pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Ways to show overlapping peptides on structure

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

Hello,

I'm exploring ways to show multiple overlapping peptides on a protein
structure (see the picture below for an example). Being able to show
overlapping peptides all at once on structure is highly desirable in the
field of hydrogen-deuterium exchange mass spectrometry and may be useful in
other fields, too, but I don't know any structure visualization program
capable of doing that. I'll explain how I made the example picture and the
problems/pitfalls with that approach, and would like to hear your
suggestions for how to improve or alternative approaches.

Example picture:
https://pymolwiki.org/index.php/File:Overlapping_peptides.png
[image: email.png]

What I've done was to first "de-overlap" the peptides, i.e., to sort the
peptides into separate groups so that every group contains non-overlapping
peptides only. Each group of non-overlapping peptides was then shown in the
usual way on a "track". From pymol's perspective, a track is really just an
ordinary structure (only backbone atoms, no sidechains); the coordinates of
the backbone atoms are carefully offset from the real structure of the
protein, so that when all the tracks are displayed, they look like forming
an integral structure --- and this is where things get hacky:

1)  I need to know the orientation-/normal-/tangent-vectors that pymol uses
to draw secondary structure elements. Those vectors are calculated from
atomic coordinates in pymol. With them I can back-calculate the coordinates
of each track's atoms such that when pymol reads these coordinates and
displays as cartoon, the secondary structure elements align nicely across
all tracks and the final result looks like one integral structure. The
problem is pymol does not provide APIs to get those vectors, so I ended up
having to duplicate the relevant logic from pymol's source code
(layer2/RepCartoon.cpp) in my code to calculate those vectors. And that
made my code tied to a specific version of pymol, neither forward- nor
backward-compatible. Whenever pymol changes the way those vectors are
calculated, my code breaks.

2)  With how pymol calculates those vectors (~November 2018), there are
corner cases where the conversion between atomic coordinates and those
vectors are not easily reversible (for some beta-strands), which caused
ugly twists in some tracks.

3)  Because the atoms in the tracks are offset from the real structure in
different directions, by different amounts, to make the cartoon look nice,
the distances between bonding atoms often became longer, and I had to
increase 'connect_cutoff' to keep them connected, which sometimes screwed
up other parts of the structure.

4)  For large structures with many tracks, the number of atoms that pymol
needs to handle becomes huge, and the impact to performance and file size
is appreciable.

So, the above summarized my current effort, which mostly works, although
with its many pitfalls/drawbacks. As I said, I'm looking forward to
suggestions, alternatives, or any other ways to approach the central
problem: to display overlapping peptides on a structure.

Thank you,
Yang

[PyMOL] label color

[Oganesyan, V. <vah...@as...>]

Hello PyMOLers,

In version 2.2.3 under Win upon ray-tracing label color changes. Is there a way to prevent that from happening?

Thank you.

Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics
____________________________________________________________________
AstraZeneca
R&D | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-4640  M:  240-398-0046
Vah...@as...<mailto:Oga...@me...>

Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

[Istvan K. <iko...@gm...>]

Yeping, not sure the question was addressed to me, but per the Pymol Align
wiki page the numbers you are referring to are

   1. RMSD after refinement
   2. Number of aligned atoms after refinement
   3. Number of refinement cycles
   4. RMSD before refinement
   5. Number of aligned atoms before refinement
   6. Raw alignment score
   7. Number of residues aligned

   Istvan

On Mon, Aug 19, 2019 at 11:16 PM sunyeping <sun...@al...> wrote:

