pymol-users Mailing List for PyMOL Molecular Graphics System

Hello,

When I load local pdb files with metal LINK records, e.g. magnesium ion and
surrounding waters, I couldn't get the dash line to show up with
sticks+spheres representation. I think there should be a setting to turn
the dash lines on, because when fetching pdb from server the dash lines are
there. I would appreciate the instructions on how to do it correctly.

Best,

Wei

Nice tutorial here
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html (click on
surface properties)
(with chimera not pymol, no need to install apbs)

El mié., 27 de jun. de 2018 a la(s) 19:07, Joel Tyndall (
joe...@ot...) escribió:

> It can easily be done in PyMOL
>
>
>
> Select your molecule, then in the right side select
> A(Action)->Generate->Vacuum Electrostatic
>
>
>
> Or there are plenty of tutorials on the web for APBS
>
>
>
> Hope this helps
>
>
>
> J
>
>
>
>
>
> *From:* Clarisa Alvarez <cla...@gm...>
> *Sent:* Thursday, 28 June 2018 3:05 AM
> *To:* pym...@li...
> *Subject:* [PyMOL] Columb coloring
>
>
>
> Dir Sir/Madam,
>
> I need coloring my protein surface by electrostatic characteristics.
>
> Do I need to install APBS? because i could not do it. If you could help me
> it will be greatful.
>
> Thanks in advance,
>
> Yours,
>
> Clarisa.
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Is there a way to add a ramp*  (i.e. a way to look at colors and feel the
numbers) to the colorbyrmsd.py** script?

* https://pymolwiki.org/index.php/Ramp_New
** https://pymolwiki.org/index.php/ColorByRMSD

Same goes to the "b factor putty" preset....


Thank you.

Hi Nathan,

Thank you very much for the files and instructions. I can reproduce the problem. I haven't seen this before and don't know yet what's going wrong, we will investigate.

Cheers,
  Thomas

> On Jun 28, 2018, at 10:50 AM, ncl...@cs... wrote:
> 
> The alignment in this example is nearly perfect. Even the residues left
> out of the fitting have perfect matches at the sequence level (as can be
> seen by saving the super object and turning on the sequence alignment and
> contact_all).
> 
> PyMOL>load 1AY7_u.pdb, test
> CmdLoad: "1AY7_u.pdb" loaded as "test".
> PyMOL>load 1AY7_b.pdb, gold
> CmdLoad: "1AY7_b.pdb" loaded as "gold".
> PyMOL>select contact_rec, gold & chain R & (all within 10 of gold & chain
> L) & n. ca
> Selector: selection "contact_rec" defined with 33 atoms.
> PyMOL>select contact_lig, gold & chain L & (all within 10 of gold & chain
> R) & n. ca
> Selector: selection "contact_lig" defined with 33 atoms.
> PyMOL>select contact_all, contact_rec + contact_lig
> Selector: selection "contact_all" defined with 66 atoms.
> PyMOL>super gold & contact_all, test, cycles=0
> MatchAlign: aligning residues (66 vs 185)...
> MatchAlign: score 143.882
> ExecutiveAlign: 58 atoms aligned.
> Executive: RMS =    0.524 (58 to 58 atoms)
> 
> <1AY7_u.pdb><1AY7_b.pdb>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi everybody,

we got the same error (Failed to create menus) on Windows 10. We selected 'Ignore' and Pymol 2.1.1 was unable to start successfully. We had to find the .exe in the installation folder since there was no shortcut, as mentioned before.

In our case the solution was to:

  1.  Uninstall/remove the broken installation of Pymol 2.1.1.
  2.  Install again but this time we chose the option to install for all users. We were asked for administrative rights, confirmed that and the installation finished succesfully.

Could it be an permission issue?

Best regards,
Matic

On 26. 06. 2018 11:23, puneet garg wrote:
Ok, I'll check it out.

