pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] CASTp

[Vitali J. <jir...@gm...>]

Dear PyMOl users

Can you please help to know how to view the data downloaded from the CASTp
server.
I install the plugin but cant view the data obtained from the CASTp
http://sts.bioe.uic.edu/castp/index.html?3igg

best
James

Re: [PyMOL] Visualisation clashed structures

[Magnus, M. <mm...@fa...>]

Hey,

(I sent the structure in the second e-mail as a zip file, but apparently, the Harvard mail system blocked it)

I also understood what was going on. The structure [2] is a very raw, early stage of our simulation, full of clashes (and the file has no CONECT in it).

When I `set connect_mode, 1` [1] ( = CONECT records), I don’t see any bonds (which makes sense, as there is no CONECT in my PDB file) and PyMOL does not calculate bonds and loads the structure immediately!

Thus, the fix is to `set connect_mode, 1` and use explicit CONECT in my file or load file without CONECT  and use Surface representation to get insights into what’s going on (and calculate RMSD, etc.).

Thanks, the issue is solved.

Magnus

[1] https://pymolwiki.org/index.php/Connect_mode
[2] https://www.dropbox.com/t/kz4LISig75hlwCMj
[sc 2024-10-31 at 12.58.22 2.jpg.jpeg]

Re: [PyMOL] Visualisation clashed structures

[Magnus, M. <mm...@fa...>]

Interestingly,

set auto_show_classified, off

is the best way to solve it (the Line representation works)!

Magnus

[sc 2024-10-31 at 18.56.17.jpeg]

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

Re: [PyMOL] Visualisation clashed structures

[Jarrett J. <jar...@sc...>]

Hello,

Hard to say at first glance, but it may be easier to postulate if we have
an example file that hangs.

Best,
Jarrett J

On Wed, Oct 30, 2024 at 7:57 PM Magnus, Marcin <mm...@fa...>
wrote:

> Hey,
>
> I’m working a new method for RNA 3D structure prediction. And yeah, I see
> that the structure is a mess, but I want to be able to load the structure
> into PyMOL. I can do that with Chimera, but PyMOL apparently is trying to
> do something, and this something takes forever to load the model. I love
> PyMOL and have lots of my own plugins to work with RNA 3D structures, I
> would love to be able to use PyMOL for analysis what’s going on in here.
>
> Any ideas, hints, why it takes so long to load it. Is it that PyMOL is
> calculcate bonds between all the atoms and it’s getting overwhelmed but
> this mess?
>
> Any hints are welocome,
>
> Magnus
>
> Elena Rivas lab, MCB, Harvard
> mm...@fa...
> https://mmagnus.github.io/
>
> [image: sc 2024-10-30 at 13.27.07.jpeg.jpeg]
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] Visualisation clashed structures

[Magnus, M. <mm...@fa...>]

Hey,

I’m working a new method for RNA 3D structure prediction. And yeah, I see that the structure is a mess, but I want to be able to load the structure into PyMOL. I can do that with Chimera, but PyMOL apparently is trying to do something, and this something takes forever to load the model. I love PyMOL and have lots of my own plugins to work with RNA 3D structures, I would love to be able to use PyMOL for analysis what’s going on in here.

Any ideas, hints, why it takes so long to load it. Is it that PyMOL is calculcate bonds between all the atoms and it’s getting overwhelmed but this mess?

Any hints are welocome,

Magnus

Elena Rivas lab, MCB, Harvard
mm...@fa...<mailto:mm...@fa...>
https://mmagnus.github.io/

[sc 2024-10-30 at 13.27.07.jpeg.jpeg]

[PyMOL] local resolution map

[jp d <yo...@ya...>]

hi,
is it possible to use the local resolution maps from cryosparc
in pymol ?
specifically we want to color the primary map based on the
local resolution map.

thanks
jpd

Re: [PyMOL] 16th Annual CCP4/APS Crystallographic School (2024) in the US

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

A couple seats have become available. If you're  in the U.S., particularly an existing APS user, and are interested in attending, please get in touch with us.

Charles, Andrey, Garib and Qingping

________________________________

Subject: 16th Annual CCP4/APS Crystallographic School (2024) in the US

Dear Colleagues,

We are pleased to announce the 16th annual CCP4/APS crystallographic
school “From data collection to structure refinement and beyond” will be
held on Oct 28th to Nov 4th, 2024 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-2024/index.php. This will be our first
work post the APS-U upgrade.