> Hello Mat,
>
> Thank you for your reply.
> I followed your codes in the second line and get a series of output, which
> look like:
>
> (9.949092864990234, 267, 0, 9.949092864990234, 267, 420.0, 226)
>
> I guess the first and the fourth float numbers are the rmsd, but what are
> other numbers in the line?
>
> Best regards.
>
> Yeping
>
> ------------------------------------------------------------------
> From:Istvan Kolossvary <iko...@gm...>
> Sent At:2019 Aug. 20 (Tue.) 00:29
> To:Mateusz Bieniek <bie...@gm...>
> Cc:孙业平 <sun...@al...>; pymol-users <
> pym...@li...>
> Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD
> simulation trajectory and a reference structure?
>
> Superpose all states of an object to one of the states.
> print cmd.intra_fit("my-traj////CA", 1)Do the same, but this time the
> target/reference is a different object.
> for s in range(cmd.count_states()): print(cmd.align('my-traj', 'ref',
> mobile_state=s + 1, target_state=1, cycles=0, transform=0))
>
> On Mon, Aug 19, 2019 at 9:25 AM Mateusz Bieniek <bie...@gm...>
> wrote:
> There is also intra_rms and instra_fit commands:
> https://pymol.org/pymol-command-ref.html#intra_rms
> https://pymol.org/pymol-command-ref.html#intra_fit
>
> For example:
> intra_fit name CA and resid 1326-1350, 0
>
> Maybe they will be useful.
>
> Best, Mat
>
> On Mon, 19 Aug 2019 at 13:54, sunyeping <sun...@al...> wrote:
> Hello Mateusz,
>
> Thank you very much for your reply to my inquiry. Before I try the PyMOL
> extension you mentioned, I want to try scripting language in pymol. I wrote
> a attemptive one (align.py):
>
> cmd.load("A.gro")
> cmd.load("A.xtc")
> cmd.load("ref.pdb")
> for i in range(1, 5001):
>    cmd.align(ref, A,target_state=i)
>
> I ran it in pymol command line, but it doesn't work. I am new to pymol
> scripting. Could you write a correct one for me? Thank you very much.
>
> Best regards,
>
> Yeping
>
>
> ------------------------------------------------------------------
> From:Mateusz Bieniek <bie...@gm...>
> Sent At:2019 Aug. 19 (Mon.) 20:32
> To:孙业平 <sun...@al...>
> Cc:pymol-users <pym...@li...>
> Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD
> simulation trajectory and a reference structure?
>
> Hi Sunyeping,
>
> Besides using the scripting language in pymol, you might want to consider
> the experimental PyMOL extension created by the PyMOL Fellows (me and Paul
> Smith, https://pymol.org/fellowship/). The extension relies on the
> MDAnalysis package and so far includes RMSD as an example. Here is the link
> to the right github branch
> https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
>
> If you compile it, you can use the RMSD this way:
> mda_load systemX.gro
> mda_load_traj systemX.xtc
> mda_rmsd
>
>
> Kind Regards,
> Mateusz
>
>
> On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users <
> pym...@li...> wrote:
> Dear everyall,
>
> I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames
> and a reference structure (B.pdb) into pymol. I wish to get the rmsd value
> between each state of the MD simulation trajectory and the
> reference structure, but I don't know how. I can use the align command as:
> "align A, B", but this only gives one rmsd value. Could you tell me how to
> get the rmsd value between each state of the MD simulation trajectory and
> the reference structure?
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>

Re: [PyMOL] aberrant behavior of mouse clicks in PyMOL

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

Hi Vaheh,

Which version of PyMOL do you use? Could it be this issue? https://github.com/schrodinger/pymol-open-source/issues/35

Cheers,
  Thomas

> On Aug 21, 2019, at 10:04 PM, Oganesyan, Vaheh <vah...@as...> wrote:
> 
> Hi All,
>  
>  
> I’m experiencing very annoying behavior of mouse clicks when there are more than one molecule in ASU. Upon opening the window cartoon mode is showing. If I click on the part of first listed molecule then all look good. However, if I click on the part of the second molecule then another residue gets picked up from the first one. Now, if I do “show as cartoon” while it is already showing cartoon, then the behavior goes back to normal.
> Question: Do I have computer hardware issue, (personal hardware issue 😊), or this is a bug?
> Thank you.
>  
> Regards,
>  
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> ____________________________________________________________________
> AstraZeneca
> R&D | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T:  301-398-4640  M:  240-398-0046
> Vah...@as...
>  
>  
>  
> _______________________________________________
> 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] custom labels losing their colors on ray tracing [EXTERNAL]

[Rochtus, A. <Ann...@ch...>]

Please unsubscribe

Op 21-08-19 20:28 heeft Dyda via PyMOL-users <pym...@li...> geschreven:

    Hi Thomas,
    
    Thanks.
    
    In the meantime I figured that the problem was a larger than 0.0 setting of
    spec_direct that washes out the label colors.
    Setting it 0.0 solves it at a price of some image degradation.
    
    Fred
    ?[32m*******************************************************************************
    Fred Dyda, Ph.D.                       Phone:301-402-4496
    Laboratory of Molecular Biology        Fax: 301-496-0201
    DHHS/NIH/NIDDK                         e-mail:Fre...@ni...  
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[PyMOL] aberrant behavior of mouse clicks in PyMOL

[Oganesyan, V. <vah...@as...>]

Hi All,


I’m experiencing very annoying behavior of mouse clicks when there are more than one molecule in ASU. Upon opening the window cartoon mode is showing. If I click on the part of first listed molecule then all look good. However, if I click on the part of the second molecule then another residue gets picked up from the first one. Now, if I do “show as cartoon” while it is already showing cartoon, then the behavior goes back to normal.
Question: Do I have computer hardware issue, (personal hardware issue 😊), or this is a bug?
Thank you.

Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics
____________________________________________________________________
AstraZeneca
R&D | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-4640  M:  240-398-0046
Vah...@as...<mailto:Oga...@me...>

Re: [PyMOL] custom labels losing their colors on ray tracing

[Dyda <dy...@ul...>]

Hi Thomas,

Thanks.

In the meantime I figured that the problem was a larger than 0.0 setting of
spec_direct that washes out the label colors.
Setting it 0.0 solves it at a price of some image degradation.

Fred
*******************************************************************************
Fred Dyda, Ph.D.                       Phone:301-402-4496
Laboratory of Molecular Biology        Fax: 301-496-0201
DHHS/NIH/NIDDK                         e-mail:Fre...@ni...  
Bldg. 5. Room 303             
Bethesda, MD 20892-0560      URGENT message e-mail: 202...@mm...
Google maps coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
*******************************************************************************

Re: [PyMOL] HELIX and SHEET records not read by Pymol

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

Hi Thomas,

I have no idea why, but it seems to work for me when following
your instructions. Perhaps because I deleted everything except for the ATOM
records?

Thanks for looking into it!

Best wishes,
Chris

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On Wed, Aug 21, 2019 at 4:48 PM Thomas Holder <tho...@sc...>
wrote:

> Hi Chris,
>
> Works for me. Do you have an example file that doesn't work for you?
>
> "Works for me" steps to reproduce:
> - remove everything but ATOM records from 1ubq.pdb (raw.pdb)
> - run stride on raw.pdb
> - paste stride output on website
> - paste website result into PDB file (stride.pdb)
> - load stride.pdb and raw.pdb with PyMOL
> -> Result: Cartoons differ
>
> Cheers,
>   Thomas
>
> > On Aug 20, 2019, at 11:05 AM, Chris Fage <fa...@GM...> wrote:
> >
> > Dear All,
> >
> > Pymol seems to ignore the HELIX and SHEET records in my coordinate file,
> and instead assigns secondary structural features according to the default
> method. Unless my understanding is flawed, these records should override
> Pymol's assignment...?
> >
> > I generated the records with the Stride Web Interface and converted them
> to PDB format with Emma Rath's website (
> http://www.canoz.com/sdh/STRIDEtoPDBsecondarystruct.pl).
> >
> > Does anyone have any ideas? Thanks!
> >
> > Best wishes,
> > Chris
> >
> >       Virus-free. www.avg.com
> > _______________________________________________
> > 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] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

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

Hi Yeping,

The return value of cmd.align() is documented here:

https://pymolwiki.org/index.php/Align#PyMOL_API

Cheers,
  Thomas

> On Aug 20, 2019, at 5:15 AM, sunyeping via PyMOL-users <pym...@li...> wrote:
> 
> Hello Mat,
> 
> Thank you for your reply.
> I followed your codes in the second line and get a series of output, which look like:
> 
> (9.949092864990234, 267, 0, 9.949092864990234, 267, 420.0, 226)
> 
> I guess the first and the fourth float numbers are the rmsd, but what are other numbers in the line?
> 
> Best regards.
> 
> Yeping
> ------------------------------------------------------------------
> From:Istvan Kolossvary <iko...@gm...>
> Sent At:2019 Aug. 20 (Tue.) 00:29
> To:Mateusz Bieniek <bie...@gm...>
> Cc:孙业平 <sun...@al...>; pymol-users <pym...@li...>
> Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?
> 
> Superpose all states of an object to one of the states.
> print cmd.intra_fit("my-traj////CA", 1)Do the same, but this time the target/reference is a different object.
> for s in range(cmd.count_states()): print(cmd.align('my-traj', 'ref', mobile_state=s + 1, target_state=1, cycles=0, transform=0))
> 
> On Mon, Aug 19, 2019 at 9:25 AM Mateusz Bieniek <bie...@gm...> wrote:
> There is also intra_rms and instra_fit commands: 
> https://pymol.org/pymol-command-ref.html#intra_rms
> https://pymol.org/pymol-command-ref.html#intra_fit
> 
> For example:
> intra_fit name CA and resid 1326-1350, 0
> 
> Maybe they will be useful. 
> 
> Best, Mat
> 
> On Mon, 19 Aug 2019 at 13:54, sunyeping <sun...@al...> wrote:
> Hello Mateusz,
> 
> Thank you very much for your reply to my inquiry. Before I try the PyMOL extension you mentioned, I want to try scripting language in pymol. I wrote a attemptive one (align.py):
> 
> cmd.load("A.gro")
> cmd.load("A.xtc")
> cmd.load("ref.pdb")
> for i in range(1, 5001):
>    cmd.align(ref, A,target_state=i)
> 
> I ran it in pymol command line, but it doesn't work. I am new to pymol scripting. Could you write a correct one for me? Thank you very much.
> 
> Best regards,
> 
> Yeping 
> 
> 
> ------------------------------------------------------------------
> From:Mateusz Bieniek <bie...@gm...>
> Sent At:2019 Aug. 19 (Mon.) 20:32
> To:孙业平 <sun...@al...>
> Cc:pymol-users <pym...@li...>
> Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?
> 
> Hi Sunyeping,
> 
> Besides using the scripting language in pymol, you might want to consider the experimental PyMOL extension created by the PyMOL Fellows (me and Paul Smith, https://pymol.org/fellowship/). The extension relies on the MDAnalysis package and so far includes RMSD as an example. Here is the link to the right github branch https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
> 
> If you compile it, you can use the RMSD this way: 
> mda_load systemX.gro
> mda_load_traj systemX.xtc
> mda_rmsd 
> 
> 
> Kind Regards, 
> Mateusz
>  
> 
> On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users <pym...@li...> wrote:
> Dear everyall,
> 
> I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and a reference structure (B.pdb) into pymol. I wish to get the rmsd value between each state of the MD simulation trajectory and the reference structure, but I don't know how. I can use the align command as: "align A, B", but this only gives one rmsd value. Could you tell me how to get the rmsd value between each state of the MD simulation trajectory and the reference structure?
> _______________________________________________
> 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] HELIX and SHEET records not read by Pymol

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

Hi Chris,

Works for me. Do you have an example file that doesn't work for you?

"Works for me" steps to reproduce:
- remove everything but ATOM records from 1ubq.pdb (raw.pdb)
- run stride on raw.pdb
- paste stride output on website
- paste website result into PDB file (stride.pdb)
- load stride.pdb and raw.pdb with PyMOL
-> Result: Cartoons differ

Cheers,
  Thomas

> On Aug 20, 2019, at 11:05 AM, Chris Fage <fa...@GM...> wrote:
> 
> Dear All,
> 
> Pymol seems to ignore the HELIX and SHEET records in my coordinate file, and instead assigns secondary structural features according to the default method. Unless my understanding is flawed, these records should override Pymol's assignment...?
> 
> I generated the records with the Stride Web Interface and converted them to PDB format with Emma Rath's website (http://www.canoz.com/sdh/STRIDEtoPDBsecondarystruct.pl). 
> 
> Does anyone have any ideas? Thanks!
> 
> Best wishes,
> Chris
> 
> 	Virus-free. www.avg.com
> _______________________________________________
> 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] custom labels losing their colors on ray tracing

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

Hi Fred,

I can't reproduce this. Do you have a complete example?

This is how I tested it:

pseudoatom labelname, pos=[1,2,3], label=some_string
set label_color, red
ray
# -> label is red
set label_color, blue, labelname
ray
# -> label is blue
set label_color, green, (labelname)
ray
# -> label is green

Cheers,
  Thomas


> On Aug 19, 2019, at 7:32 PM, Dyda via PyMOL-users <pym...@li...> wrote:
> 
> 
> It appears that customs labels created with
> 
> pseudoatom labelname, pos=[x,y,z], label=some_string
> 
> lose their colors when the image is raytraced.
> 
> Does anyone know whether a workaround exist?
> 
> Thanks.
> 
> Fred
> *******************************************************************************
> Fred Dyda, Ph.D.                       Phone:301-402-4496
> Laboratory of Molecular Biology        Fax: 301-496-0201
> DHHS/NIH/NIDDK                         e-mail:Fre...@ni...  
> Bldg. 5. Room 303             
> Bethesda, MD 20892-0560      URGENT message e-mail: 202...@mm...
> Google maps coords: 39.000597, -77.102102
> http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
> *******************************************************************************
> 
> 
> _______________________________________________
> 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] HELIX and SHEET records not read by Pymol

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

Dear All,

Pymol seems to ignore the HELIX and SHEET records in my coordinate file,
and instead assigns secondary structural features according to the default
method. Unless my understanding is flawed, these records should override
Pymol's assignment...?

I generated the records with the Stride Web Interface and converted them to
PDB format with Emma Rath's website (
http://www.canoz.com/sdh/STRIDEtoPDBsecondarystruct.pl).

Does anyone have any ideas? Thanks!

Best wishes,
Chris

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Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

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

Hello Mat,

Thank you for your reply.
I followed your codes in the second line and get a series of output, which look like:

(9.949092864990234, 267, 0, 9.949092864990234, 267, 420.0, 226)

I guess the first and the fourth float numbers are the rmsd, but what are other numbers in the line?

Best regards.

Yeping
------------------------------------------------------------------
From:Istvan Kolossvary <iko...@gm...>
Sent At:2019 Aug. 20 (Tue.) 00:29
To:Mateusz Bieniek <bie...@gm...>
Cc:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

Superpose all states of an object to one of the states.
print cmd.intra_fit("my-traj////CA", 1)Do the same, but this time the target/reference is a different object.
for s in range(cmd.count_states()): print(cmd.align('my-traj', 'ref', mobile_state=s + 1, target_state=1, cycles=0, transform=0))
On Mon, Aug 19, 2019 at 9:25 AM Mateusz Bieniek <bie...@gm...> wrote:
There is also intra_rms and instra_fit commands: 
https://pymol.org/pymol-command-ref.html#intra_rms
https://pymol.org/pymol-command-ref.html#intra_fit

For example:
intra_fit name CA and resid 1326-1350, 0

Maybe they will be useful. 

Best, Mat
On Mon, 19 Aug 2019 at 13:54, sunyeping <sun...@al...> wrote:
Hello Mateusz,

Thank you very much for your reply to my inquiry. Before I try the PyMOL extension you mentioned, I want to try scripting language in pymol. I wrote a attemptive one (align.py):

cmd.load("A.gro")
cmd.load("A.xtc")
cmd.load("ref.pdb")
for i in range(1, 5001):
   cmd.align(ref, A,target_state=i)

I ran it in pymol command line, but it doesn't work. I am new to pymol scripting. Could you write a correct one for me? Thank you very much.

Best regards,

Yeping 


------------------------------------------------------------------
From:Mateusz Bieniek <bie...@gm...>
Sent At:2019 Aug. 19 (Mon.) 20:32
To:孙业平 <sun...@al...>
Cc:pymol-users <pym...@li...>
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

Hi Sunyeping,

Besides using the scripting language in pymol, you might want to consider the experimental PyMOL extension created by the PyMOL Fellows (me and Paul Smith, https://pymol.org/fellowship/). The extension relies on the MDAnalysis package and so far includes RMSD as an example. Here is the link to the right github branch https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018

If you compile it, you can use the RMSD this way: 
mda_load systemX.gro
mda_load_traj systemX.xtc
mda_rmsd 


Kind Regards, 
Mateusz

On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users <pym...@li...> wrote:
Dear everyall,

I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and a reference structure (B.pdb) into pymol. I wish to get the rmsd value between each state of the MD simulation trajectory and the reference structure, but I don't know how. I can use the align command as: "align A, B", but this only gives one rmsd value. Could you tell me how to get the rmsd value between each state of the MD simulation trajectory and the reference structure?_______________________________________________
 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] custom labels losing their colors on ray tracing

[Dyda <dy...@ul...>]

It appears that customs labels created with

pseudoatom labelname, pos=[x,y,z], label=some_string

lose their colors when the image is raytraced.

Does anyone know whether a workaround exist?

Thanks.

Fred
*******************************************************************************
Fred Dyda, Ph.D.                       Phone:301-402-4496
Laboratory of Molecular Biology        Fax: 301-496-0201
DHHS/NIH/NIDDK                         e-mail:Fre...@ni...  
Bldg. 5. Room 303             
Bethesda, MD 20892-0560      URGENT message e-mail: 202...@mm...
Google maps coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
*******************************************************************************

Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

[Istvan K. <iko...@gm...>]

Superpose all states of an object to one of the states.
print cmd.intra_fit("my-traj////CA", 1)Do the same, but this time the
target/reference is a different object.
for s in range(cmd.count_states()): print(cmd.align('my-traj', 'ref',
mobile_state=s + 1, target_state=1, cycles=0, transform=0))

On Mon, Aug 19, 2019 at 9:25 AM Mateusz Bieniek <bie...@gm...>
wrote:

> There is also intra_rms and instra_fit commands:
> https://pymol.org/pymol-command-ref.html#intra_rms
> https://pymol.org/pymol-command-ref.html#intra_fit
>
> For example:
> intra_fit name CA and resid 1326-1350, 0
>
> Maybe they will be useful.
>
> Best, Mat
>
> On Mon, 19 Aug 2019 at 13:54, sunyeping <sun...@al...> wrote:
>
>> Hello Mateusz,
>>
>> Thank you very much for your reply to my inquiry. Before I try the PyMOL
>> extension you mentioned, I want to try scripting language in pymol. I
>> wrote a attemptive one (align.py):
>>
>> cmd.load("A.gro")
>> cmd.load("A.xtc")
>> cmd.load("ref.pdb")
>> for i in range(1, 5001):
>>    cmd.align(ref, A,target_state=i)
>>
>> I ran it in pymol command line, but it doesn't work. I am new to pymol
>> scripting. Could you write a correct one for me? Thank you very much.
>>
>> Best regards,
>>
>> Yeping
>>
>>
>> ------------------------------------------------------------------
>> From:Mateusz Bieniek <bie...@gm...>
>> Sent At:2019 Aug. 19 (Mon.) 20:32
>> To:孙业平 <sun...@al...>
>> Cc:pymol-users <pym...@li...>
>> Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD
>> simulation trajectory and a reference structure?
>>
>> Hi Sunyeping,
>>
>> Besides using the scripting language in pymol, you might want to consider
>> the experimental PyMOL extension created by the PyMOL Fellows (me and Paul
>> Smith, https://pymol.org/fellowship/). The extension relies on the
>> MDAnalysis package and so far includes RMSD as an example. Here is the link
>> to the right github branch
>> https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
>>
>> If you compile it, you can use the RMSD this way:
>> mda_load systemX.gro
>> mda_load_traj systemX.xtc
>> mda_rmsd
>>
>>
>> Kind Regards,
>> Mateusz
>>
>>
>> On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users <
>> pym...@li...> wrote:
>> Dear everyall,
>>
>> I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000
>> frames and a reference structure (B.pdb) into pymol. I wish to get the rmsd
>> value between each state of the MD simulation trajectory and the
>> reference structure, but I don't know how. I can use the align command as:
>> "align A, B", but this only gives one rmsd value. Could you tell me how to
>> get the rmsd value between each state of the
>> MD simulation trajectory and the reference structure?
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
>> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

[Mateusz B. <bie...@gm...>]

There is also intra_rms and instra_fit commands:
https://pymol.org/pymol-command-ref.html#intra_rms
https://pymol.org/pymol-command-ref.html#intra_fit

For example:
intra_fit name CA and resid 1326-1350, 0

Maybe they will be useful.

Best, Mat

On Mon, 19 Aug 2019 at 13:54, sunyeping <sun...@al...> wrote:

> Hello Mateusz,
>
> Thank you very much for your reply to my inquiry. Before I try the PyMOL
> extension you mentioned, I want to try scripting language in pymol. I
> wrote a attemptive one (align.py):
>
> cmd.load("A.gro")
> cmd.load("A.xtc")
> cmd.load("ref.pdb")
> for i in range(1, 5001):
>    cmd.align(ref, A,target_state=i)
>
> I ran it in pymol command line, but it doesn't work. I am new to pymol
> scripting. Could you write a correct one for me? Thank you very much.
>
> Best regards,
>
> Yeping
>
>
> ------------------------------------------------------------------
> From:Mateusz Bieniek <bie...@gm...>
> Sent At:2019 Aug. 19 (Mon.) 20:32
> To:孙业平 <sun...@al...>
> Cc:pymol-users <pym...@li...>
> Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD
> simulation trajectory and a reference structure?
>
> Hi Sunyeping,
>
> Besides using the scripting language in pymol, you might want to consider
> the experimental PyMOL extension created by the PyMOL Fellows (me and Paul
> Smith, https://pymol.org/fellowship/). The extension relies on the
> MDAnalysis package and so far includes RMSD as an example. Here is the link
> to the right github branch
> https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
>
> If you compile it, you can use the RMSD this way:
> mda_load systemX.gro
> mda_load_traj systemX.xtc
> mda_rmsd
>
>
> Kind Regards,
> Mateusz
>
>
> On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users <
> pym...@li...> wrote:
> Dear everyall,
>
> I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames
> and a reference structure (B.pdb) into pymol. I wish to get the rmsd value
> between each state of the MD simulation trajectory and the
> reference structure, but I don't know how. I can use the align command as:
> "align A, B", but this only gives one rmsd value. Could you tell me how to
> get the rmsd value between each state of the MD simulation trajectory and
> the reference structure?
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>

Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

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

Hello Mateusz,

Thank you very much for your reply to my inquiry. Before I try the PyMOL extension you mentioned, I want to try scripting language in pymol. I wrote a attemptive one (align.py):

cmd.load("A.gro")
cmd.load("A.xtc")
cmd.load("ref.pdb")
for i in range(1, 5001):
   cmd.align(ref, A,target_state=i)

I ran it in pymol command line, but it doesn't work. I am new to pymol scripting. Could you write a correct one for me? Thank you very much.

Best regards,

Yeping 



------------------------------------------------------------------
From:Mateusz Bieniek <bie...@gm...>
Sent At:2019 Aug. 19 (Mon.) 20:32
To:孙业平 <sun...@al...>
Cc:pymol-users <pym...@li...>
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

Hi Sunyeping,

Besides using the scripting language in pymol, you might want to consider the experimental PyMOL extension created by the PyMOL Fellows (me and Paul Smith, https://pymol.org/fellowship/). The extension relies on the MDAnalysis package and so far includes RMSD as an example. Here is the link to the right github branch https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018

If you compile it, you can use the RMSD this way: 
mda_load systemX.gro
mda_load_traj systemX.xtc
mda_rmsd 


Kind Regards, 
Mateusz

On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users <pym...@li...> wrote:
Dear everyall,

I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and a reference structure (B.pdb) into pymol. I wish to get the rmsd value between each state of the MD simulation trajectory and the reference structure, but I don't know how. I can use the align command as: "align A, B", but this only gives one rmsd value. Could you tell me how to get the rmsd value between each state of the MD simulation trajectory and the reference structure?_______________________________________________
 PyMOL-users mailing list
 Archives: http://www.mail-archive.com/pym...@li...
 Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

[Mateusz B. <bie...@gm...>]

Hi Sunyeping,

Besides using the scripting language in pymol, you might want to consider
the experimental PyMOL extension created by the PyMOL Fellows (me and Paul
Smith, https://pymol.org/fellowship/). The extension relies on the
MDAnalysis package and so far includes RMSD as an example. Here is the link
to the right github branch
https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018

If you compile it, you can use the RMSD this way:
mda_load systemX.gro
mda_load_traj systemX.xtc
mda_rmsd


Kind Regards,
Mateusz


On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users <
pym...@li...> wrote:

> Dear everyall,
>
> I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames
> and a reference structure (B.pdb) into pymol. I wish to get the rmsd value
> between each state of the MD simulation trajectory and the
> reference structure, but I don't know how. I can use the align command as:
> "align A, B", but this only gives one rmsd value. Could you tell me how to
> get the rmsd value between each state of the MD simulation trajectory and
> the reference structure?
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

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

Dear everyall,

I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and a reference structure (B.pdb) into pymol. I wish to get the rmsd value between each state of the MD simulation trajectory and the reference structure, but I don't know how. I can use the align command as: "align A, B", but this only gives one rmsd value. Could you tell me how to get the rmsd value between each state of the MD simulation trajectory and the reference structure?

[PyMOL] Custom plugin requirements

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

Hi,

Did you know the R function install.packages() or its cousin
devtools::install_github()?

The devtools::install_github() is a function provided by the RStudio
environment. RStudio in this context would be akin to PyMOL, a software for
final users in general.

install.packages() is provided by R itself.

Both are capable to install custom libraries directly into the user's
environment.

If PyMOL had some function like that any developer could share its plugins
without the burden that is right now.

Would be a neat function and not very tricky either.

Maybe install_package(CONDA, "scikit-learn") or install_package(PIP,
"requests"). And then run these after import pymol, but before the
remaining imports.

Or maybe some special variable like __REQUIREMENTS__ = {"conda": "lxml"}
would be possible also. Of course would not be possible to run the file
before evaluating the variable, the ast module would work nice for this.

I never saw nothing like that for any software except R, RStudio or Golang,
but would be a great addition for PyMOL, and a very easy one. Just import
the conda and pip API and fetch the packages. But in my opinion it is very
clever.

The commercial version of PyMOL is already shipped with its own version of
Python (and conda I guess). But would not be that messy for user local pip
packages, after all is for this kind of reason to encourage user local
packages instead of system wide.

What do you think?

Best wishes,
Have a great weekend,
Pedro Lacerda

Re: [PyMOL] How to download and install

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

It is very hard!

I give up last week and installed the trial version to show some session to
my coworkers.

And only PyMOL is installed, there isn't anything like install.packaged()
from R, so I can't even share my commands with custom requirements to them.

Em qui, 15 de ago de 2019 19:46, Joel Tyndall <joe...@ot...>
escreveu:

> Details of where to get the appropriate files are available here.
>
>
>
> https://pymolwiki.org/index.php/Windows_Install
>
>
>
> With a little bit of tinkering I was able to install this
>
>
>
> J
>
>
>
> *From:* Pedro Lacerda <psl...@gm...>
> *Sent:* Wednesday, 14 August 2019 11:22 PM
> *To:* pym...@li...
> *Subject:* [PyMOL] How to download and install
>
>
>
> Hi,
>
>
>
> I'm unable to build or download and install PyMOL for Windows for free in
> our laboratory.
>
>
>
> How can I find a valid license or a free build? Don't need all the
> features of the professional version, but would be very useful.
>

Em qui, 15 de ago de 2019 19:46, Joel Tyndall <joe...@ot...>
escreveu:

> Details of where to get the appropriate files are available here.
>
>
>
> https://pymolwiki.org/index.php/Windows_Install
>
>
>
> With a little bit of tinkering I was able to install this
>
>
>
> J
>
>
>
> *From:* Pedro Lacerda <psl...@gm...>
> *Sent:* Wednesday, 14 August 2019 11:22 PM
> *To:* pym...@li...
> *Subject:* [PyMOL] How to download and install
>
>
>
> Hi,
>
>
>
> I'm unable to build or download and install PyMOL for Windows for free in
> our laboratory.
>
>
>
> How can I find a valid license or a free build? Don't need all the
> features of the professional version, but would be very useful.
>

Re: [PyMOL] Label volume

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

Hi Thomas,

Cool, I did something like that, copied the selection "%obj and index 1"
then labeled it. So I got an independent label.

Multi-line labels was somewhat hackish:

cmd.label(
    label_obj_name,
    '"' + "\\n".join([
        f'ID {i}',
        f'Class {ensemble.klass}',
        f'S {ensemble.strength}',
    ]) + '"'
)


I give up of volumes right now because I didn't figured out how to align
them. The behaviour I wanted was achieved with an "pseudo" atom.

Cheers,

Em qui, 15 de ago de 2019 às 05:49, Thomas Holder <
tho...@sc...> escreveu:

> Hi Pedro,
>
> it's only possible to label atoms. If you need an independent label,
> create a pseudo atom:
>
> pseudoatom label="Hello World"
>
> You can move the atom (or the label) in 3-Button Editing mouse mode while
> holding CTRL and dragging with the left mouse button.
>
> Cheers,
>   Thomas
>
> > On Aug 12, 2019, at 7:01 PM, Pedro Lacerda <psl...@gm...> wrote:
> >
> > And how to place a single arbitrary label on the object or segment?
> >
> > Em seg, 12 de ago de 2019 às 13:55, Pedro Lacerda <psl...@gm...>
> escreveu:
> > Hi PyMOL list,
> >
> > Is possible toshow  a label independent of the associated object be
> enabled?
> >
> > Or is possible to label a volume or map?
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> >
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > _______________________________________________
> > 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.
>
>

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] count_atoms and states

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

Hi,

Thank you for your effort.

This would be the very best option? Thinking the use case that users need
all the states would be a lot harder.

I would rather let state 0 refer to all the states like now, but upper
nonexistent states give an error. This would remove some errors by 1, and
would work as is for single state objects.

Em qui, 15 de ago de 2019 05:56, Thomas Holder <
tho...@sc...> escreveu:

>
> > On Aug 12, 2019, at 2:56 PM, Christian Cole French <
> chr...@sc...> wrote:
> >
> > Maybe the nonexistent state warning is something that should be
> implemented elsewhere as well.
>
> Selecting state 0 is now an error:
>
>
> https://github.com/schrodinger/pymol-open-source/commit/c09ce287d447e6c703e57d31ae3e5d53f8359ee1
>
> Cheers,
>   Thomas
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Re: [PyMOL] count_atoms and states

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

> On Aug 12, 2019, at 2:56 PM, Christian Cole French <chr...@sc...> wrote:
> 
> Maybe the nonexistent state warning is something that should be implemented elsewhere as well.

Selecting state 0 is now an error:

https://github.com/schrodinger/pymol-open-source/commit/c09ce287d447e6c703e57d31ae3e5d53f8359ee1

Cheers,
  Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Label volume

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

Hi Pedro,

it's only possible to label atoms. If you need an independent label, create a pseudo atom:

pseudoatom label="Hello World"

You can move the atom (or the label) in 3-Button Editing mouse mode while holding CTRL and dragging with the left mouse button.

Cheers,
  Thomas

> On Aug 12, 2019, at 7:01 PM, Pedro Lacerda <psl...@gm...> wrote:
> 
> And how to place a single arbitrary label on the object or segment?
> 
> Em seg, 12 de ago de 2019 às 13:55, Pedro Lacerda <psl...@gm...> escreveu:
> Hi PyMOL list,
> 
> Is possible toshow  a label independent of the associated object be enabled?
> 
> Or is possible to label a volume or map?
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> _______________________________________________
> 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.