On Tue, Jun 26, 2018 at 2:34 PM Thomas Holder <tho...@sc...<mailto:tho...@sc...>> wrote:
Hi Puneet,

This is a know issue with the installer, which can have a variety of reasons.

https://docs.anaconda.com/anaconda/user-guide/troubleshooting#windows-error-failed-to-create-anaconda-menus-or-failed-to-add-anaconda-to-the-system-path

PyMOL might still be properly installed and only missing the start menu entries. As far as I can tell from your screenshot, you can launch C:\pymoll\PyMOLWin.exe

Cheers,
  Thomas

> On Jun 25, 2018, at 10:37 PM, puneet garg <pun...@gm...<mailto:pun...@gm...>> wrote:
>
> Dear Sir,
> I am installing PyMOL (education version PyMOL-2.1.1_0-Windows-x86_64) on my new windows 7 computer. I am getting an error "Failed to create menu's" while installing. If I ignore it the installation fails. Please advice me on this issue. I have attached a picture of same.
> Thanks
>
>
> --
> Puneet
> Structural Biology Lab
> Biotechnology Dept.
> IIT Madras
> Chennai-600036
> <pymol error.jpg>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



--
Puneet
Structural Biology Lab
Biotechnology Dept.
IIT Madras
Chennai-600036



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The alignment in this example is nearly perfect. Even the residues left
out of the fitting have perfect matches at the sequence level (as can be
seen by saving the super object and turning on the sequence alignment and
contact_all).

PyMOL>load 1AY7_u.pdb, test
 CmdLoad: "1AY7_u.pdb" loaded as "test".
PyMOL>load 1AY7_b.pdb, gold
 CmdLoad: "1AY7_b.pdb" loaded as "gold".
PyMOL>select contact_rec, gold & chain R & (all within 10 of gold & chain
L) & n. ca
 Selector: selection "contact_rec" defined with 33 atoms.
PyMOL>select contact_lig, gold & chain L & (all within 10 of gold & chain
R) & n. ca
 Selector: selection "contact_lig" defined with 33 atoms.
PyMOL>select contact_all, contact_rec + contact_lig
 Selector: selection "contact_all" defined with 66 atoms.
PyMOL>super gold & contact_all, test, cycles=0
 MatchAlign: aligning residues (66 vs 185)...
 MatchAlign: score 143.882
 ExecutiveAlign: 58 atoms aligned.
 Executive: RMS =    0.524 (58 to 58 atoms)

It can easily be done in PyMOL

Select your molecule, then in the right side select A(Action)->Generate->Vacuum Electrostatic

Or there are plenty of tutorials on the web for APBS

Hope this helps

J


From: Clarisa Alvarez <cla...@gm...>
Sent: Thursday, 28 June 2018 3:05 AM
To: pym...@li...
Subject: [PyMOL] Columb coloring

Dir Sir/Madam,
I need coloring my protein surface by electrostatic characteristics.
Do I need to install APBS? because i could not do it. If you could help me it will be greatful.
Thanks in advance,
Yours,
Clarisa.

Dir Sir/Madam,
I need coloring my protein surface by electrostatic characteristics.
Do I need to install APBS? because i could not do it. If you could help me
it will be greatful.
Thanks in advance,
Yours,
Clarisa.

Hi Nathan,

Sounds like you are doing everything correct. Would it be possible to send me the input files?

Thanks,
  Thomas

> On Jun 26, 2018, at 10:58 AM, Nathan Clement <nat...@gm...> wrote:
> 
> Hi,
> 
> I'm trying to compute the interface RMSD (iRMSD) between two protein pairs that are highly similar (might have a few missing residues, but are otherwise identical). Right now, my code does something like the following for protein pairs "gold" and "test" (receptor has chains A+B and ligand has chains C):
> 
> PyMOL>select contact_rec, (gold & chain A+B) & all within 10 of (gold & chain C) & n. ca
> PyMOL>select contact_lig, (gold & chain C) & all within 10 of (gold & chain A+B) & n. ca
> PyMOL>align gold & contact_rec + contact_lig, test, cycles=0
>  Match: read scoring matrix.
>  Match: assigning 82 x 445 pairwise scores.
>  MatchAlign: aligning residues (82 vs 445)...
>  MatchAlign: score 257.500
>  ExecutiveAlign: 67 atoms aligned.
>  Executive: RMS =   14.161 (67 to 67 atoms)
> 
> This seems to suggest that, even with cycles=0, 82-67=15 atoms were not included in the alignment. When I look at the alignment (object=aln), it appears that most of the "missing" residues from this alignment have the same residue name, are matches in the sequence alignment, and are in a nearby location.
> 
> Is it possible to force align to give the full RMSD calculation? super has the same issue, and I'm concerned that using something like rms or fit won't work because the "gold" and "test" have different residue numbering (and might be missing residues so it's not always possible to give them an equivalent numbering).
> 
> Does anybody have any suggestions?
> 
> Thanks in advance,
> 
> Nathan

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

I have an EM map which has been surface coloured in multiple different colours using the ramp_new command and follows the colour scheme of multiple fitted pdb chains using the ‘atomic’ special color function. I want to now slice my EM map to generate a cross section and then surface cap the interior sections following the equivalent ramp_new colour scheme. Using set ray_interior_color I have managed to color the surface cap of the whole map to one colour. So my question is can multiple capping colors be assigned to a single EM map based on the ramp_new colour scheme?

Tips would be very much appreciated!
Thank you









______________________________
Dr. Harry Low
Wellcome Trust Research Fellow
Department of Life Sciences
503 Sir Ernst Chain Building
Imperial College
London, SW7 2AZ
+44 207 594 3064

Ok, I'll check it out.

On Tue, Jun 26, 2018 at 2:34 PM Thomas Holder <tho...@sc...>
wrote:

> Hi Puneet,
>
> This is a know issue with the installer, which can have a variety of
> reasons.
>
>
> https://docs.anaconda.com/anaconda/user-guide/troubleshooting#windows-error-failed-to-create-anaconda-menus-or-failed-to-add-anaconda-to-the-system-path
>
> PyMOL might still be properly installed and only missing the start menu
> entries. As far as I can tell from your screenshot, you can launch
> C:\pymoll\PyMOLWin.exe
>
> Cheers,
>   Thomas
>
> > On Jun 25, 2018, at 10:37 PM, puneet garg <pun...@gm...> wrote:
> >
> > Dear Sir,
> > I am installing PyMOL (education version PyMOL-2.1.1_0-Windows-x86_64)
> on my new windows 7 computer. I am getting an error "Failed to create
> menu's" while installing. If I ignore it the installation fails. Please
> advice me on this issue. I have attached a picture of same.
> > Thanks
> >
> >
> > --
> > Puneet
> > Structural Biology Lab
> > Biotechnology Dept.
> > IIT Madras
> > Chennai-600036
> > <pymol error.jpg>
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Puneet
Structural Biology Lab
Biotechnology Dept.
IIT Madras
Chennai-600036

Hi Puneet,

This is a know issue with the installer, which can have a variety of reasons.

https://docs.anaconda.com/anaconda/user-guide/troubleshooting#windows-error-failed-to-create-anaconda-menus-or-failed-to-add-anaconda-to-the-system-path

PyMOL might still be properly installed and only missing the start menu entries. As far as I can tell from your screenshot, you can launch C:\pymoll\PyMOLWin.exe

Cheers,
  Thomas

> On Jun 25, 2018, at 10:37 PM, puneet garg <pun...@gm...> wrote:
> 
> Dear Sir,
> I am installing PyMOL (education version PyMOL-2.1.1_0-Windows-x86_64) on my new windows 7 computer. I am getting an error "Failed to create menu's" while installing. If I ignore it the installation fails. Please advice me on this issue. I have attached a picture of same.
> Thanks
> 
> 
> -- 
> Puneet
> Structural Biology Lab
> Biotechnology Dept.
> IIT Madras
> Chennai-600036
> <pymol error.jpg>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi,

I'm trying to compute the interface RMSD (iRMSD) between two protein pairs
that are highly similar (might have a few missing residues, but are
otherwise identical). Right now, my code does something like the following
for protein pairs "gold" and "test" (receptor has chains A+B and ligand has
chains C):

PyMOL>select contact_rec, (gold & chain A+B) & all within 10 of (gold &
chain C) & n. ca
PyMOL>select contact_lig, (gold & chain C) & all within 10 of (gold & chain
A+B) & n. ca
PyMOL>align gold & contact_rec + contact_lig, test, cycles=0
 Match: read scoring matrix.
 Match: assigning 82 x 445 pairwise scores.
 MatchAlign: aligning residues (82 vs 445)...
 MatchAlign: score 257.500
 ExecutiveAlign: 67 atoms aligned.
 Executive: RMS =   14.161 (67 to 67 atoms)

This seems to suggest that, even with cycles=0, 82-67=15 atoms were not
included in the alignment. When I look at the alignment (object=aln), it
appears that most of the "missing" residues from this alignment have the
same residue name, are matches in the sequence alignment, and are in a
nearby location.

Is it possible to force align to give the full RMSD calculation? super has
the same issue, and I'm concerned that using something like rms or fit
won't work because the "gold" and "test" have different residue numbering
(and might be missing residues so it's not always possible to give them an
equivalent numbering).

Does anybody have any suggestions?

Thanks in advance,

Nathan

 Dear Sir,
I am installing PyMOL (education version PyMOL-2.1.1_0-Windows-x86_64) on
my new windows 7 computer. I am getting an error "Failed to create menu's"
while installing. If I ignore it the installation fails. Please advice me
on this issue. I have attached a picture of same.
Thanks


-- 
Puneet
Structural Biology Lab
Biotechnology Dept.
IIT Madras
Chennai-600036

Hi,

I tried to install pymol on Ubuntu 18.04, but when I call it on terminal,
the following error message appears:

/usr/local/bin/python2.7: No module named _collections

What can I do to fix it ?

Best Regards,

Bruno

Hi everyone,

We've migrated the PyMOL open-source SVN repository to github:

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

The SourceForge project will be phased out. We will no longer update the SVN repository. Bugs should be reported on the new github page.

We will continue to use the pymol-users mailing list provided by SourceForge.

Cheers,
  Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Murpholino,

This should be the correct selection expression:

    sele = '(sc. or name CA) and i. {}'.format(stored.x)

Cheers,
  Thomas

> On Jun 20, 2018, at 3:11 PM, Murpholino Peligro <mur...@gm...> wrote:
> 
> I have waters and ions in my structures.
> 
> If I add the "sc." it works for non-glycine residues. (The error is "ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.")
> How to tweak it so that F1 works for all my residues?
> 
> Ps I was thinking to include the alpha carbon in the selection so the sidechain does not look truncated
>     sele = 'sc. and i. or name ca and i. {}'.format(stored.x)
> This works but it centers on the ca and not the sc. Plus... sticks are not drawn.
> Ps. Sorry for the delay. I was very sick.
> 
> 
> 
> 2018-06-18 5:12 GMT-05:00 Thomas Holder <tho...@sc...>:
> 
> > It works ...but the F1 key now zooms farther away from the residues..... :P
> 
> Are there other atoms with residue number 1? Ligands? Solvent? I had removed the "sc." selector, so that it works on Glycine as well. You can add it back to the sele string in the zoomnext function.
> 
>     sele = 'sc. and i. {}'.format(stored.x)
> 
> Cheers,
>   Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Thanks.
It works perfect this time.



2018-06-20 15:00 GMT-05:00 Thomas Holder <tho...@sc...>:

> Hi Murpholino,
>
> This should be the correct selection expression:
>
>     sele = '(sc. or name CA) and i. {}'.format(stored.x)
>
> Cheers,
>   Thomas
>
> > On Jun 20, 2018, at 3:11 PM, Murpholino Peligro <mur...@gm...>
> wrote:
> >
> > I have waters and ions in my structures.
> >
> > If I add the "sc." it works for non-glycine residues. (The error is
> "ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.")
> > How to tweak it so that F1 works for all my residues?
> >
> > Ps I was thinking to include the alpha carbon in the selection so the
> sidechain does not look truncated
> >     sele = 'sc. and i. or name ca and i. {}'.format(stored.x)
> > This works but it centers on the ca and not the sc. Plus... sticks are
> not drawn.
> > Ps. Sorry for the delay. I was very sick.
> >
> >
> >
> > 2018-06-18 5:12 GMT-05:00 Thomas Holder <tho...@sc...>:
> >
> > > It works ...but the F1 key now zooms farther away from the
> residues..... :P
> >
> > Are there other atoms with residue number 1? Ligands? Solvent? I had
> removed the "sc." selector, so that it works on Glycine as well. You can
> add it back to the sele string in the zoomnext function.
> >
> >     sele = 'sc. and i. {}'.format(stored.x)
> >
> > Cheers,
> >   Thomas
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

I have waters and ions in my structures.

If I add the "sc." it works for non-glycine residues. (The error is
"ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.")
How to tweak it so that F1 works for all my residues?

Ps I was thinking to include the alpha carbon in the selection so the
sidechain does not look truncated
    sele = 'sc. and i. or name ca and i. {}'.format(stored.x)
This works but it centers on the ca and not the sc. Plus... sticks are not
drawn.
Ps. Sorry for the delay. I was very sick.



2018-06-18 5:12 GMT-05:00 Thomas Holder <tho...@sc...>:

>
> > It works ...but the F1 key now zooms farther away from the residues.....
> :P
>
> Are there other atoms with residue number 1? Ligands? Solvent? I had
> removed the "sc." selector, so that it works on Glycine as well. You can
> add it back to the sele string in the zoomnext function.
>
>     sele = 'sc. and i. {}'.format(stored.x)
>
> Cheers,
>   Thomas
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

> It works ...but the F1 key now zooms farther away from the residues..... :P

Are there other atoms with residue number 1? Ligands? Solvent? I had removed the "sc." selector, so that it works on Glycine as well. You can add it back to the sele string in the zoomnext function.

    sele = 'sc. and i. {}'.format(stored.x)

Cheers,
  Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

resending...
I hope you can see the link to the screenshots in my gdrive

Here is the code merged.
It works ...but the F1 key now zooms farther away from the residues..... :P
​
 firstF1.png
<" rel="nofollow">https://drive.google.com/file/d/0B9tqXyDsq9YIYWxTSlhaa2hoUlR3dkFhZzE0Tm83YmZjQ1pN/view?usp=drive_web>
​​
 manualorient.png
<" rel="nofollow">https://drive.google.com/file/d/0B9tqXyDsq9YIMUFvNGNxZE9iekNic0Y4eXU0eGx4blBBZ2ZN/view?usp=drive_web>
​​
 secondF1.png
<" rel="nofollow">https://drive.google.com/file/d/0B9tqXyDsq9YIal9aanptTS04ekREeVZkZGVMTXRKc2VuSlpN/view?usp=drive_web>
​

2018-06-15 14:03 GMT-05:00 Murpholino Peligro <mur...@gm...>:

> Wow. I like it. Thanks.
>
> I got 8 structures with their respective maps. So in order to view them
> all at once, interactively, I think I only need to merge my code with yours
> and ...add a ramp for every map? I am gonna try that now.
> Here's my code (pml attached)
>
> If you want to have my maps and pdbs please tell me.
>
>
> 2018-06-15 13:22 GMT-05:00 Thomas Holder <tho...@sc...>:
>
>> Hi Murpholino,
>>
>> How about an interactive version instead of a fix-speed movie? The
>> attached script maps the F1 key to advance to the next residue, and F2 to
>> go back. It also colors atoms by density fit (red if they don't fit into
>> the 1.2 sigma shell). It will only show sticks for the current residue, to
>> make it more visible.
>>
>> Cheers,
>>   Thomas
>>
>>
>>
>>
>>
>> > On Jun 15, 2018, at 4:36 PM, Murpholino Peligro <mur...@gm...>
>> wrote:
>> >
>> > Dear PyMOL users......
>> > I found this bb_inspector at https://pymolwiki.org/index.ph
>> p/MovieSchool_4
>> > It kinda does what I want, so I tweak it little bit ... (*.pml attached)
>> > If you run the script and play the movie you'll see that sometimes the
>> sidechain is a little bit obscured by some density/atoms in the front. How
>> do I make them more visible?
>> >
>> > Lots of thanks
>> >
>> >
>> >
>> >
>> >
>> > 2018-06-15 8:31 GMT-05:00 Murpholino Peligro <mur...@gm...>:
>> > Dear PyMOL users...
>> >
>> > Is there a way to orient every sidechain and take a picture to produce
>> a movie?
>> >
>> > Idea: By aligning the pdbs and maps and having them in the grid mode,
>> with this movie I could f take a quick look at how well my electron density
>> fits to all my models...
>> >
>> > Thanks
>> >
>> > <sc_inspector.pml>------------------------------------------
>> ------------------------------------
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
>>
>>
>

Wow. I like it. Thanks.

I got 8 structures with their respective maps. So in order to view them all
at once, interactively, I think I only need to merge my code with yours and
...add a ramp for every map? I am gonna try that now.
Here's my code (pml attached)

If you want to have my maps and pdbs please tell me.


2018-06-15 13:22 GMT-05:00 Thomas Holder <tho...@sc...>:

> Hi Murpholino,
>
> How about an interactive version instead of a fix-speed movie? The
> attached script maps the F1 key to advance to the next residue, and F2 to
> go back. It also colors atoms by density fit (red if they don't fit into
> the 1.2 sigma shell). It will only show sticks for the current residue, to
> make it more visible.
>
> Cheers,
>   Thomas
>
>
>
>
>
> > On Jun 15, 2018, at 4:36 PM, Murpholino Peligro <mur...@gm...>
> wrote:
> >
> > Dear PyMOL users......
> > I found this bb_inspector at https://pymolwiki.org/index.
> php/MovieSchool_4
> > It kinda does what I want, so I tweak it little bit ... (*.pml attached)
> > If you run the script and play the movie you'll see that sometimes the
> sidechain is a little bit obscured by some density/atoms in the front. How
> do I make them more visible?
> >
> > Lots of thanks
> >
> >
> >
> >
> >
> > 2018-06-15 8:31 GMT-05:00 Murpholino Peligro <mur...@gm...>:
> > Dear PyMOL users...
> >
> > Is there a way to orient every sidechain and take a picture to produce a
> movie?
> >
> > Idea: By aligning the pdbs and maps and having them in the grid mode,
> with this movie I could f take a quick look at how well my electron density
> fits to all my models...
> >
> > Thanks
> >
> > <sc_inspector.pml>------------------------------------------
> ------------------------------------
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
>

Hi Murpholino,

How about an interactive version instead of a fix-speed movie? The attached script maps the F1 key to advance to the next residue, and F2 to go back. It also colors atoms by density fit (red if they don't fit into the 1.2 sigma shell). It will only show sticks for the current residue, to make it more visible.

Cheers,
  Thomas

"The bug" is currently being fixed by the phenix developers.

And also I found out that there's a way to superpose maps in PyMOL. Look at
the second example in https://pymolwiki.org/index.php/Matrix_Copy

:)


2018-06-14 17:34 GMT-05:00 Murpholino Peligro <mur...@gm...>:

> Dear PyMOL users...
> Have you tried to compare several structures and maps?
> I am talking about something like this (https://www.phenix-online.
> org/documentation/reference/structure_comparison.html)
>
> Are there any good pymol scripts that can make this easier?
>
> Although the table phenix outputs looks very nice I am happy with just
> aligning the pdbs (that's easy) and the maps* (that I do not know how to
> do).
>
> map* i.e. in ccp4 or mtz format.
>
> Ps. I would normally use the phenix program in the url above, but a bug is
> standing in the way.
>

Dear PyMOL users......
I found this bb_inspector at https://pymolwiki.org/index.php/MovieSchool_4
It kinda does what I want, so I tweak it little bit ... (*.pml attached)
If you run the script and play the movie you'll see that sometimes the
sidechain is a little bit obscured by some density/atoms in the front. How
do I make them more visible?

Lots of thanks





2018-06-15 8:31 GMT-05:00 Murpholino Peligro <mur...@gm...>:

> Dear PyMOL users...
>
> Is there a way to orient every sidechain and take a picture to produce a
> movie?
>
> Idea: By aligning the pdbs and maps and having them in the grid mode, with
> this movie I could f take a quick look at how well my electron density fits
> to all my models...
>
> Thanks
>