Dates: October 28 through November 4, 2024

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near

Chicago), Illinois, USA

The school comprises two parts: data collection (provisional pending APS
availability) workshop and crystallographic computing workshop. Data
collection workshop includes beamline training, data collection on
GM/CA@APS beamlines, and data processing, using only the participants'
crystals. Crystallographic computation workshop will feature many modern
crystallographic software packages taught by authors and other experts.
This workshop will also introduce elements of CryoEM. 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 draft
program can be found at the School website.

Applicants: The workshop strongly encourages students who need expert
help with difficulties/challenges in their own projects. 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.

Application: Application deadline is  August 31st, 2024. To apply,
visit  https://www.ccp4.ac.uk/schools/APS-2024/application.php

Fees: There is a $500 participation fee for the selected academic
students and $1500 for industrial researchers. No credit card will be
required for registration, students who are selected to participate will
be contacted to pay. 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, Andrey, Garib and Qingping


________________________________
From: Xu, Qingping
Sent: Monday, April 8, 2024 1:26 PM
To: CC...@JI... <CC...@JI...>; phe...@ph... <phe...@ph...>; pym...@li... <pym...@li...>
Subject: 16th Annual CCP4/APS Crystallographic School (2024) in the US

Dear Colleagues,

We are pleased to announce the 16th annual CCP4/APS crystallographic
school “From data collection to structure refinement and beyond” will be
held on Oct 28th to Nov 4th, 2024 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-2024/index.php. This will be our first
work post the APS-U upgrade.


Dates: October 28 through November 4, 2024

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near

Chicago), Illinois, USA

The school comprises two parts: data collection (provisional pending APS
availability) workshop and crystallographic computing workshop. Data
collection workshop includes beamline training, data collection on
GM/CA@APS beamlines, and data processing, using only the participants'
crystals. Crystallographic computation workshop will feature many modern
crystallographic software packages taught by authors and other experts.
This workshop will also introduce elements of CryoEM. 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 draft
program can be found at the School website.

Applicants: The workshop strongly encourages students who need expert
help with difficulties/challenges in their own projects. 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.

Application: Application deadline is  August 31st, 2024. To apply,
visit  https://www.ccp4.ac.uk/schools/APS-2024/application.php

Fees: There is a $500 participation fee for the selected academic
students and $1500 for industrial researchers. No credit card will be
required for registration, students who are selected to participate will
be contacted to pay. 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, Andrey, Garib and Qingping

[PyMOL] STL file scale

[P C <pet...@gm...>]

Apologies for what might be a trivial question: does Pymol use some
standard scale when saving stl files? I will be trying to 3D print a couple
of separate protein structures, which need to be at a consistent scale so
that they can be compared/combined. Apparently Chimera saves stl files such
that they are at 1E7 magnification, when printed at 100% scale (
https://munfred.com/proteins.pdf). Does Pymol follow the same (or other
standard) convention?

Peter

Re: [PyMOL] [pymol] Assembly

[Norbert S. <st...@bb...>]

Dear Matthias,

use:

set assembly, 1
set all_states, 1
fetch 7epp

GUI "generate symmetry mates" does not work as the unit cell is defined as:
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1
resulting in symmetry mates shifted by 1.0 Ang. in x y z.

We need a "generate biological assembly" command.

Best,

Norbert

Am 22.09.2024 um 12:02 schrieb Matthias Mayer:
> To whom it may concern,
>
> I wanted to load a cryoEM structure of a virus-like particle 
> (7epp.pdb1) into pymol 2.5.0. But instead of showing all the subunits, 
> when I open the file, it makes a movie out of it with individual 
> framesIs there a way to prevent this and just show the entire assembly?
>
> Also when I used the single file 7epp.cif and used the command 
> generate symmetry mates, it makes weird things, overlaying all the 
> structures with only a small translational offset and not rotation.
>
> Thanks for any suggestions.
>
> Best regards
>
> Matthias
>

Re: [PyMOL] [pymol] Assembly

[Joel S. <mjs...@al...>]

Hi Matthias, try dragging the pdb file into the center of the Pymol Viewing
screen, thanks:)

On Sun, Sep 22, 2024 at 12:21 PM Matthias Mayer <
m....@zm...> wrote:

> To whom it may concern,
>
> I wanted to load a cryoEM structure of a virus-like particle (7epp.pdb1)
> into pymol 2.5.0. But instead of showing all the subunits, when I open
> the file, it makes a movie out of it with individual framesIs there a
> way to prevent this and just show the entire assembly?
>
> Also when I used the single file 7epp.cif and used the command generate
> symmetry mates, it makes weird things, overlaying all the structures
> with only a small translational offset and not rotation.
>
> Thanks for any suggestions.
>
> Best regards
>
> Matthias
>
> --
> =============================================================
> Prof. Dr. Matthias P. Mayer, SFCSSI
> Center for Molecular Biology of Heidelberg University (ZMBH)
> Im Neuenheimer Feld 345, room 161
> D-69120 Heidelberg
> Germany
>
> Tel. +49 6221 546829
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

[PyMOL] [pymol] Assembly

[Matthias M. <m....@zm...>]

To whom it may concern,

I wanted to load a cryoEM structure of a virus-like particle (7epp.pdb1) 
into pymol 2.5.0. But instead of showing all the subunits, when I open 
the file, it makes a movie out of it with individual framesIs there a 
way to prevent this and just show the entire assembly?

Also when I used the single file 7epp.cif and used the command generate 
symmetry mates, it makes weird things, overlaying all the structures 
with only a small translational offset and not rotation.

Thanks for any suggestions.

Best regards

Matthias

-- 
=============================================================
Prof. Dr. Matthias P. Mayer, SFCSSI
Center for Molecular Biology of Heidelberg University (ZMBH)
Im Neuenheimer Feld 345, room 161
D-69120 Heidelberg
Germany

Tel. +49 6221 546829

Re: [PyMOL] [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

[Joel S. <mjs...@al...>]

Hello Crystallographic School please keep me in mind if in need of any
instructors, profile below in bold and attached, thanks:), Joel 🚀

*Hello HR I hope you're well:).*




*I am a 56 year old American Rutgers University PhD in Biomedical
Informatics/Nanomedicine exhibiting expertise in ion channel Pannexin1
computational transmembrane protein design towards pharmacophore ligand
discovery and am interested in the above position.SInce my PhD graduation
in 2020 I have been computationally investigating Panx1 and completed its
molecular modeling and am now optimizing the best ligand i.e. QM via ORCA.*


*Best,*

*Joel 🚀*

On Thu, Aug 15, 2024 at 10:04 PM Xu, Qingping via PyMOL-users <
pym...@li...> wrote:

> Please note that we are still accepting applications, interested students
> are encouraged to apply before the deadline. A draft program is available
> at the course website.
>
> Charles, Andrey and Qingping
>
> ------------------------------
> *From:* CCP4 bulletin board <CC...@JI...> on behalf of Qingping
> Xu <000...@JI...>
> *Sent:* Monday, April 8, 2024 1:26 PM
> *To:* CC...@JI... <CC...@JI...>
> *Subject:* [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024)
> in the US
>
> This Message Is From an External Sender
> This message came from outside your organization.
>
>
> Dear Colleagues,
>
> We are pleased to announce the 16th annual CCP4/APS crystallographic
> school “From data collection to structure refinement and beyond” will be
> held on Oct 28th to Nov 4th, 2024 at the Advanced Photon Source (APS),
> Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All
> details can be found at the school website: https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2024/index.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RU9QBjAs8$. This will be our first
> work post the APS-U upgrade.
>
>
> Dates: October 28 through November 4, 2024
>
> Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near
>
> Chicago), Illinois, USA
>
> The school comprises two parts: data collection (provisional pending APS
> availability) workshop and crystallographic computing workshop. Data
> collection workshop includes beamline training, data collection on
> GM/CA@APS beamlines, and data processing, using only the participants'
> crystals. Crystallographic computation workshop will feature many modern
> crystallographic software packages taught by authors and other experts.
> This workshop will also introduce elements of CryoEM. The daily schedule
> will be organized in three sections – lectures, tutorials, and hands-on
> (interactive trouble-shooting of the technical difficulties the
> participants face in their projects). We have had considerable success
> resolving these problems in past years, attested by resulting
> publications (see https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUPTfq2LA$). A draft
> program can be found at the School website.
>
> Applicants: The workshop strongly encourages students who need expert
> help with difficulties/challenges in their own projects. 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.
>
> Application: Application deadline is  August 31st, 2024. To apply,
> visit  https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2024/application.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUhRwAcxE$
>
> Fees: There is a $500 participation fee for the selected academic
> students and $1500 for industrial researchers. No credit card will be
> required for registration, students who are selected to participate will
> be contacted to pay. The students will be responsible for their
> transportation and lodging. The workshop organizers can assist in making
> lodging reservations at the Argonne Guest House. The workshop will cover
> all other expenses (including meals).
>
>
> We hope to see you at the school.
>
> Charles, Andrey, Garib and Qingping
>
> ########################################################################
>
> To unsubscribe from the CCP4BB list, click the following link:https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUtJdGhk8$
>
> This message was issued to members of https://urldefense.us/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUIlqrIeo$, a mailing list hosted by https://urldefense.us/v3/__http://www.jiscmail.ac.uk__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUyfFpMcY$, terms & conditions are available at https://urldefense.us/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUuFJW2bU$
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Re: [PyMOL] [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

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

Please note that we are still accepting applications, interested students are encouraged to apply before the deadline. A draft program is available at the course website.

Charles, Andrey and Qingping

________________________________
From: CCP4 bulletin board <CC...@JI...> on behalf of Qingping Xu <000...@JI...>
Sent: Monday, April 8, 2024 1:26 PM
To: CC...@JI... <CC...@JI...>
Subject: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

This Message Is From an External Sender
This message came from outside your organization.


Dear Colleagues,

We are pleased to announce the 16th annual CCP4/APS crystallographic
school “From data collection to structure refinement and beyond” will be
held on Oct 28th to Nov 4th, 2024 at the Advanced Photon Source (APS),
Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All
details can be found at the school website:
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2024/index.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RU9QBjAs8$. This will be our first
work post the APS-U upgrade.


Dates: October 28 through November 4, 2024

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near

Chicago), Illinois, USA

The school comprises two parts: data collection (provisional pending APS
availability) workshop and crystallographic computing workshop. Data
collection workshop includes beamline training, data collection on
GM/CA@APS beamlines, and data processing, using only the participants'
crystals. Crystallographic computation workshop will feature many modern
crystallographic software packages taught by authors and other experts.
This workshop will also introduce elements of CryoEM. 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
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUPTfq2LA$). A draft
program can be found at the School website.

Applicants: The workshop strongly encourages students who need expert
help with difficulties/challenges in their own projects. 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.

Application: Application deadline is  August 31st, 2024. To apply,
visit  https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2024/application.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUhRwAcxE$

Fees: There is a $500 participation fee for the selected academic
students and $1500 for industrial researchers. No credit card will be
required for registration, students who are selected to participate will
be contacted to pay. 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, Andrey, Garib and Qingping

########################################################################

To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUtJdGhk8$

This message was issued to members of https://urldefense.us/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUIlqrIeo$, a mailing list hosted by https://urldefense.us/v3/__http://www.jiscmail.ac.uk__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUyfFpMcY$, terms & conditions are available at https://urldefense.us/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUuFJW2bU$

[PyMOL] no interpolation between some scenes wanted

[Georg M. <geo...@un...>]

Dear Pymol community, I am trying since hours to turn off the 
interpolation for a few scenes in my script.

However I am just able to turn off interpolation totally by using "mview 
uninterpolate" at the end of the script.

Writing "scene 001, animate=0" seems to be obsolete.

Also using mview .... , cut=1.0 and other keywords from mview which 
should stop or change interpolation are not working. 
https://pymolwiki.org/index.php/Mview

This would be a testing script:

reinitialize
load $TUT/1hpv.pdb
util.cbc
turn x,180
orient
as cartoon
scene 001, store

show sticks, organic
orient organic
scene 002, store

hide cartoon
show lines, byres organic expand 5
turn x,45
turn y,45
scene 003, store

# 2) Specify a 30-second movie -- state 1, 900 frames at 30 frames per 
second.

mset 1 x900

mview store, 1, scene=001
mview store, 240, scene=001


turn y,-30
mview store, 70, cut=1.0
turn y,60
mview store, 170, cut=1.0


mview store, 300, scene=002
mview store, 540, scene=002

turn y,-30
mview store, 370
turn y,60
mview store, 470


mview store, 600, scene=003
mview store, 840, scene=003

turn y,-30
mview store, 670
turn y,60
mview store, 770


Many thanks in advance for any tips, br Georg.

Re: [PyMOL] Deprecation of MMTF-format files for the PDB archive

[Robert H. <ha...@st...>]

Jose, I have a few questions about the BCIF format. Adding pymol-users
because there might be interest there as well (at least among developers).

First, at PDBe, where is the link for downloading BCIF files for a given
structure?

I only see this, for example, at  https://www.ebi.ac.uk/pdbe/entry/pdb/4hhb
[image: image.png]
Any plan to include BCIF there?

Second, I am not finding a definitive description of distinguishing among
MMFF and various types of BCIF files, since the same internal MessagePack
format is used for all.

Is there a reliable and future-proof way of doing this short of parsing the
whole byte stream with a MessagePack reader and checking for map keys or
values? That does not seem to me a very efficient way of processing byte
streams.

I had thought perhaps the initial map value for "encoder" would suffice,
but now I see that that is not reliable. For example, the density server
declaration in older BCIF files now refers to "volume-server".

Suggestions?

Bob

[PyMOL] Antw: Re: .phs files in pymol

[Urban L. <urb...@bo...>]

Thank you so much!

Best, 
Urban 
>>> Takanori Nakane <tna...@os...> 30/07/2024 13:01 >>>
Hi,

Open the map in Coot and select [File]-[Export Map].
This allows you to save the map in .ccp4 (= .mrc)
format, which PyMOL can read.

Best regards,

Takanori Nakane

On 7/30/24 20:17, Urban Leitgeb via PyMOL-users wrote:
> Hi,
> 
> I calculated anomalous difference maps with shelx and got .phs 
> files as output. I can open them in coot, but not in pymol.
> I have read that I have to convert them to .mtz or rather calculate 
> a map. Can anyone tell me how to do that?
> 
> Thanks,
> Urban
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...

> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] .phs files in pymol

[Takanori N. <tna...@os...>]

Hi,

Open the map in Coot and select [File]-[Export Map].
This allows you to save the map in .ccp4 (= .mrc)
format, which PyMOL can read.

Best regards,

Takanori Nakane

On 7/30/24 20:17, Urban Leitgeb via PyMOL-users wrote:
> Hi,
> 
> I calculated anomalous difference maps with shelx and got .phs 
> files as output. I can open them in coot, but not in pymol.
> I have read that I have to convert them to .mtz or rather calculate 
> a map. Can anyone tell me how to do that?
> 
> Thanks,
> Urban
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] .phs files in pymol

[Urban L. <urb...@bo...>]

Hi, 

I calculated anomalous difference maps with shelx and got .phs files as output. I can open them in coot, but not in pymol. 
I have read that I have to convert them to .mtz or rather calculate a map. Can anyone tell me how to do that?

Thanks, 
Urban 

Re: [PyMOL] open source installation on Windows broken?

[Thomas H. <th...@th...>]

Hi Bob,

Looks like Christoph Gohlke has moved his wheels to Github:
https://github.com/cgohlke/pymol-open-source-wheels/

Another option would be the conda-forge channel:
https://anaconda.org/conda-forge/pymol-open-source

Cheers,
  Thomas

On Mon, Jul 22, 2024 at 4:46 AM Robert Hanson via PyMOL-users
<pym...@li...> wrote:
>
> At
> https://pymolwiki.org/index.php/Windows_Install
> the process fails for
>
> 3. Download the appropriate wheel files,
>
> which is a dead link.
>
> Does anyone know how to run open source PyMOL on Windows OS?
>
> Bob Hanson
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Create command with ranges of states

[Jarrett J. <jar...@sc...>]

Hi Istvan,

I have not yet come across a better way to do this (perhaps someone has a
clever way to approach this), but I do think that adding a range of states
to the create function is reasonable. The other idea that came to mind was
to do a full copy with `create` and just delete states, but it seems
deleting states is not yet implemented (although I have seen a few requests
for this before). I'll see if I can address this for PyMOL 3.1. The
Timeline programs select a range to view in the movie, but doesn't actually
alter the structure data.

Jarrett J.

On Fri, Jul 19, 2024 at 6:46 PM Istvan Kolossvary <iko...@gm...>
wrote:

> Hi,
>
> It seems that the Create command can only copy either a single state or
> all states but no ranges. The range option would be very useful in
> stitching together a trajectory from parts of other trajectories. This
> functionality is readily available in the Timeline, but AFAIK not available
> in Create. Right now the only solution seems to use a hugely inefficient
> loop copying a whole range state by state. Does anyone know a better
> solution?
>
> Thanks,
>
>    Istvan
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] open source installation on Windows broken?

[Robert H. <ha...@st...>]

At
https://pymolwiki.org/index.php/Windows_Install
the process fails for

3. Download the appropriate wheel files
<http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol-open-source>,

which is a dead link.

Does anyone know how to run open source PyMOL on Windows OS?

Bob Hanson

Re: [PyMOL] Pymol 3 Timeline issues

[Lei S. <le...@gm...>]

Hi Jarrett,

I feel it is easy enough for you to test in the scripting mode that whether
"cmd.movie.produce(moviename,mode='ray',quality=85,quiet=0)" would produce
the same with pymol3 and pymol2 after you load a 1000-frame dcd file to an
object with load_traj. If not, do you have any suggestions how to let
pymol3 behave like pymol2? Of course, I can always switch back to use
pymol2, like I am doing now.

Thanks,
Lei

On Sat, Jul 20, 2024 at 9:47 PM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Lei,
>
> I may need more details on how you're producing your movies. I would note
> that the File menu will only produce a movie based on the movie that's in
> the timeline *not* the one from PyMOL 2. So if you're using the old movie
> API to export out a movie in PyMOL 3, your results won't be as expected
> unless you use the legacy export menu. The `load_traj` command, I believe,
> was unchanged moving to PyMOL3, if you can provide more details on what has
> changed for you, that'd be great. While the interface is improved in
> PyMOL3, I've also made sure to accommodate for most use cases of the
> Timeline to be configured via scripting. The Python API for it is located
> here: https://pymolwiki.org/index.php/Timeline_Python_API.
>
> Jarrett J
>
> On Sat, Jul 20, 2024 at 12:26 PM Lei Shi <le...@gm...> wrote:
>
>> Hi Istvan,
>>
>> I have related but not the same problems with pymol3 when making the
>> movies. Using the pymol script that works for pymol 2.5, pymol3 could only
>> produce a movie for the first 240(?) frames and I could not find the
>> setting to fix this issue. In addition, I believe they also changed the
>> default options of load_traj in pymol3. Overall, it appears pymol3 counts
>> on you using the interface but this is not always ideal for heavy duty
>> work, e.g., requiring running "pymol -c" (text mode) on a linux server to
>> finish the job.
>>
>> Lei
>>
>>
>>
>> On Fri, Jul 19, 2024 at 6:12 PM Istvan Kolossvary <iko...@gm...>
>> wrote:
>>
>>> Hi,
>>>
>>> I have had these issues with the new timeline. It works fine with scenes
>>> and short multi-state objects (like those showcased in the Pymol 3 online
>>> visualization course) but when it comes to real life MD trajectories I
>>> found two "dealbreaker" issues.
>>>
>>> 1) With complex movies based on MD trajectories and not scenes, the Draw
>>> mode is not working. If I select Draw to generate a movie file quickly for
>>> testing then (a) it takes almost as long as Ray Tracing and (b) the movie
>>> is complete garbage, showing only random parts of the system.
>>>
>>> 2) The Ray Tracing mode works fine, but processing time is prohibitively
>>> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
>>> automatically uses all the available cores for ray tracing. The way Pymol 3
>>> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
>>> only 100 seconds.
>>>
>>> Has anyone encountered similar issues?
>>>
>>> Thanks,
>>>
>>>    Istvan
>>> _______________________________________________
>>> 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
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

Re: [PyMOL] Pymol 3 Timeline issues

[Jarrett J. <jar...@sc...>]

Hi Lei,

I may need more details on how you're producing your movies. I would note
that the File menu will only produce a movie based on the movie that's in
the timeline *not* the one from PyMOL 2. So if you're using the old movie
API to export out a movie in PyMOL 3, your results won't be as expected
unless you use the legacy export menu. The `load_traj` command, I believe,
was unchanged moving to PyMOL3, if you can provide more details on what has
changed for you, that'd be great. While the interface is improved in
PyMOL3, I've also made sure to accommodate for most use cases of the
Timeline to be configured via scripting. The Python API for it is located
here: https://pymolwiki.org/index.php/Timeline_Python_API.

