunately, the DNA chains are sequentially numbered, so you can do something like:
> 
> for i in range(1, 80): cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P")
> for i in range(81, 160): cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P")
> 
> The offending bond lengths are much longer than a typical P–O bond, which is why PyMOL's default distance-based bonding doesn't pick it up.
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> 
> 
> From: h. adam steinberg <h.a...@gm...><mailto:h.a...@gm...>
> Reply: h. adam steinberg <h.a...@gm...><mailto:h.a...@gm...>
> Date: March 20, 2020 at 9:59:45 PM
> To: pymol-users <pym...@li...><mailto:pym...@li...>
> Subject:  [PyMOL] broken DNA cartoon
> 
> Hi All,
> 
> When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken and mostly missing (it should span from left to right). Any ideas on how to get the cartoon to work?
> 
> Pymol version 2.3.4
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ZC2vp55wsN9oFwgr_7x8uTkJWSRtOjFf-57C6a5eaPE&s=KSnVSB_1bn5_DFbGDbFWEcHlPnycwLNU9F17YUusNjw&e=>
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> 

Re: [PyMOL] [EXTERNAL] Re: broken DNA cartoon

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

Hi Adam,

On my first attempt with Jared's commands, I pasted both for loops at the top PyMOL prompt with a semicolon between the commands.
This failed because I created a Python syntax error. 

When I issued Jared's commands one at a time, they worked.

Alternatively, rewrite Jared's for loops as list comprehensions.
Now you can paste the two list comprehensions separated by a semicolon at the PyMOL prompt.

[cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P") for i in range(1, 80)]; [cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P") for i in range(81, 160)]

This worked for me. I am using PyMOL 2.3.4, the incentive product, but it should work for older versions, even PyMOL 0.99.

You can issue many commands on one line if they are separated by semicolons. There are some restrictions and limitations.
For more details, https://github.com/MooersLab/EasyPyMOL and https://www.ncbi.nlm.nih.gov/pubmed/27488983

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: h. adam steinberg [h.a...@gm...]
Sent: Sunday, March 22, 2020 8:16 AM
To: Jared Sampson
Cc: pymol-users
Subject: [EXTERNAL] Re: [PyMOL] broken DNA cartoon

Thank you Jared!

The commands didn’t work, but at least I now know why, and how to manually fix this.

On Mar 20, 2020, at 10:37 PM, Jared Sampson <jar...@co...<mailto:jar...@co...>> wrote:

Hi Adam -

That's a fun one.  It appears that most of these O3' atoms are not bonded to the P atom of the following nucleotide, which you can see if you show the DNA chains as sticks.  Creating a bond via `bond atom1, atom2` results in a normal cartoon.  Fortunately, the DNA chains are sequentially numbered, so you can do something like:

for i in range(1, 80): cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P")
for i in range(81, 160): cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P")

The offending bond lengths are much longer than a typical P–O bond, which is why PyMOL's default distance-based bonding doesn't pick it up.

Hope that helps.

Cheers,
Jared



From: h. adam steinberg <h.a...@gm...><mailto:h.a...@gm...>
Reply: h. adam steinberg <h.a...@gm...><mailto:h.a...@gm...>
Date: March 20, 2020 at 9:59:45 PM
To: pymol-users <pym...@li...><mailto:pym...@li...>
Subject:  [PyMOL] broken DNA cartoon

Hi All,

When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken and mostly missing (it should span from left to right). Any ideas on how to get the cartoon to work?

Pymol version 2.3.4


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Re: [PyMOL] [EXTERNAL] broken DNA cartoon

[h. a. s. <h.a...@gm...>]

Thank you Blaine!

Now I know why, and how to manually fix this.

> On Mar 20, 2020, at 10:52 PM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:
> 
> The O3' to P bond lengths are 2.2 Angstroms when they should 1.6 Angstroms.
> This is outside the bond length range that PyMOL accepts so the bond is absent when you display the model as line or stick model.
> This is why the cartoon is missing or broken.
> 5FUR is a 8.5 Angstrom cryo EM structure.
> Perhaps the associated paper explains this discrepancy. 
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: h. adam steinberg [h.a...@gm...]
> Sent: Friday, March 20, 2020 8:57 PM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] broken DNA cartoon
> 
> Hi All,
> 
> When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken and mostly missing (it should span from left to right). Any ideas on how to get the cartoon to work?
> 
> Pymol version 2.3.4
> 
> 

Re: [PyMOL] broken DNA cartoon

[h. a. s. <h.a...@gm...>]

Thank you Jared!

The commands didn’t work, but at least I now know why, and how to manually fix this.

> On Mar 20, 2020, at 10:37 PM, Jared Sampson <jar...@co...> wrote:
> 
> Hi Adam - 
> 
> That's a fun one.  It appears that most of these O3' atoms are not bonded to the P atom of the following nucleotide, which you can see if you show the DNA chains as sticks.  Creating a bond via `bond atom1, atom2` results in a normal cartoon.  Fortunately, the DNA chains are sequentially numbered, so you can do something like:
> 
> for i in range(1, 80): cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P")
> for i in range(81, 160): cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P")
> 
> The offending bond lengths are much longer than a typical P–O bond, which is why PyMOL's default distance-based bonding doesn't pick it up.
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> 
> 
> From: h. adam steinberg <h.a...@gm...> <mailto:h.a...@gm...>
> Reply: h. adam steinberg <h.a...@gm...> <mailto:h.a...@gm...>
> Date: March 20, 2020 at 9:59:45 PM
> To: pymol-users <pym...@li...> <mailto:pym...@li...>
> Subject:  [PyMOL] broken DNA cartoon 
> 
>> Hi All,
>> 
>> When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken and mostly missing (it should span from left to right). Any ideas on how to get the cartoon to work?
>> 
>> Pymol version 2.3.4
>> 
>> 
>> _______________________________________________ 
>> PyMOL-users mailing list 
>> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...> 
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>

Re: [PyMOL] API for connect_mode

[Jake V. <jak...@gm...>]

Ah I see. So that setting is for setting how bonds are interpreted when
opening a PDB, the setting you are looking for is pdb_connect_all. Again,
the setting needs to be sent in as a string, as with most things using the
PyMol API.

I made a simple script to make sure it works:

from pymol import cmd
import sys
cmd.load(sys.argv[1])
cmd.set("pdb_conect_all", "on")
cmd.save(sys.argv[1][:-4] + "_With_Connect.pdb", "all")


Running the command "pymol -c script.py -- XXXX.pdb" will then generate the
file "XXXX_With_Connect.pdb".
Hope this is what you are looking for!


On Sat, Mar 21, 2020 at 8:14 PM Marcelo Depólo <mar...@gm...>
wrote:

> Hello there!
>
> I am running a python script within pymol and I am trying to set
> connect_mode to 1 by using:
>
> cmd.set(connect_mode,1)
>
> But pymol 1.8.4 does not recognize 'connect_mode' ("NameError: name
> 'connect_mode' is not defined")
>
> All I want is to save my .pdb file with the CONNECT section. Is there a
> way to do that not by hand?
>
> Cheers!
> --
> Marcelo Depólo Polêto
> Postdoctoral Researcher
> BIOAGRO - Room T07
> Department of General Biology - UFV
> Contact: + 55 31 3612-2464
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] API for connect_mode

[Marcelo D. <mar...@gm...>]

Hello there!

I am running a python script within pymol and I am trying to set
connect_mode to 1 by using:

cmd.set(connect_mode,1)

But pymol 1.8.4 does not recognize 'connect_mode' ("NameError: name
'connect_mode' is not defined")

All I want is to save my .pdb file with the CONNECT section. Is there a way
to do that not by hand?

Cheers!
--
Marcelo Depólo Polêto
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464

Re: [PyMOL] [EXTERNAL] broken DNA cartoon

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

The O3' to P bond lengths are 2.2 Angstroms when they should 1.6 Angstroms.
This is outside the bond length range that PyMOL accepts so the bond is absent when you display the model as line or stick model.
This is why the cartoon is missing or broken.
5FUR is a 8.5 Angstrom cryo EM structure.
Perhaps the associated paper explains this discrepancy. 

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: h. adam steinberg [h.a...@gm...]
Sent: Friday, March 20, 2020 8:57 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] broken DNA cartoon

Hi All,

When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken and mostly missing (it should span from left to right). Any ideas on how to get the cartoon to work?

Pymol version 2.3.4

Re: [PyMOL] broken DNA cartoon

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

Hi Adam - 

That's a fun one.  It appears that most of these O3' atoms are not bonded to the P atom of the following nucleotide, which you can see if you show the DNA chains as sticks.  Creating a bond via `bond atom1, atom2` results in a normal cartoon.  Fortunately, the DNA chains are sequentially numbered, so you can do something like:

for i in range(1, 80): cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P")
for i in range(81, 160): cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P")

The offending bond lengths are much longer than a typical P–O bond, which is why PyMOL's default distance-based bonding doesn't pick it up.

Hope that helps.

Cheers,
Jared



From: h. adam steinberg <h.a...@gm...>
Reply: h. adam steinberg <h.a...@gm...>
Date: March 20, 2020 at 9:59:45 PM
To: pymol-users <pym...@li...>
Subject:  [PyMOL] broken DNA cartoon  

Hi All,

When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken and mostly missing (it should span from left to right). Any ideas on how to get the cartoon to work?

Pymol version 2.3.4


_______________________________________________  
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Archives: http://www.mail-archive.com/pym...@li...  
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] broken DNA cartoon

[h. a. s. <h.a...@gm...>]

Hi All,

When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken and mostly missing (it should span from left to right). Any ideas on how to get the cartoon to work?

Pymol version 2.3.4

Re: [PyMOL] Selection of elements in object

[Marko H. <mh...@ca...>]

<html>
  <head>
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
  </head>
  <body>
    <tt>Hello Henrik, <br>
      <br>
      your syntax is not correct:<br>
      select name_for_selection, selected_parts<br>
      <a class="moz-txt-link-freetext" href="https://pymolwiki.org/index.php/Select">https://pymolwiki.org/index.php/Select</a><br>
      <br>
      eg. <br>
      select my_carbons, elem C &amp; obj <br>
      will select atoms that are element C AND in obj and calls this
      selection my_carbons. <br>
      <br>
      hth, Marko<br>
    </tt><br>
    <div class="moz-cite-prefix">On 20/03/2020 13:40, Henrik Gotfredsen
      wrote:<br>
    </div>
    <blockquote type="cite"
cite="mid:CAD...@ma...">
      <meta http-equiv="content-type" content="text/html; charset=UTF-8">
      <div dir="ltr">Dear Pymol users
        <div><br>
        </div>
        <div>Would anyone be able to help with the correct syntax used
          for selecting specific elements within an object?</div>
        <div><br>
        </div>
        <div>For example, I would like to be able to select only carbon
          or hydrogen. </div>
        <div><br>
        </div>
        <div>select elem c (works but selects all the carbons in my
          project)</div>
        <div>select elem c, obj (this selects all atoms within 'obj' as
          selection 'elem_c')</div>
        <div><br>
        </div>
        <div>Any suggestions are much appreciated :)</div>
        <div><br>
        </div>
        <div>Many thanks!</div>
        <div>Henrik </div>
      </div>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <pre class="moz-quote-pre" wrap="">_______________________________________________
PyMOL-users mailing list
Archives: <a class="moz-txt-link-freetext" href="http://www.mail-archive.com/pym...@li...">http://www.mail-archive.com/pym...@li...</a>
Unsubscribe: <a class="moz-txt-link-freetext" href="https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe">https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe</a></pre>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">-- 

Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
 

</pre>
  </body>
</html>

[PyMOL] Selection of elements in object

[Henrik G. <hen...@ch...>]

Dear Pymol users

Would anyone be able to help with the correct syntax used for selecting
specific elements within an object?

For example, I would like to be able to select only carbon or hydrogen.

select elem c (works but selects all the carbons in my project)
select elem c, obj (this selects all atoms within 'obj' as selection
'elem_c')

Any suggestions are much appreciated :)

Many thanks!
Henrik

[PyMOL] Accessibility Conformance Report

[William M. Jr <ma...@cl...>]

My university is aking me to provide the following information:


Please include an Accessibility Conformance Report (ACR) for this solution as an attachment<https://itsolutions.app.clemson.edu/assessments/submit.php?edit=1317#>. The vendor should be able to provide an ACR that meets the following criteria:

  *   The ACR should be based on a Voluntary Product Accessibility Template® (VPAT®) version 2.1 or higher, provided by the Industry Technology Industry Council<https://www.itic.org/policy/accessibility> (ITIC).
  *   The ACR should include conformance to Web Content Accessibility Guidelines<https://www.w3.org/TR/WCAG20/> (WCAG) version 2.0 levels A and AA.

Please advise
Bill Marcotte
________________________________
William R Marcotte Jr, PhD
Professor
Department of Genetics & Biochemistry
Clemson University
📞(864) 656-0119
📱(864) 328-4089
📠(864) 656-6879

[PyMOL] How to load ~/.pymolpluginsrc.py before finish_launching()?

[Pedro L. <psl...@gm...>]

Hi,

As the title says: How to load *~/.pymolpluginsrc.py* before
*finish_launching()*?

I didn't found an way to access saved preferences in library mode.

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

Re: [PyMOL] Accessing vertex normals from surface representation within PyMOL session

[Yang Su <su...@cr...>]

Hi Thomas,

I posted a somewhat related question here before:
https://sourceforge.net/p/pymol/mailman/message/36747359/

Basically, the idea is to get normals and tangents for the cartoon
representation so that one can show multiple overlapping peptides on the
structure. See the example image below. The method I posted in that
question relies on calculating these normal and tangent values by
duplicating pymol's code, which is an ugly hack with compatibility and
performance issues. It would be nice if pymol offers an official way to
show overlapping peptides.

[image: Overlapping_peptides.png]

Best,
Yang



On Tue, Feb 25, 2020 at 6:07 AM Thomas Holder <tho...@sc...>
wrote:

> Hi Jared,
>
> Apologies for the late reply. Unfortunately such an API doesn't exist. I
> agree that it would be very useful, I will file a feature request.
>
> Cheers,
>   Thomas
>
> > On Feb 14, 2020, at 9:20 PM, Jared Sampson <jar...@co...>
> wrote:
> >
> > Hi all -
> >
> > Is it possible to access surface triangle mesh position and normal
> values on a per-selection basis within a PyMOL session?  I know it's
> possible to get these by writing out and parsing .obj files, but to do this
> for an entire protein surface in a per-atom/residue fashion would be
> inefficient.  I imagine there must be a function to access this similar to
> "dump" for isosurfaces, but haven't been able to find it.
> >
> > Thanks a lot!
> >
> > Cheers,
> > Jared
> >
> > _______________________________________________
> > 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.
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe