pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Mohammad,
I do not know if PyMOL can do what you want. But...
If you know how to refine using phenix*, and the pdb has electron density
data, I suggest to refine and validate your structure. In the validation
window, there is specific tab where one can see if the structure has
missing atoms.
If you do not know how to use phenix then you can use pdb-redo** Paper
here***
Good luck
* https://www.phenix-online.org/download/ tutorials @ youtube
** https://pdb-redo.eu/
*** https://pdb-redo.eu/publications/bioinformatics.pdf
El mar., 31 de jul. de 2018 a la(s) 09:24, Mohammad Goodarzi (
moh...@gm...) escribió:
> Hello,
>
> I would like to know how to check for missing or broken part of a PDB file
> using pymol?
> should i screen within each amino acid or there is a way to show it by
> pymol?
>
> Thanks
> Mohammad
>
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Hello pymol-users, fyi ...
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Hi all,
I have a peptide structure and would like to phosphorylate one of the
serine residues to test its binding capacity to a ligand. I tried the Build
function with a PyMol 2.0, but only a phosphorous can be added to the
serine. Does anyone have experiences of creating a phosphorylated residue
with PyMol or other tools?
Any suggestions would be appreciated.
Thanks,
Wei

Hello,
I would like to know how to check for missing or broken part of a PDB file
using pymol?
should i screen within each amino acid or there is a way to show it by
pymol?
Thanks
Mohammad

Hi Abhik and Jared,
There is also "intra_fit" and "multifilesave":
https://pymolwiki.org/index.php/intra_fit
https://pymolwiki.org/index.php/multifilesave
Example:
 intra_fit name CA
 multifilesave model{state:06}.pdb, state=0
Cheers,
 Thomas
> On Jul 30, 2018, at 9:46 PM, Jared Sampson <jar...@co...> wrote:
> 
> Hi ABhik - 
> 
> You'll want to have a look at the `split_states` command. Something like the following should get you going. Note the embedded multiline `python` block. 
> 
> # Using 1nmr as a sample structure
> fetch 1nmr, async=0
> split_states 1nmr, prefix=model
> 
> python
> # starting at state 2, align each model to state 1
> for i in range(2, cmd.count_states('1nmr') + 1):
> this_model = 'model{:04d}'.format(i)
> cmd.super(this_model, 'model0001')
> cmd.save('{}.pdb'.format(this_model), this_model)
> python end
> 
> For your 100000 structures you'll also need more zero-padding (e.g. '{:07d}'). You can save this as super_states.pml and run from PyMOL with the command: @super_states.pml
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> On July 30, 2018 at 2:16:54 AM, abh...@bo... (abh...@bo...) wrote:
> 
>> Hello All 
>> I have a pdb file containing 100000 frames . Now I want to align all frame 
>> one by one in pymol and then want to save the final coordinate. How it can 
>> be done? 
>> All suggestions are welcome 
>> Thanking you. 
>> ABhik 
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi ABhik - 
You'll want to have a look at the `split_states` command. Something like the following should get you going. Note the embedded multiline `python` block. 
# Using 1nmr as a sample structure
fetch 1nmr, async=0
split_states 1nmr, prefix=model
python
# starting at state 2, align each model to state 1
for i in range(2, cmd.count_states('1nmr') + 1):
  this_model = 'model{:04d}'.format(i)
  cmd.super(this_model, 'model0001')
  cmd.save('{}.pdb'.format(this_model), this_model)
python end
For your 100000 structures you'll also need more zero-padding (e.g. '{:07d}'). You can save this as super_states.pml and run from PyMOL with the command: @super_states.pml
Hope that helps.
Cheers,
Jared
On July 30, 2018 at 2:16:54 AM, abh...@bo... (abh...@bo...) wrote:
Hello All 
I have a pdb file containing 100000 frames . Now I want to align all frame 
one by one in pymol and then want to save the final coordinate. How it can 
be done? 
All suggestions are welcome 
Thanking you. 
ABhik 
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Hello All
I have a pdb file containing 100000 frames . Now I want to align all frame
one by one in pymol and then want to save the final coordinate. How it can
be done?
All suggestions are welcome
Thanking you.
ABhik

I now know that I can select specific residues to display the "volume data".
Something like `volume mol1-2MGyvol, mol1_2MGy, 1.0 blue .5 2.0 yellow 0,
resname CYS and mol1, 4.0, carve=4.0` works.
>From there I can choose to display the volume à la Fo-Fc
:)
El jue., 26 de jul. de 2018 a la(s) 10:14, Murpholino Peligro (
mur...@gm...) escribió:
> Dear PyMOL users.
> I got a ccp4 difference map and a structure. If I load the structure in
> Coot and then load the map (ticking the "Is a difference map" box). Coot
> loads the map onto the structure, showing me the holes and peaks in
> electron density.
> How can I achieve this in PyMOL?
> When I open the structure and the map in PyMOL, they are unaligned.
>
> Thanks
>

Hi all,
 I've encountered an odd problem with the file type defaults in the external gui for Pymol 2.1.0. Whenever I try to open a file, or save a file, or whatnot, the gui defaults to the file type at the bottom of the file type list, rather than at the top. So I by default search for MMFT files on open, rather than 'all readable'. I assume there's a setting that's wrong somewhere - anybody know what it might be?
William P. Katt
Cerione Research Group
Department of Molecular Medicine
Cornell University

Dear PyMOL users.
I got a ccp4 difference map and a structure. If I load the structure in
Coot and then load the map (ticking the "Is a difference map" box). Coot
loads the map onto the structure, showing me the holes and peaks in
electron density.
How can I achieve this in PyMOL?
When I open the structure and the map in PyMOL, they are unaligned.
Thanks

Thanks Marko and Thomas,
It works removing the lines at the end as indicated by Marko. I also 
tried for other ligands. Indeed, I have the v1.5.0.5 version. Thanks a lot.
Cheers,
Baptiste
Le 26/07/2018 à 10:32, Marko Hyvonen a écrit :
> Hi Thomas
>
> Perhaps this is a Pymol version issue? I just tried this (with the 
> second command of yours) with the original coords and get the same as 
> Baptiste. I tried this on v. 1.8.2 open source Pymol in Win10 laptop.
>
> With the fixed coords I just sent back, the result is the correct 
> 0.032 A.
>
> cheers, Marko
>
> On 26/07/2018 09:26, Thomas Holder wrote:
>> Hi Baptiste,
>>
>> These files look good to me, I get:
>>
>> PyMOL>rms Crystal_Rfp, Vina_Rfp
>> Executive: RMSD = 0.032 (51 to 51 atoms)
>>
>> Is it possible that you tried with a multi-model (multiple poses) pdbqt file before? If that's the case, specify "mobile_state" and/or "target_state":
>>
>> PyMOL>rms Crystal_Rfp, Vina_Rfp, mobile_state=1, target_state=1
>> Executive: RMSD = 0.032 (51 to 51 atoms)
>>
>> See also "Notes" section here:https://pymolwiki.org/index.php/Align#Notes
>>
>> Cheers,
>> Thomas
>>
>>> On Jul 26, 2018, at 9:42 AM, Baptiste Legrand<bap...@gm...> wrote:
>>>
>>> Thanks for your answers. The molecule is the rifampicin. Please find attached the pdb from the crystal structure and the pdbqt from autodock vina. May be the format of one or both files is not correct.
>>>
>>> Best,
>>>
>>> Baptiste
>>>
>>>
>>> Le 25/07/2018 à 18:57, Markus Heller a écrit :
>>>> Not knowing what your molecule looks like, could it be automorphism?
>>>>
>>>>> -----Original Message-----
>>>>> From: Baptiste Legrand<bap...@gm...>
>>>>> Sent: Wednesday, July 25, 2018 9:17 AM
>>>>> To:pym...@li...
>>>>> Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and
>>>>> from a docking
>>>>>
>>>>> Dear all,
>>>>>
>>>>> I tried to calculate a rmsd value between ligands from a crystal structure and
>>>>> after docking. The two molecules share similar nomenclatures and are really
>>>>> well superimposed. I think that the RMSD should be < 1 A. I used the following
>>>>> lines:
>>>>>
>>>>> alter all,segi=""
>>>>> alter all,chain =""
>>>>> rms /ligand_crystal////*, /ligand_docking////*
>>>>>
>>>>> It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the
>>>>> pair_fit function, pymol completely return one molecule and also write
>>>>> "ExecutiveRMS: RMS = 6.146 (51 to 51 atoms)". I should have missed
>>>>> something...
>>>>>
>>>>> thanks for the help,
>>>>> All the Best.
>>>>>
>>>>> Baptiste
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org!http://sdm.link/slashdot
>> _______________________________________________
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>> Info Page:https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives:http://www.mail-archive.com/pym...@li...
>
> -- 
>
> Marko Hyvonen
> Department of Biochemistry, University of Cambridge
> mh...@ca...
> +44 (0)1223 766 044
> @HyvonenGroup
> http://hyvonen.bioc.cam.ac.uk
> 
>
>
>
> ------------------------------------------------------------------------------
> 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...

<html>
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 </head>
 <body text="#000000" bgcolor="#FFFFFF">
 <tt>Hi Thomas <br>
 <br>
 Perhaps this is a Pymol version issue? I just tried this (with the
 second command of yours) with the original coords and get the same
 as Baptiste. I tried this on v. 1.8.2 open source Pymol in Win10
 laptop. <br>
 <br>
 With the fixed coords I just sent back, the result is the correct
 0.032 A. <br>
 <br>
 cheers, Marko<br>
 </tt><br>
 <div class="moz-cite-prefix">On 26/07/2018 09:26, Thomas Holder
 wrote:<br>
 </div>
 <blockquote type="cite"
 cite="mid:B4A...@sc...">
 <pre wrap="">Hi Baptiste,
These files look good to me, I get:
PyMOL&gt;rms Crystal_Rfp, Vina_Rfp
 Executive: RMSD = 0.032 (51 to 51 atoms)
Is it possible that you tried with a multi-model (multiple poses) pdbqt file before? If that's the case, specify "mobile_state" and/or "target_state":
PyMOL&gt;rms Crystal_Rfp, Vina_Rfp, mobile_state=1, target_state=1
 Executive: RMSD = 0.032 (51 to 51 atoms)
See also "Notes" section here: <a class="moz-txt-link-freetext" href="https://pymolwiki.org/index.php/Align#Notes">https://pymolwiki.org/index.php/Align#Notes</a>
Cheers,
 Thomas
</pre>
 <blockquote type="cite">
 <pre wrap="">On Jul 26, 2018, at 9:42 AM, Baptiste Legrand <a class="moz-txt-link-rfc2396E" href="mailto:bap...@gm...">&lt;bap...@gm...&gt;</a> wrote:
Thanks for your answers. The molecule is the rifampicin. Please find attached the pdb from the crystal structure and the pdbqt from autodock vina. May be the format of one or both files is not correct.
Best,
Baptiste
Le 25/07/2018 à 18:57, Markus Heller a écrit :
</pre>
 <blockquote type="cite">
 <pre wrap="">Not knowing what your molecule looks like, could it be automorphism?
</pre>
 <blockquote type="cite">
 <pre wrap="">-----Original Message-----
From: Baptiste Legrand <a class="moz-txt-link-rfc2396E" href="mailto:bap...@gm...">&lt;bap...@gm...&gt;</a>
Sent: Wednesday, July 25, 2018 9:17 AM
To: <a class="moz-txt-link-abbreviated" href="mailto:pym...@li...">pym...@li...</a>
Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and
from a docking
Dear all,
I tried to calculate a rmsd value between ligands from a crystal structure and
after docking. The two molecules share similar nomenclatures and are really
well superimposed. I think that the RMSD should be &lt; 1 A. I used the following
lines:
alter all,segi=""
alter all,chain =""
rms /ligand_crystal////*, /ligand_docking////*
It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the
pair_fit function, pymol completely return one molecule and also write
"ExecutiveRMS: RMS = 6.146 (51 to 51 atoms)". I should have missed
something...
thanks for the help,
All the Best.
Baptiste
</pre>
 </blockquote>
 </blockquote>
 </blockquote>
 <pre wrap="">
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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_______________________________________________
PyMOL-users mailing list (<a class="moz-txt-link-abbreviated" href="mailto:PyM...@li...">PyM...@li...</a>)
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 </blockquote>
 <br>
 <pre class="moz-signature" cols="72">-- 
Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
 
</pre>
 </body>
</html>

Forget my last reply ;-) Marko is right, I didn't notice first because this is fixed in PyMOL 2.1. Some PDBQT atom types were not imported correctly in previous versions.
Cheers,
 Thomas
> On Jul 26, 2018, at 10:21 AM, Marko Hyvonen <mh...@ca...> wrote:
> 
> Hi Baptiste, 
> 
> removing the data at the end of the HETATM lines from ca. character 70 onwards fixed it. Not sure what these are. According to PDB 3.30 format, 67-76 should be empty. Some of the elements were non-standard also (NA for N, OA for O), but looks to be the numbers in the "empty" columns that bother PyMOL (perhaps it should just ignore these?).
> 
> A lot of other things I do not recognise in PDB files in you docked rifampicin too, but those seem not to bother the analysis. 
> 
> See attached. RMSD 0.032 for 51 atoms. Not a bad docking pose!
> 
> cheers, Marko
> 
> On 26/07/2018 08:42, Baptiste Legrand wrote:
>> Thanks for your answers. The molecule is the rifampicin. Please find attached the pdb from the crystal structure and the pdbqt from autodock vina. May be the format of one or both files is not correct. 
>> 
>> Best, 
>> 
>> Baptiste 
>> 
>> 
>> Le 25/07/2018 à 18:57, Markus Heller a écrit : 
>>> Not knowing what your molecule looks like, could it be automorphism? 
>>> 
>>>> -----Original Message----- 
>>>> From: Baptiste Legrand <bap...@gm...> 
>>>> Sent: Wednesday, July 25, 2018 9:17 AM 
>>>> To: pym...@li... 
>>>> Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and 
>>>> from a docking 
>>>> 
>>>> Dear all, 
>>>> 
>>>> I tried to calculate a rmsd value between ligands from a crystal structure and 
>>>> after docking. The two molecules share similar nomenclatures and are really 
>>>> well superimposed. I think that the RMSD should be < 1 A. I used the following 
>>>> lines: 
>>>> 
>>>> alter all,segi="" 
>>>> alter all,chain ="" 
>>>> rms /ligand_crystal////*, /ligand_docking////* 
>>>> 
>>>> It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the 
>>>> pair_fit function, pymol completely return one molecule and also write 
>>>> "ExecutiveRMS: RMS = 6.146 (51 to 51 atoms)". I should have missed 
>>>> something... 
>>>> 
>>>> thanks for the help, 
>>>> All the Best. 
>>>> 
>>>> Baptiste 
> 
> -- 
> 
> Marko Hyvonen
> Department of Biochemistry, University of Cambridge
> 
> mh...@ca...
> 
> +44 (0)1223 766 044
> @HyvonenGroup
> 
> http://hyvonen.bioc.cam.ac.uk
> 
> <Vina_Rfp3.pdb>
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Baptiste,
These files look good to me, I get:
PyMOL>rms Crystal_Rfp, Vina_Rfp
 Executive: RMSD = 0.032 (51 to 51 atoms)
Is it possible that you tried with a multi-model (multiple poses) pdbqt file before? If that's the case, specify "mobile_state" and/or "target_state":
PyMOL>rms Crystal_Rfp, Vina_Rfp, mobile_state=1, target_state=1
 Executive: RMSD = 0.032 (51 to 51 atoms)
See also "Notes" section here: https://pymolwiki.org/index.php/Align#Notes
Cheers,
 Thomas
> On Jul 26, 2018, at 9:42 AM, Baptiste Legrand <bap...@gm...> wrote:
> 
> Thanks for your answers. The molecule is the rifampicin. Please find attached the pdb from the crystal structure and the pdbqt from autodock vina. May be the format of one or both files is not correct.
> 
> Best,
> 
> Baptiste
> 
> 
> Le 25/07/2018 à 18:57, Markus Heller a écrit :
>> Not knowing what your molecule looks like, could it be automorphism?
>> 
>>> -----Original Message-----
>>> From: Baptiste Legrand <bap...@gm...>
>>> Sent: Wednesday, July 25, 2018 9:17 AM
>>> To: pym...@li...
>>> Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and
>>> from a docking
>>> 
>>> Dear all,
>>> 
>>> I tried to calculate a rmsd value between ligands from a crystal structure and
>>> after docking. The two molecules share similar nomenclatures and are really
>>> well superimposed. I think that the RMSD should be < 1 A. I used the following
>>> lines:
>>> 
>>> alter all,segi=""
>>> alter all,chain =""
>>> rms /ligand_crystal////*, /ligand_docking////*
>>> 
>>> It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the
>>> pair_fit function, pymol completely return one molecule and also write
>>> "ExecutiveRMS: RMS = 6.146 (51 to 51 atoms)". I should have missed
>>> something...
>>> 
>>> thanks for the help,
>>> All the Best.
>>> 
>>> Baptiste
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

<html>
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 </head>
 <body text="#000000" bgcolor="#FFFFFF">
 <tt>Hi Baptiste, <br>
 <br>
 removing the data at the end of the HETATM lines from ca.
 character 70 onwards fixed it. Not sure what these are. According
 to PDB 3.30 format, 67-76 should be empty. Some of the elements
 were non-standard also (NA for N, OA for O), but looks to be the
 numbers in the "empty" columns that bother PyMOL (perhaps it
 should just ignore these?).<br>
 <br>
 A lot of other things I do not recognise in PDB files in you docked
 rifampicin too, but those seem not to bother the analysis. <br>
 <br>
 See attached. RMSD 0.032 for 51 atoms. Not a bad docking pose!<br>
 <br>
 cheers, Marko<br>
 </tt><br>
 <div class="moz-cite-prefix">On 26/07/2018 08:42, Baptiste Legrand
 wrote:<br>
 </div>
 <blockquote type="cite"
 cite="mid:4cf...@gm...">Thanks
 for your answers. The molecule is the rifampicin. Please find
 attached the pdb from the crystal structure and the pdbqt from
 autodock vina. May be the format of one or both files is not
 correct.
 <br>
 <br>
 Best,
 <br>
 <br>
 Baptiste
 <br>
 <br>
 <br>
 Le 25/07/2018 à 18:57, Markus Heller a écrit :
 <br>
 <blockquote type="cite">Not knowing what your molecule looks like,
 could it be automorphism?
 <br>
 <br>
 <blockquote type="cite">-----Original Message-----
 <br>
 From: Baptiste Legrand <a class="moz-txt-link-rfc2396E" href="mailto:bap...@gm...">&lt;bap...@gm...&gt;</a>
 <br>
 Sent: Wednesday, July 25, 2018 9:17 AM
 <br>
 To: <a class="moz-txt-link-abbreviated" href="mailto:pym...@li...">pym...@li...</a>
 <br>
 Subject: [PyMOL] Calculate RMSD between ligands from a crystal
 structure and
 <br>
 from a docking
 <br>
 <br>
 Dear all,
 <br>
 <br>
 I tried to calculate a rmsd value between ligands from a
 crystal structure and
 <br>
 after docking. The two molecules share similar nomenclatures
 and are really
 <br>
 well superimposed. I think that the RMSD should be &lt; 1 A. I
 used the following
 <br>
 lines:
 <br>
 <br>
 alter all,segi=""
 <br>
 alter all,chain =""
 <br>
 rms /ligand_crystal////*, /ligand_docking////*
 <br>
 <br>
 It works but I obtained an abnormal high RMSD value of 6.146
 A. When I use the
 <br>
 pair_fit function, pymol completely return one molecule and
 also write
 <br>
 "ExecutiveRMS: RMS =  6.146 (51 to 51 atoms)". I should have
 missed
 <br>
 something...
 <br>
 <br>
 thanks for the help,
 <br>
 All the Best.
 <br>
 <br>
 Baptiste
 <br>
 <br>
 <br>
 <br>
------------------------------------------------------------------------------
 <br>
 Check out the vibrant tech community on one of the world's
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 <br>
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 <pre wrap="">_______________________________________________
PyMOL-users mailing list (<a class="moz-txt-link-abbreviated" href="mailto:PyM...@li...">PyM...@li...</a>)
Info Page: <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/pymol-users">https://lists.sourceforge.net/lists/listinfo/pymol-users</a>
Archives: <a class="moz-txt-link-freetext" href="http://www.mail-archive.com/pym...@li...">http://www.mail-archive.com/pym...@li...</a></pre>
 </blockquote>
 <br>
 <pre class="moz-signature" cols="72">-- 
Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
 
</pre>
 </body>
</html>

Thanks for your answers. The molecule is the rifampicin. Please find 
attached the pdb from the crystal structure and the pdbqt from autodock 
vina. May be the format of one or both files is not correct.
Best,
Baptiste
Le 25/07/2018 à 18:57, Markus Heller a écrit :
> Not knowing what your molecule looks like, could it be automorphism?
>
>> -----Original Message-----
>> From: Baptiste Legrand <bap...@gm...>
>> Sent: Wednesday, July 25, 2018 9:17 AM
>> To: pym...@li...
>> Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and
>> from a docking
>>
>> Dear all,
>>
>> I tried to calculate a rmsd value between ligands from a crystal structure and
>> after docking. The two molecules share similar nomenclatures and are really
>> well superimposed. I think that the RMSD should be < 1 A. I used the following
>> lines:
>>
>> alter all,segi=""
>> alter all,chain =""
>> rms /ligand_crystal////*, /ligand_docking////*
>>
>> It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the
>> pair_fit function, pymol completely return one molecule and also write
>> "ExecutiveRMS: RMS =  6.146 (51 to 51 atoms)". I should have missed
>> something...
>>
>> thanks for the help,
>> All the Best.
>>
>> Baptiste
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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...

Not knowing what your molecule looks like, could it be automorphism?
> -----Original Message-----
> From: Baptiste Legrand <bap...@gm...>
> Sent: Wednesday, July 25, 2018 9:17 AM
> To: pym...@li...
> Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and
> from a docking
> 
> Dear all,
> 
> I tried to calculate a rmsd value between ligands from a crystal structure and
> after docking. The two molecules share similar nomenclatures and are really
> well superimposed. I think that the RMSD should be < 1 A. I used the following
> lines:
> 
> alter all,segi=""
> alter all,chain =""
> rms /ligand_crystal////*, /ligand_docking////*
> 
> It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the
> pair_fit function, pymol completely return one molecule and also write
> "ExecutiveRMS: RMS =  6.146 (51 to 51 atoms)". I should have missed
> something...
> 
> thanks for the help,
> All the Best.
> 
> Baptiste
> 
> 
> 
> ------------------------------------------------------------------------------
> 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...

Dear all,
I tried to calculate a rmsd value between ligands from a crystal 
structure and after docking. The two molecules share similar 
nomenclatures and are really well superimposed. I think that the RMSD 
should be < 1 A. I used the following lines:
alter all,segi=""
alter all,chain =""
rms /ligand_crystal////*, /ligand_docking////*
It works but I obtained an abnormal high RMSD value of 6.146 A. When I 
use the pair_fit function, pymol completely return one molecule and also 
write "ExecutiveRMS: RMS =  6.146 (51 to 51 atoms)". I should have 
missed something...
thanks for the help,
All the Best.
Baptiste

Awesome. This is exactly what I was looking for.
Nathan
On Mon, Jul 23, 2018 at 11:16 AM Jarrett Johnson <
jar...@sc...> wrote:
> Hello Nathan,
>
> While we prepare to rollout the "quiet" argument for pair_fit, in the
> meantime try:
>
> cmd.feedback("disable", "executive", "results")
>
> Jarrett J.
>
> On Sun, Jul 22, 2018 at 6:47 PM, Jarrett Johnson <
> jar...@sc...> wrote:
>
>> Hello Nathan,
>>
>> We actually just implemented a 'quiet' argument for the pair_fit command
>> on Friday. This should be live in an upcoming update.
>>
>> Jarrett J.
>>
>> On Sun, Jul 22, 2018 at 6:32 PM, <ncl...@cs...> wrote:
>>
>>> Hi,
>>>
>>> Consider the following (simplified) Pymol script, test.py:
>>>
>>> -----
>>> import sys
>>> cmd.load(sys.argv[1], 'prot1')
>>> cmd.load(sys.argv[2], 'prot2')
>>> rms = cmd.pair_fit('prot1 & n. ca','prot2 & n. ca')
>>> print 'This should print', rms
>>>
>>> -----
>>>
>>> I would like the only output for this program to be created by the line,
>>> 'This should print.' However, here is what I actually get, with a few
>>> different options:
>>>
>>> $ pymol -qc test.py -- protein.pdb protein.pdb
>>> ExecutiveRMS: RMS = 0.000 (96 to 96 atoms)
>>> This should print 0.0
>>> $ pymol -Qc test.py -- protein.pdb protein.pdb
>>> $
>>>
>>> (The first prints output from ExecutiveRMS, and the second prints nothing
>>> at all.)
>>> Is there any way to prevent the ExecutiveRMS output? Either
>>> programmatically or on the command line?
>>>
>>> Thanks much,
>>>
>>> Nathan
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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...
>>>
>>
>>
>>
>> --
>> Jarrett Johnson,
>> Schrödinger
>>
>
>
>
> --
> Jarrett Johnson,
> Schrödinger
>

Thanks Marko for reminding us of good and professional communication practices.
We have removed the three email addresses from the mailing list.
If anyone else needs to be unsubscribed and doesn't know how to do it themselves, please email me directly.
Thanks,
 Thomas
> On Jul 24, 2018, at 4:49 PM, Marko Hyvonen <mh...@ca...> wrote:
> 
> Sorry, but is this a joke of some sort? Or a piss-take?
> 
> If one of the above, can we stop it, please. It is not "handy" to receive this spam either.
> 
> If these are serious requests to be unsubscribed, follow the link below for page where you can unsubscribe. Presumably you subscribed to this in the first instance???
> 
> Am I the only one annoyed also of this propagation of social media (?) custom of not signing emails with your name? This is a professional mailing list where you can expect the very people (the real experts!) who wrote the software etc to reply to you and the replies come from individuals with real names and affiliations. (the same goes for ccp4, phenix, coot.. bulletin boards)
> 
> best, Marko
> 
> On 24/07/2018 14:27, Nahuel Naum Foressi wrote:
>> Dear Mr. and Mrs,
>> 
>> Please remove my account from pymol-user mailing list.
>> it is not handy to receive all these e mails.
>> 
>> 
>> Thanks
>> 
>> 
>> 2018年07月24日 4:10 GMT-03:00 <m.t...@nk...>:
>> Dear Mr. and Mrs,
>> 
>> 
>> Please remove my account from pymol-user mailing list.
>> 
>> it is not handy to receive all these e mails.
>> 
>> 
>> 
>> Thanks
>> 
>> 
>> 
>> 
>> 
>> From: 신현길 [mailto:hyu...@ki...] 
>> Sent: dinsdag 24 juli 2018 2:44
>> To: pym...@li...
>> Subject: [PyMOL] Unsubscribe pymol user mails
>> 
>> 
>> Dear Mr. or Mrs. 
>> 
>> 
>> I don't want to recieve pymol user mails.
>> 
>> Please remove my account from pymol-user mailing list.
>> 
>> 
>> Thanks 
>> 
>> 
>> 
>> <image001.jpg>
> 
> -- 
> 
> Marko Hyvonen
> Department of Biochemistry, University of Cambridge
> 
> mh...@ca...
> 
> +44 (0)1223 766 044
> @HyvonenGroup
> 
> http://hyvonen.bioc.cam.ac.uk
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

<html>
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 </head>
 <body text="#000000" bgcolor="#FFFFFF">
 <tt>Sorry, but is this a joke of some sort? Or a piss-take?<br>
 <br>
 If one of the above, can we stop it, please. It is not "handy" to
 receive this spam either.<br>
 <br>
 If these are serious requests to be unsubscribed, follow the link
 below for page where you can unsubscribe. Presumably you
 subscribed to this in the first instance???<br>
 <br>
 Am I the only one annoyed also of this propagation of social media
 (?) custom of not signing emails with your name? This is a
 professional mailing list where you can expect the very people
 (the real experts!) who wrote the software etc to reply to you and
 the replies come from individuals with real names and
 affiliations. (the same goes for ccp4, phenix, coot.. bulletin
 boards)<br>
 <br>
 best, Marko<br>
 <br>
 </tt>
 <div class="moz-cite-prefix">On 24/07/2018 14:27, Nahuel Naum
 Foressi wrote:<br>
 </div>
 <blockquote type="cite"
cite="mid:CAA...@ma...">
 <meta http-equiv="content-type" content="text/html; charset=utf-8">
 <div dir="ltr">
 <p class="MsoNormal" style="margin:0px
0cm;font-size:12pt;font-family:Gulim,sans-serif;text-decoration-style:initial;text-decoration-color:initial"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Dear
 Mr. and Mrs,</span></p>
 <span class="gmail-im"
style="color:rgb(80,0,80);font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial">
 <p class="MsoNormal" style="margin:0px
 0cm;font-size:12pt;font-family:Gulim,sans-serif"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></p>
 <p class="MsoNormal" style="margin:0px
 0cm;font-size:12pt;font-family:Gulim,sans-serif"><span
 style="font-family:Dotum,sans-serif">Please remove my
 account from pymol-user mailing list.</span></p>
 </span>
 <p class="MsoNormal" style="margin:0px
0cm;font-size:12pt;font-family:Gulim,sans-serif;text-decoration-style:initial;text-decoration-color:initial"><span
 style="font-family:Dotum,sans-serif">it is not handy to
 receive all these e mails.</span></p>
 <p class="MsoNormal" style="margin:0px
0cm;font-size:12pt;font-family:Gulim,sans-serif;text-decoration-style:initial;text-decoration-color:initial"><span
 style="font-family:Dotum,sans-serif"> </span></p>
 <p class="MsoNormal" style="margin:0px
0cm;font-size:12pt;font-family:Gulim,sans-serif;text-decoration-style:initial;text-decoration-color:initial"><span
 style="font-family:Dotum,sans-serif"> </span></p>
 <p class="MsoNormal" style="margin:0px
0cm;font-size:12pt;font-family:Gulim,sans-serif;text-decoration-style:initial;text-decoration-color:initial"><span
 style="font-family:Dotum,sans-serif">Thanks</span></p>
 <br>
 </div>
 <div class="gmail_extra"><br>
 <div class="gmail_quote">2018年07月24日 4:10 GMT-03:00 <span
 dir="ltr">&lt;<a href="mailto:m.t...@nk..."
 target="_blank" moz-do-not-send="true">m.t...@nk...</a>&gt;</span>:<br>
 <blockquote class="gmail_quote" style="margin:0 0 0
 .8ex;border-left:1px #ccc solid;padding-left:1ex">
 <div link="blue" vlink="purple" lang="EN-US">
 <div class="m_6100001841272857512WordSection1">
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style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">Dear
 Mr. and Mrs,</span></p>
 <span class="">
 <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"> </span></p>
 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;">Please remove
 my account from pymol-user mailing list.</span></p>
 </span>
 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;">it
 is not handy to receive all these e mails.</span></p>
 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;"> </span></p>
 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;"> </span></p>
 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;">Thanks</span></p>
 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;"> </span></p>
 <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"> </span></p>
 <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"> </span></p>
 <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"> </span></p>
 <p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span
style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">
 </span><span style="font-size:10.0pt" lang="KO">신현길</span><span
style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">
 [mailto:<a href="mailto:hyu...@ki..."
 target="_blank" moz-do-not-send="true">hyu...@ki....<wbr>kr</a>]
 <br>
 <b>Sent:</b> dinsdag 24 juli 2018 2:44<br>
 <b>To:</b> <a
 href="mailto:pym...@li..."
 target="_blank" moz-do-not-send="true">pym...@li....<wbr>net</a><br>
 <b>Subject:</b> [PyMOL] Unsubscribe pymol user mails</span></p>
 <div>
 <div class="h5">
 <p class="MsoNormal"> </p>
 <div>
 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;">Dear
 Mr. or Mrs. </span></p>
 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;"> </span></p>
 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;">I
 don't want to recieve pymol user mails.</span></p>
 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;">Please remove
 my account from pymol-user mailing list.</span></p>
 <p class="MsoNormal"><span
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 <p class="MsoNormal"><span
 style="font-family:&quot;Dotum&quot;,&quot;sans-serif&quot;">Thanks </span></p>
 </div>
 <p class="MsoNormal"><br>
 <br>
 <img id="m_6100001841272857512_x0000_i1025"
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 class="" height="100" width="600"></p>
 </div>
 </div>
 </div>
 </div>
 <br>
 ------------------------------<wbr>------------------------------<wbr>------------------<br>
 Check out the vibrant tech community on one of the world's
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 href="http://sdm.link/slashdot" rel="noreferrer"
 target="_blank" moz-do-not-send="true">http://sdm.link/slashdot</a><br>
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 href="mailto:PyM...@li..."
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 </blockquote>
 <br>
 <pre class="moz-signature" cols="72">-- 
Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
 
</pre>
 </body>
</html>

Dear Mr. and Mrs,
Please remove my account from pymol-user mailing list.
it is not handy to receive all these e mails.
Thanks
2018年07月24日 4:10 GMT-03:00 <m.t...@nk...>:
> Dear Mr. and Mrs,
>
>
>
> Please remove my account from pymol-user mailing list.
>
> it is not handy to receive all these e mails.
>
>
>
>
>
> Thanks
>
>
>
>
>
>
>
>
>
> *From:* 신현길 [mailto:hyu...@ki...]
> *Sent:* dinsdag 24 juli 2018 2:44
> *To:* pym...@li...
> *Subject:* [PyMOL] Unsubscribe pymol user mails
>
>
>
> Dear Mr. or Mrs.
>
>
>
> I don't want to recieve pymol user mails.
>
> Please remove my account from pymol-user mailing list.
>
>
>
> Thanks
>
>
>
>
> ------------------------------------------------------------
> ------------------
> 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...
>

Greetings,
We are happy to announce the release of PyMOL 2.2. Download ready-to-use installers from https://pymol.org/ or update your installation with "conda update -c schrodinger pymol".
New features include:
- MAE (Maestro) format export with styling, properties, and group hierarchy
- Nucleic acid mutagenesis wizard
- Stereochemistry labeling with RDKit or $SCHRODINGER backend
Find the complete release notes at:
https://pymol.org/d/media:new22 
We welcome any feedback and bug reports.
Cheers,
- The PyMOL Team at Schrödinger
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Mr. and Mrs,
Please remove my account from pymol-user mailing list.
it is not handy to receive all these e mails.
Thanks
From: 신현길 [mailto:hyu...@ki...]
Sent: dinsdag 24 juli 2018 2:44
To: pym...@li...
Subject: [PyMOL] Unsubscribe pymol user mails
Dear Mr. or Mrs.
I don't want to recieve pymol user mails.
Please remove my account from pymol-user mailing list.
Thanks
[cid:image001.jpg@01D4232D.DD88D660]

Dear Mr. or Mrs. 
 
I don't want to recieve pymol user mails.
Please remove my account from pymol-user mailing list.
 
Thanks