Jarrett J

On Sat, Jul 20, 2024 at 12:26 PM Lei Shi <le...@gm...> wrote:

> Hi Istvan,
>
> I have related but not the same problems with pymol3 when making the
> movies. Using the pymol script that works for pymol 2.5, pymol3 could only
> produce a movie for the first 240(?) frames and I could not find the
> setting to fix this issue. In addition, I believe they also changed the
> default options of load_traj in pymol3. Overall, it appears pymol3 counts
> on you using the interface but this is not always ideal for heavy duty
> work, e.g., requiring running "pymol -c" (text mode) on a linux server to
> finish the job.
>
> Lei
>
>
>
> On Fri, Jul 19, 2024 at 6:12 PM Istvan Kolossvary <iko...@gm...>
> wrote:
>
>> Hi,
>>
>> I have had these issues with the new timeline. It works fine with scenes
>> and short multi-state objects (like those showcased in the Pymol 3 online
>> visualization course) but when it comes to real life MD trajectories I
>> found two "dealbreaker" issues.
>>
>> 1) With complex movies based on MD trajectories and not scenes, the Draw
>> mode is not working. If I select Draw to generate a movie file quickly for
>> testing then (a) it takes almost as long as Ray Tracing and (b) the movie
>> is complete garbage, showing only random parts of the system.
>>
>> 2) The Ray Tracing mode works fine, but processing time is prohibitively
>> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
>> automatically uses all the available cores for ray tracing. The way Pymol 3
>> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
>> only 100 seconds.
>>
>> Has anyone encountered similar issues?
>>
>> Thanks,
>>
>>    Istvan
>> _______________________________________________
>> 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



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] Pymol 3 Timeline issues

[Lei S. <le...@gm...>]

Hi Istvan,

I have related but not the same problems with pymol3 when making the
movies. Using the pymol script that works for pymol 2.5, pymol3 could only
produce a movie for the first 240(?) frames and I could not find the
setting to fix this issue. In addition, I believe they also changed the
default options of load_traj in pymol3. Overall, it appears pymol3 counts
on you using the interface but this is not always ideal for heavy duty
work, e.g., requiring running "pymol -c" (text mode) on a linux server to
finish the job.

Lei



On Fri, Jul 19, 2024 at 6:12 PM Istvan Kolossvary <iko...@gm...>
wrote:

> Hi,
>
> I have had these issues with the new timeline. It works fine with scenes
> and short multi-state objects (like those showcased in the Pymol 3 online
> visualization course) but when it comes to real life MD trajectories I
> found two "dealbreaker" issues.
>
> 1) With complex movies based on MD trajectories and not scenes, the Draw
> mode is not working. If I select Draw to generate a movie file quickly for
> testing then (a) it takes almost as long as Ray Tracing and (b) the movie
> is complete garbage, showing only random parts of the system.
>
> 2) The Ray Tracing mode works fine, but processing time is prohibitively
> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
> automatically uses all the available cores for ray tracing. The way Pymol 3
> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
> only 100 seconds.
>
> Has anyone encountered similar issues?
>
> Thanks,
>
>    Istvan
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Pymol 3 Timeline issues

[Jarrett J. <jar...@sc...>]

Hi Istvan,

With regards to CPU ray tracing only running on a single core, that sounds
like a major regression; we haven't changed anything in regards to that so
I'll investigate. As for your first issue, do you have any examples that I
can inspect myself to see what the issue is?

Jarrett J.

On Fri, Jul 19, 2024 at 6:11 PM Istvan Kolossvary <iko...@gm...>
wrote:

> Hi,
>
> I have had these issues with the new timeline. It works fine with scenes
> and short multi-state objects (like those showcased in the Pymol 3 online
> visualization course) but when it comes to real life MD trajectories I
> found two "dealbreaker" issues.
>
> 1) With complex movies based on MD trajectories and not scenes, the Draw
> mode is not working. If I select Draw to generate a movie file quickly for
> testing then (a) it takes almost as long as Ray Tracing and (b) the movie
> is complete garbage, showing only random parts of the system.
>
> 2) The Ray Tracing mode works fine, but processing time is prohibitively
> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
> automatically uses all the available cores for ray tracing. The way Pymol 3
> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
> only 100 seconds.
>
> Has anyone encountered similar issues?
>
> Thanks,
>
>    Istvan
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL