From prathvi at iitk.ac.in  Tue Nov  2 03:53:56 2021
From: prathvi at iitk.ac.in (Prathvi Singh)
Date: Tue, 2 Nov 2021 16:23:56 +0530
Subject: [Chimera-users] Counting the number of water molecules
Message-ID: <CAD3Hi5YV4=RuXDbrsYpQYqr6nS5g6yf6EUyyg=k1X1Z-+Fn-4g@mail.gmail.com>

Hi,

Is there a command in UCSF chimera to count the total no. of water
molecules in a PDB file? Can we also count, say the total number of alanine
residues in a PDB file or any other other residue for that matter?

-- 
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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From meng at cgl.ucsf.edu  Tue Nov  2 09:50:13 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 2 Nov 2021 09:50:13 -0700
Subject: [Chimera-users] Counting the number of water molecules
In-Reply-To: <CAD3Hi5YV4=RuXDbrsYpQYqr6nS5g6yf6EUyyg=k1X1Z-+Fn-4g@mail.gmail.com>
References: <CAD3Hi5YV4=RuXDbrsYpQYqr6nS5g6yf6EUyyg=k1X1Z-+Fn-4g@mail.gmail.com>
Message-ID: <0BF388C6-2DC2-4751-A5E8-C1B599B6C740@cgl.ucsf.edu>

Hi Prathvi,
You can use selection, then look at the Selection Inspector to see number of residues.

For example, command:

select :hoh

.... or menu:

Select... Residues... HOH

...and then open the Selection Inspector by clicking the green magnifying glass at the lower right corner of the Chimera window.  The top part of that dialog will say how many residues are selected.

See selection
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
Selection Inspector
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 2, 2021, at 3:53 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> 
> Is there a command in UCSF chimera to count the total no. of water molecules in a PDB file? Can we also count, say the total number of alanine residues in a PDB file or any other other residue for that matter?
> 
> -- 
> Prathvi Singh,
> Research Fellow,
> Department of Biological Sciences & Bioengineering,
> Indian Institute of Technology, Kanpur-208016
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From francesca.magarotto2 at studio.unibo.it  Wed Nov  3 06:53:38 2021
From: francesca.magarotto2 at studio.unibo.it (Francesca Magarotto - francesca.magarotto2@studio.unibo.it)
Date: Wed, 3 Nov 2021 13:53:38 +0000
Subject: [Chimera-users] Showbox
Message-ID: <VI1PR0102MB32458287A35F852D5E13A588808C9@VI1PR0102MB3245.eurprd01.prod.exchangelabs.com>

Hi,
I know that the program showbox is related to Dock, but I can't find a mailing list still active for Dock users...
Maybe someone could help me here.
I don't understand if ligands that are docked inside the binding site can exit in part from the box the user defines for grid calculation.
I think that maybe if sphere centers are very near the boundaries of the box, it could be possible, but I'm not sure.
Does anyone know it?
Thanks and regards.
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From saniyatkate99 at gmail.com  Wed Nov  3 06:57:17 2021
From: saniyatkate99 at gmail.com (Saniya Kate)
Date: Wed, 3 Nov 2021 19:27:17 +0530
Subject: [Chimera-users] error while running chimera
Message-ID: <CAA_jpDvDh0qiJ7SAV7AWCjm7D6jTSXPH2Jmiq0J=vFbxdVNt9g@mail.gmail.com>

Good evening,
i am Student and Installed chimera for WINDOWS (chimera-1.15-win64.exe
<https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/chimera-1.15-win64.exe>)
from
your website but I am unable to run it on my system since it is a 64 bit
release and my system is 32 bit. I urgently need chimera for my project
work but I'm not able to use it since the 32 bit release of chimera isn't
available.
please let me know what can be done
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From meng at cgl.ucsf.edu  Wed Nov  3 08:48:56 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 3 Nov 2021 08:48:56 -0700
Subject: [Chimera-users] old 32-bit Chimera versions
In-Reply-To: <CAA_jpDvDh0qiJ7SAV7AWCjm7D6jTSXPH2Jmiq0J=vFbxdVNt9g@mail.gmail.com>
References: <CAA_jpDvDh0qiJ7SAV7AWCjm7D6jTSXPH2Jmiq0J=vFbxdVNt9g@mail.gmail.com>
Message-ID: <54E18E46-C02C-4392-B6E4-4C39D5F9290F@cgl.ucsf.edu>

Dear Saniya Kate,
If you look at the download page, there is a link to older releases including 32-bit versions.  Here is the link for that old releases page... you have to go to the bottom half for the 32-bit releases:
<https://www.rbvi.ucsf.edu/chimera/olddownload.html>

However, these are very old and may not have the features you want, if the features were added later than 2016.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Nov 3, 2021, at 6:57 AM, Saniya Kate via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Good evening,
> i am Student and Installed chimera for WINDOWS (chimera-1.15-win64.exe) from your website but I am unable to run it on my system since it is a 64 bit release and my system is 32 bit. I urgently need chimera for my project work but I'm not able to use it since the 32 bit release of chimera isn't available. 
> please let me know what can be done



From meng at cgl.ucsf.edu  Wed Nov  3 09:02:25 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 3 Nov 2021 09:02:25 -0700
Subject: [Chimera-users] Showbox
In-Reply-To: <VI1PR0102MB32458287A35F852D5E13A588808C9@VI1PR0102MB3245.eurprd01.prod.exchangelabs.com>
References: <VI1PR0102MB32458287A35F852D5E13A588808C9@VI1PR0102MB3245.eurprd01.prod.exchangelabs.com>
Message-ID: <2B66AAAF-B2F6-42BC-AF25-61B0210C499C@cgl.ucsf.edu>

This page at the UCSF Dock website says to use dock_fans at googlegroups.com ... did you try that one?

<http://dock.compbio.ucsf.edu/Contact_Info/index.htm>

We (Chimera/X developers) are not the UCSF DOCK developers.  I personally worked on early versions of DOCK, but that was >25 years ago!!

I might have written that showbox thing a LONG time ago, but I've forgotten the details.  To the best of my memory, it is just to help in setting up the calculation of scoring grids.  The user (you) are the one who decides the scoring grid box size and location, and showbox is just for displaying a given box size and location so you can decide whether it is appropriate or not before calculating the grid.  Docking does not actually use that box.  If I remember correctly, the ligand could possibly fall outside of it, which just means that the ligand part outside the box will not contribute to its score.  Hopefully you would choose a grid box location that would enclose the spheres you want to use for docking, plus some additional space, so that most ligand poses would be fully inside of it.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 3, 2021, at 6:53 AM, Francesca Magarotto - francesca.magarotto2--- via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> I know that the program showbox is related to Dock, but I can't find a mailing list still active for Dock users...
> Maybe someone could help me here.
> I don't understand if ligands that are docked inside the binding site can exit in part from the box the user defines for grid calculation.
> I think that maybe if sphere centers are very near the boundaries of the box, it could be possible, but I'm not sure.
> Does anyone know it?
> Thanks and regards.



From saniyatkate99 at gmail.com  Wed Nov  3 09:50:08 2021
From: saniyatkate99 at gmail.com (Saniya Kate)
Date: Wed, 3 Nov 2021 22:20:08 +0530
Subject: [Chimera-users] old 32-bit Chimera versions
In-Reply-To: <54E18E46-C02C-4392-B6E4-4C39D5F9290F@cgl.ucsf.edu>
References: <CAA_jpDvDh0qiJ7SAV7AWCjm7D6jTSXPH2Jmiq0J=vFbxdVNt9g@mail.gmail.com>
 <54E18E46-C02C-4392-B6E4-4C39D5F9290F@cgl.ucsf.edu>
Message-ID: <CAA_jpDs_Ce1u0oNXZNPxUtFnxYE6bHL-YAZQQp1e0nd-5iyGvA@mail.gmail.com>

Thanks, I'll check them out.

On Wed, 3 Nov 2021, 9:19 pm Elaine Meng, <meng at cgl.ucsf.edu> wrote:

> Dear Saniya Kate,
> If you look at the download page, there is a link to older releases
> including 32-bit versions.  Here is the link for that old releases page...
> you have to go to the bottom half for the 32-bit releases:
> <https://www.rbvi.ucsf.edu/chimera/olddownload.html>
>
> However, these are very old and may not have the features you want, if the
> features were added later than 2016.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Nov 3, 2021, at 6:57 AM, Saniya Kate via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Good evening,
> > i am Student and Installed chimera for WINDOWS (chimera-1.15-win64.exe)
> from your website but I am unable to run it on my system since it is a 64
> bit release and my system is 32 bit. I urgently need chimera for my project
> work but I'm not able to use it since the 32 bit release of chimera isn't
> available.
> > please let me know what can be done
>
>
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From roberto.santos.p.s at outlook.com  Sat Nov  6 18:49:28 2021
From: roberto.santos.p.s at outlook.com (Paulo Roberto da Silva Santos)
Date: Sun, 7 Nov 2021 01:49:28 +0000
Subject: [Chimera-users] Chimera Laucher Error
Message-ID: <RO1P152MB0219942BCDF03F99F1780AC596909@RO1P152MB0219.LAMP152.PROD.OUTLOOK.COM>

Hi,

 I was intalated Chimera 1.5 64bit under Windows 10 64 bit, I was intalated Chimera 1.5 64bit under Windows 10 64 bit, and all was fine until I started executed,  ?Chimera crashed and now it gives me an error at launch and quits, so I cannot run it anymore.

After launch, the error window shows:

--------------------------------------------------------------------------------
Chimera exited abnormally; the exit code was: -1073741819. Use the --debug command line option for the full error message.
--------------------------------------------------------------------------------

Paulo Roberto da Silva Santos
Bacharel em Qu?mica - UFPB
Mestrando em Qu?mica  - UFPB
LCCQS - Laborat?rio de Compostos de Coordena??o e Qu?mica de Superf?cie
(83) 99915-5963

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From eunice.gsh1990 at gmail.com  Mon Nov  8 03:18:34 2021
From: eunice.gsh1990 at gmail.com (Eunice Gwee)
Date: Mon, 8 Nov 2021 22:18:34 +1100
Subject: [Chimera-users] Selecting and listing all residues in a specific
	area
Message-ID: <CAD+2CwuRscXG=WH_KBCkK1CXUO2hVuWwT4AkG4WcAzZEfdjvBA@mail.gmail.com>

To whom this may concern,

I have been using the Autodock Vina function on Chimera for my studies and
I was wondering if it is possible to list the residues in the selected area
of the protein used in docking.

Thank you.

With regards,
Eunice
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From prathvi at iitk.ac.in  Mon Nov  8 03:39:26 2021
From: prathvi at iitk.ac.in (Prathvi Singh)
Date: Mon, 8 Nov 2021 17:09:26 +0530
Subject: [Chimera-users] Writing data to a text file
Message-ID: <CAD3Hi5aQk+gK=vi7G0reXp-7MgJyXS1FM+SqtPf-+9fHwTLrxA@mail.gmail.com>

Hi,

Suppose I want to find the distance between all atoms of residue-A and
residue-B & write the distances to a file. Is it possible to do so in a
meaningful way?

-- 
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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From meng at cgl.ucsf.edu  Mon Nov  8 07:53:40 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 8 Nov 2021 07:53:40 -0800
Subject: [Chimera-users] Selecting and listing all residues in a
 specific area
In-Reply-To: <CAD+2CwuRscXG=WH_KBCkK1CXUO2hVuWwT4AkG4WcAzZEfdjvBA@mail.gmail.com>
References: <CAD+2CwuRscXG=WH_KBCkK1CXUO2hVuWwT4AkG4WcAzZEfdjvBA@mail.gmail.com>
Message-ID: <AEBF8601-0347-4D71-BB3F-88E4BA0E2B9D@cgl.ucsf.edu>

Hi Eunice,
Not exactly, but if you can "select" a set of residues by any method, e.g. by Ctrl-click-dragging a box around them, or by distance zone from an atom or residue (first select the atom or residue, and then use menu Select... Zone...), then you can write a list of what is selected (menu Actions... Write List...).

Many different ways to select residues:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

Actions menu including Write LIst
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuactions>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 8, 2021, at 3:18 AM, Eunice Gwee via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> To whom this may concern,
> I have been using the Autodock Vina function on Chimera for my studies and I was wondering if it is possible to list the residues in the selected area of the protein used in docking.
> Thank you.
> With regards,
> Eunice



From meng at cgl.ucsf.edu  Mon Nov  8 08:05:18 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 8 Nov 2021 08:05:18 -0800
Subject: [Chimera-users] Writing data to a text file
In-Reply-To: <CAD3Hi5aQk+gK=vi7G0reXp-7MgJyXS1FM+SqtPf-+9fHwTLrxA@mail.gmail.com>
References: <CAD3Hi5aQk+gK=vi7G0reXp-7MgJyXS1FM+SqtPf-+9fHwTLrxA@mail.gmail.com>
Message-ID: <8C452DFD-F7CD-4F87-AB0C-C662E268FB52@cgl.ucsf.edu>

Hi Prathvi,
You can get all-by-all distances written to a file or the Reply Log by using Find Clashes/Contacts or the clashes command, by defining residue-A as the first set of atoms, residue-B as the second set of atoms, and and using a large negative cutoff value that will just get everything.  For example, if it's residue 10 in chain A of model 0 versus residue 50 in chain B of model 1, the command to send info to the Log could be something like

findclash #0:10.A  test #1:50.B overlap -1000 log true

(and/or use the saveFile option to save to file)

Find Clashes/Contacts tool
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>

findclash command and its options
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

ChimeraX (our newer program) also has a tool and command to do this same thing, if you're interested.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 8, 2021, at 3:39 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way?



From gregc at cgl.ucsf.edu  Mon Nov  8 09:54:00 2021
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 8 Nov 2021 09:54:00 -0800
Subject: [Chimera-users] Chimera Laucher Error
In-Reply-To: <RO1P152MB0219942BCDF03F99F1780AC596909@RO1P152MB0219.LAMP152.PROD.OUTLOOK.COM>
References: <RO1P152MB0219942BCDF03F99F1780AC596909@RO1P152MB0219.LAMP152.PROD.OUTLOOK.COM>
Message-ID: <26b530ad-659c-1071-ea6d-9a660f5dd265@cgl.ucsf.edu>

Do you have AMD Radeon graphics by any chance?? If so, you need to get 
the latest driver from amd.com.? If not, update your graphics driver 
anyway.? The most common cause of weird errors like this are buggy 
graphics drivers.


 ??? HTH,


 ??? Greg


On 11/6/2021 6:49 PM, Paulo Roberto da Silva Santos via Chimera-users wrote:
> Hi,
>
> ?I was intalated Chimera 1.5 64bit under Windows 10 64 bit,?I was 
> intalated Chimera 1.5 64bit under Windows 10 64 bit, and all was fine 
> until I started executed, ??Chimera crashed and now it gives me an 
> error at launch and quits, so I cannot run it anymore.
>
> After launch, the error window shows:
>
> --------------------------------------------------------------------------------
> Chimera exited abnormally; the exit code was: -1073741819. Use the 
> --debug command line option for the full error message.
> --------------------------------------------------------------------------------
>
> *Paulo Roberto da Silva Santos*
> *Bacharel em Qu?mica - UFPB*
> *Mestrando em Qu?mica? - UFPB*
> *LCCQS - Laborat?rio?de Compostos de Coordena??o e Qu?mica de 
> **Superf?cie*
> *(83) 99915-5963*
>
>
> _______________________________________________
> Chimera-users mailing list:Chimera-users at cgl.ucsf.edu
> Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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From nazarychev at imc.macro.ru  Mon Nov  8 10:35:45 2021
From: nazarychev at imc.macro.ru (Victor Nazarychev)
Date: Mon, 8 Nov 2021 21:35:45 +0300
Subject: [Chimera-users] the version of Ambertools that are used in the
 command "Write prmtop"?
In-Reply-To: <1E6617CD-F733-4583-B0F6-6605DF4AA31D@cgl.ucsf.edu>
References: <CALpHq2dxB9e9kEmpM3bd3B52tTg445edMN1bi2MR+Ad4ahFQ0Q@mail.gmail.com>
 <588D3708-F0EA-4BE3-9152-D67A2A03DC66@cgl.ucsf.edu>
 <CALpHq2cnuAFH1VY7aWy_P2t0ftY=7qrEqts+No5yrEKybQZUkA@mail.gmail.com>
 <1E6617CD-F733-4583-B0F6-6605DF4AA31D@cgl.ucsf.edu>
Message-ID: <CALpHq2f99wO-cov8aMZbhHZ3RoudxDwGb6y+=raNS_xZ1cYMUg@mail.gmail.com>

Hello, Eric,

Sorry for the delay with response. But when I chose the Tools>Amder>Write
Prmtop> in the menu Select force field type I only can select 6 force
fields, and GAFF could not be chosen.

Could you please direct where in the Chimera menu I can select the option
to build a GAFF force field using the menu "Write Prmtop"?

Best regards,
Victor

??, 27 ???. 2021 ?. ? 20:58, Eric Pettersen <pett at cgl.ucsf.edu>:

> Hi Victor,
> I'm not sure I understand the question.  The Write Prmtop tool will write
> a .prmtop file using GAFF types if necessary.  That prmtop file uses a
> somewhat older version of the prmtop format, but most tools will still read
> it.
>
> --Eric
>
> On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <nazarychev at imc.macro.ru>
> wrote:
>
> Dear Eric,
>
> Thank you for your help.
>
> Maybe you know how to build *.prmtop file of substance namely in the GAFF
> force field, using Chimera's tools?
>
> Best regards,
> Victor
>
> ??, 26 ???. 2021 ?. ? 20:14, Eric Pettersen <pett at cgl.ucsf.edu>:
>
>> Hi Victor,
>>         Most of Chimera uses AmberTools18 (e.g. minimization; charge
>> addition), but specifically the tools in the Tools?Amber menu use
>> functionality provided by sleap, which is not distributed with current
>> versions of AmberTools.  Those tools use AmberTools 1.5, which was released
>> in 2011.
>>
>> --Eric
>>
>>         Eric Pettersen
>>         UCSF Computer Graphics Lab
>>
>>
>> > On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users <
>> chimera-users at cgl.ucsf.edu> wrote:
>> >
>> > Dear Chimera's users,
>> >
>> > I built amber's .inpcrd and prmtop files using command write prmtop
>> from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how
>> could I figure out what version of AmberTools is incorporated in this
>> Chimera release?
>> >
>> > Best regards,
>> > Victor
>> > _______________________________________________
>> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> > Manage subscription:
>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>
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From pett at cgl.ucsf.edu  Mon Nov  8 11:19:16 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 8 Nov 2021 11:19:16 -0800
Subject: [Chimera-users] the version of Ambertools that are used in the
 command "Write prmtop"?
In-Reply-To: <CALpHq2f99wO-cov8aMZbhHZ3RoudxDwGb6y+=raNS_xZ1cYMUg@mail.gmail.com>
References: <CALpHq2dxB9e9kEmpM3bd3B52tTg445edMN1bi2MR+Ad4ahFQ0Q@mail.gmail.com>
 <588D3708-F0EA-4BE3-9152-D67A2A03DC66@cgl.ucsf.edu>
 <CALpHq2cnuAFH1VY7aWy_P2t0ftY=7qrEqts+No5yrEKybQZUkA@mail.gmail.com>
 <1E6617CD-F733-4583-B0F6-6605DF4AA31D@cgl.ucsf.edu>
 <CALpHq2f99wO-cov8aMZbhHZ3RoudxDwGb6y+=raNS_xZ1cYMUg@mail.gmail.com>
Message-ID: <A030C576-65B0-4303-ACE2-64E7A3BE08BB@cgl.ucsf.edu>

Hi Victor,
	Chimera will use GAFF types for non-standard residues in all those forcefields, and regular AMBER types for standard residues.  There is no option to use GAFF types for all residues.

--Eric

> On Nov 8, 2021, at 10:35 AM, Victor Nazarychev <nazarychev at imc.macro.ru> wrote:
> 
> Hello, Eric,
> 
> Sorry for the delay with response. But when I chose the Tools>Amder>Write Prmtop> in the menu Select force field type I only can select 6 force fields, and GAFF could not be chosen. 
> 
> Could you please direct where in the Chimera menu I can select the option to build a GAFF force field using the menu "Write Prmtop"? 
> 
> Best regards, 
> Victor
> 
> ??, 27 ???. 2021 ?. ? 20:58, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>>:
> Hi Victor,
> 	I'm not sure I understand the question.  The Write Prmtop tool will write a .prmtop file using GAFF types if necessary.  That prmtop file uses a somewhat older version of the prmtop format, but most tools will still read it.
> 
> --Eric
> 
>> On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <nazarychev at imc.macro.ru <mailto:nazarychev at imc.macro.ru>> wrote:
>> 
>> Dear Eric, 
>> 
>> Thank you for your help.  
>> 
>> Maybe you know how to build *.prmtop file of substance namely in the GAFF force field, using Chimera's tools?
>> 
>> Best regards, 
>> Victor 
>> 
>> ??, 26 ???. 2021 ?. ? 20:14, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>>:
>> Hi Victor,
>>         Most of Chimera uses AmberTools18 (e.g. minimization; charge addition), but specifically the tools in the Tools?Amber menu use functionality provided by sleap, which is not distributed with current versions of AmberTools.  Those tools use AmberTools 1.5, which was released in 2011.
>> 
>> --Eric
>> 
>>         Eric Pettersen
>>         UCSF Computer Graphics Lab
>> 
>> 
>> > On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>> wrote:
>> > 
>> > Dear Chimera's users, 
>> > 
>> > I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release? 
>> > 
>> > Best regards, 
>> > Victor
>> > _______________________________________________
>> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>> 
> 

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From nazarychev at imc.macro.ru  Mon Nov  8 11:53:47 2021
From: nazarychev at imc.macro.ru (Victor Nazarychev)
Date: Mon, 8 Nov 2021 22:53:47 +0300
Subject: [Chimera-users] the version of Ambertools that are used in the
 command "Write prmtop"?
In-Reply-To: <A030C576-65B0-4303-ACE2-64E7A3BE08BB@cgl.ucsf.edu>
References: <CALpHq2dxB9e9kEmpM3bd3B52tTg445edMN1bi2MR+Ad4ahFQ0Q@mail.gmail.com>
 <588D3708-F0EA-4BE3-9152-D67A2A03DC66@cgl.ucsf.edu>
 <CALpHq2cnuAFH1VY7aWy_P2t0ftY=7qrEqts+No5yrEKybQZUkA@mail.gmail.com>
 <1E6617CD-F733-4583-B0F6-6605DF4AA31D@cgl.ucsf.edu>
 <CALpHq2f99wO-cov8aMZbhHZ3RoudxDwGb6y+=raNS_xZ1cYMUg@mail.gmail.com>
 <A030C576-65B0-4303-ACE2-64E7A3BE08BB@cgl.ucsf.edu>
Message-ID: <CALpHq2fhKnvktqLAumZVn0pNvkW_UaKiQtiik5K=wdnWvbBZKQ@mail.gmail.com>

Eric,

Thank you for your answer!

Victor

??, 8 ????. 2021 ?. ? 22:19, Eric Pettersen <pett at cgl.ucsf.edu>:

> Hi Victor,
> Chimera will use GAFF types for non-standard residues in all those
> forcefields, and regular AMBER types for standard residues.  There is no
> option to use GAFF types for all residues.
>
> --Eric
>
> On Nov 8, 2021, at 10:35 AM, Victor Nazarychev <nazarychev at imc.macro.ru>
> wrote:
>
> Hello, Eric,
>
> Sorry for the delay with response. But when I chose the Tools>Amder>Write
> Prmtop> in the menu Select force field type I only can select 6 force
> fields, and GAFF could not be chosen.
>
> Could you please direct where in the Chimera menu I can select the option
> to build a GAFF force field using the menu "Write Prmtop"?
>
> Best regards,
> Victor
>
> ??, 27 ???. 2021 ?. ? 20:58, Eric Pettersen <pett at cgl.ucsf.edu>:
>
>> Hi Victor,
>> I'm not sure I understand the question.  The Write Prmtop tool will write
>> a .prmtop file using GAFF types if necessary.  That prmtop file uses a
>> somewhat older version of the prmtop format, but most tools will still read
>> it.
>>
>> --Eric
>>
>> On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <nazarychev at imc.macro.ru>
>> wrote:
>>
>> Dear Eric,
>>
>> Thank you for your help.
>>
>> Maybe you know how to build *.prmtop file of substance namely in the GAFF
>> force field, using Chimera's tools?
>>
>> Best regards,
>> Victor
>>
>> ??, 26 ???. 2021 ?. ? 20:14, Eric Pettersen <pett at cgl.ucsf.edu>:
>>
>>> Hi Victor,
>>>         Most of Chimera uses AmberTools18 (e.g. minimization; charge
>>> addition), but specifically the tools in the Tools?Amber menu use
>>> functionality provided by sleap, which is not distributed with current
>>> versions of AmberTools.  Those tools use AmberTools 1.5, which was released
>>> in 2011.
>>>
>>> --Eric
>>>
>>>         Eric Pettersen
>>>         UCSF Computer Graphics Lab
>>>
>>>
>>> > On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users <
>>> chimera-users at cgl.ucsf.edu> wrote:
>>> >
>>> > Dear Chimera's users,
>>> >
>>> > I built amber's .inpcrd and prmtop files using command write prmtop
>>> from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how
>>> could I figure out what version of AmberTools is incorporated in this
>>> Chimera release?
>>> >
>>> > Best regards,
>>> > Victor
>>> > _______________________________________________
>>> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>> > Manage subscription:
>>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>>
>>
>
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From prathvi at iitk.ac.in  Mon Nov  8 17:41:30 2021
From: prathvi at iitk.ac.in (Prathvi Singh)
Date: Tue, 9 Nov 2021 07:11:30 +0530
Subject: [Chimera-users] Writing data to a text file
In-Reply-To: <8C452DFD-F7CD-4F87-AB0C-C662E268FB52@cgl.ucsf.edu>
References: <CAD3Hi5aQk+gK=vi7G0reXp-7MgJyXS1FM+SqtPf-+9fHwTLrxA@mail.gmail.com>
 <8C452DFD-F7CD-4F87-AB0C-C662E268FB52@cgl.ucsf.edu>
Message-ID: <CAD3Hi5axUWQ3z9spLpEhPtkF+AzqwrcwmyRWXRBX+E6Cn+6D7g@mail.gmail.com>

Thanks Elaine for the help. I checked out ChimeraX & it is definitely much
more user-friendly. The presence of the reply log at the right side really
helps keep track of the actions one is performing and THANKS A LOT for the
undo feature. I really miss it in Chimera. Still, I wonder if there is a
way or a plugin to incorporate the "undo" command in chimera...


On Mon, Nov 8, 2021 at 9:35 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Prathvi,
> You can get all-by-all distances written to a file or the Reply Log by
> using Find Clashes/Contacts or the clashes command, by defining residue-A
> as the first set of atoms, residue-B as the second set of atoms, and and
> using a large negative cutoff value that will just get everything.  For
> example, if it's residue 10 in chain A of model 0 versus residue 50 in
> chain B of model 1, the command to send info to the Log could be something
> like
>
> findclash #0:10.A  test #1:50.B overlap -1000 log true
>
> (and/or use the saveFile option to save to file)
>
> Find Clashes/Contacts tool
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
> >
>
> findclash command and its options
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
>
> ChimeraX (our newer program) also has a tool and command to do this same
> thing, if you're interested.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Nov 8, 2021, at 3:39 AM, Prathvi Singh via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hi,
> > Suppose I want to find the distance between all atoms of residue-A and
> residue-B & write the distances to a file. Is it possible to do so in a
> meaningful way?
>
>

-- 
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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From meng at cgl.ucsf.edu  Mon Nov  8 17:51:51 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 8 Nov 2021 17:51:51 -0800
Subject: [Chimera-users] Writing data to a text file
In-Reply-To: <CAD3Hi5axUWQ3z9spLpEhPtkF+AzqwrcwmyRWXRBX+E6Cn+6D7g@mail.gmail.com>
References: <CAD3Hi5aQk+gK=vi7G0reXp-7MgJyXS1FM+SqtPf-+9fHwTLrxA@mail.gmail.com>
 <8C452DFD-F7CD-4F87-AB0C-C662E268FB52@cgl.ucsf.edu>
 <CAD3Hi5axUWQ3z9spLpEhPtkF+AzqwrcwmyRWXRBX+E6Cn+6D7g@mail.gmail.com>
Message-ID: <8D90D06A-787B-47F4-B04B-8247CC9C7926@cgl.ucsf.edu>

Sorry, no.  It is actually quite difficult to implement undo, or so I'm told (I'm not the one doing it).  Chimera has an "Undo Move" tool but that's pretty much it, and we are not actively developing Chimera to add features any more.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/undomove/undomove.html>

Our development focus is now on ChimeraX.  The ChimeraX undo doesn't include everything, but we tried to include many common actions.  Glad you like it!

ChimeraX undo:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/undo.html>

ChimeraX short list of advantages over Chimera:
<https://rbvi.ucsf.edu/chimerax/docs/user/advantages.html>

Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Nov 8, 2021, at 5:41 PM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Thanks Elaine for the help. I checked out ChimeraX & it is definitely much more user-friendly. The presence of the reply log at the right side really helps keep track of the actions one is performing and THANKS A LOT for the undo feature. I really miss it in Chimera. Still, I wonder if there is a way or a plugin to incorporate the "undo" command in chimera...
> 
> 
> On Mon, Nov 8, 2021 at 9:35 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Prathvi,
> You can get all-by-all distances written to a file or the Reply Log by using Find Clashes/Contacts or the clashes command, by defining residue-A as the first set of atoms, residue-B as the second set of atoms, and and using a large negative cutoff value that will just get everything.  For example, if it's residue 10 in chain A of model 0 versus residue 50 in chain B of model 1, the command to send info to the Log could be something like
> 
> findclash #0:10.A  test #1:50.B overlap -1000 log true
> 
> (and/or use the saveFile option to save to file)
> 
> Find Clashes/Contacts tool
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
> 
> findclash command and its options
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
> 
> ChimeraX (our newer program) also has a tool and command to do this same thing, if you're interested.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Nov 8, 2021, at 3:39 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > 
> > Hi,
> > Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way?
> 
> 
> 
> -- 
> Prathvi Singh,
> Research Fellow,
> Department of Biological Sciences & Bioengineering,
> Indian Institute of Technology, Kanpur-208016
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From prathvi at iitk.ac.in  Mon Nov  8 18:49:25 2021
From: prathvi at iitk.ac.in (Prathvi Singh)
Date: Tue, 9 Nov 2021 08:19:25 +0530
Subject: [Chimera-users] Writing data to a text file
In-Reply-To: <8D90D06A-787B-47F4-B04B-8247CC9C7926@cgl.ucsf.edu>
References: <CAD3Hi5aQk+gK=vi7G0reXp-7MgJyXS1FM+SqtPf-+9fHwTLrxA@mail.gmail.com>
 <8C452DFD-F7CD-4F87-AB0C-C662E268FB52@cgl.ucsf.edu>
 <CAD3Hi5axUWQ3z9spLpEhPtkF+AzqwrcwmyRWXRBX+E6Cn+6D7g@mail.gmail.com>
 <8D90D06A-787B-47F4-B04B-8247CC9C7926@cgl.ucsf.edu>
Message-ID: <CAD3Hi5Y77yB94FhRHbcN6rAkG3m+ZDF4Dtq3ncoAjtvhfnxFPA@mail.gmail.com>

I got it. Thanks Elaine.

On Tue, Nov 9, 2021 at 7:21 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Sorry, no.  It is actually quite difficult to implement undo, or so I'm
> told (I'm not the one doing it).  Chimera has an "Undo Move" tool but
> that's pretty much it, and we are not actively developing Chimera to add
> features any more.
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/undomove/undomove.html
> >
>
> Our development focus is now on ChimeraX.  The ChimeraX undo doesn't
> include everything, but we tried to include many common actions.  Glad you
> like it!
>
> ChimeraX undo:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/undo.html>
>
> ChimeraX short list of advantages over Chimera:
> <https://rbvi.ucsf.edu/chimerax/docs/user/advantages.html>
>
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Nov 8, 2021, at 5:41 PM, Prathvi Singh via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Thanks Elaine for the help. I checked out ChimeraX & it is definitely
> much more user-friendly. The presence of the reply log at the right side
> really helps keep track of the actions one is performing and THANKS A LOT
> for the undo feature. I really miss it in Chimera. Still, I wonder if there
> is a way or a plugin to incorporate the "undo" command in chimera...
> >
> >
> > On Mon, Nov 8, 2021 at 9:35 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Prathvi,
> > You can get all-by-all distances written to a file or the Reply Log by
> using Find Clashes/Contacts or the clashes command, by defining residue-A
> as the first set of atoms, residue-B as the second set of atoms, and and
> using a large negative cutoff value that will just get everything.  For
> example, if it's residue 10 in chain A of model 0 versus residue 50 in
> chain B of model 1, the command to send info to the Log could be something
> like
> >
> > findclash #0:10.A  test #1:50.B overlap -1000 log true
> >
> > (and/or use the saveFile option to save to file)
> >
> > Find Clashes/Contacts tool
> > <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
> >
> >
> > findclash command and its options
> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
> >
> > ChimeraX (our newer program) also has a tool and command to do this same
> thing, if you're interested.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Nov 8, 2021, at 3:39 AM, Prathvi Singh via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> > >
> > > Hi,
> > > Suppose I want to find the distance between all atoms of residue-A and
> residue-B & write the distances to a file. Is it possible to do so in a
> meaningful way?
> >
> >
> >
> > --
> > Prathvi Singh,
> > Research Fellow,
> > Department of Biological Sciences & Bioengineering,
> > Indian Institute of Technology, Kanpur-208016
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>

-- 
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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From heather.noriega at bison.howard.edu  Tue Nov  9 12:28:52 2021
From: heather.noriega at bison.howard.edu (Noriega, Heather)
Date: Tue, 9 Nov 2021 15:28:52 -0500
Subject: [Chimera-users] Solvation question
Message-ID: <CA+YTS9Xy09vP=cTyL=6J61jLendLCmfDxXBc1rXRHm6tdN6iyQ@mail.gmail.com>

Hello,

I have a quick question. I am running the solvate command before the
minimization, equilibrium, and production run in Chimera. I click the start
solvate tool and put my water box size and apply. This gives me my box and
in the command line it says created...with however many water molecules. I
then go run parameters, set up everything. Once I hit run, the water box
dissappears. I just want to make sure that the solvation did occur even
though the water box dissappears from the screen. Everything else ran
smoothly to show simulation. I just want to be certain and have
confirmation that the solvation does occur as long as I use apply and do
not close out of the window. Thanks in advance for your help.

Thank you,

Heather Noriega
PhD-Pharmaceutical Science student
College of Pharmacy
Howard University
heather.noriega at bison.howard.edu
520-203-1883
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From meng at cgl.ucsf.edu  Tue Nov  9 13:07:00 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 9 Nov 2021 13:07:00 -0800
Subject: [Chimera-users] Solvation question
In-Reply-To: <CA+YTS9Xy09vP=cTyL=6J61jLendLCmfDxXBc1rXRHm6tdN6iyQ@mail.gmail.com>
References: <CA+YTS9Xy09vP=cTyL=6J61jLendLCmfDxXBc1rXRHm6tdN6iyQ@mail.gmail.com>
Message-ID: <E75FEFE3-D6BE-477A-A4CF-4DBA7791482A@cgl.ucsf.edu>

Hello Heather,
It may be a quick question but not that quick of an answer...

It sounds like you are using the separate solvation command or tool instead of the Solvation tab in the Molecular Dynamics tool.  Instead, you need to use only the tabs in that tool: first Prep Structure, then Solvation, then Run Parameters. 

The problem is if you solvate separately first, then the Molecular Dynamics tool sees that prepping still needs to be done and calls Dock Prep, which automatically deletes the waters.

I really hope you aren't trying to run this on your capsid model!!  That is waaaay too huge and Chimera's MD calculations way too slow to give any meaningful results.  Please see the gray box with the caveats to this tool in the Molecular Dynamics Simulation documentation:

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 9, 2021, at 12:28 PM, Noriega, Heather via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I have a quick question. I am running the solvate command before the minimization, equilibrium, and production run in Chimera. I click the start solvate tool and put my water box size and apply. This gives me my box and in the command line it says created...with however many water molecules. I then go run parameters, set up everything. Once I hit run, the water box dissappears. I just want to make sure that the solvation did occur even though the water box dissappears from the screen. Everything else ran smoothly to show simulation. I just want to be certain and have confirmation that the solvation does occur as long as I use apply and do not close out of the window. Thanks in advance for your help. 
> Thank you,
> Heather Noriega



From heather.noriega at bison.howard.edu  Tue Nov  9 14:05:34 2021
From: heather.noriega at bison.howard.edu (Noriega, Heather)
Date: Tue, 9 Nov 2021 17:05:34 -0500
Subject: [Chimera-users] Solvation question
In-Reply-To: <E75FEFE3-D6BE-477A-A4CF-4DBA7791482A@cgl.ucsf.edu>
References: <CA+YTS9Xy09vP=cTyL=6J61jLendLCmfDxXBc1rXRHm6tdN6iyQ@mail.gmail.com>
 <E75FEFE3-D6BE-477A-A4CF-4DBA7791482A@cgl.ucsf.edu>
Message-ID: <CA+YTS9UB=JbUWD42v6Pw5Cup2Wttv_edGuhY2S1yFQa3QVH1Ug@mail.gmail.com>

Hello, Elaine,

No, not on my capsid model. I am working on am example monomer. Ok, so in
the Molecular Dynamics Simulation box. I have dock prepped, created my
solvation box, have all the default settings for minimization, equilibrium,
and production. Added a number for the trajectories so they save where I
want them to. Now, the screen goes black around the 8th frame. Do you know
why?

Thank you,

Heather Noriega
PhD-Pharmaceutical Science student
College of Pharmacy
Howard University
heather.noriega at bison.howard.edu
520-203-1883

On Tue, Nov 9, 2021, 4:07 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Heather,
> It may be a quick question but not that quick of an answer...
>
> It sounds like you are using the separate solvation command or tool
> instead of the Solvation tab in the Molecular Dynamics tool.  Instead, you
> need to use only the tabs in that tool: first Prep Structure, then
> Solvation, then Run Parameters.
>
> The problem is if you solvate separately first, then the Molecular
> Dynamics tool sees that prepping still needs to be done and calls Dock
> Prep, which automatically deletes the waters.
>
> I really hope you aren't trying to run this on your capsid model!!  That
> is waaaay too huge and Chimera's MD calculations way too slow to give any
> meaningful results.  Please see the gray box with the caveats to this tool
> in the Molecular Dynamics Simulation documentation:
>
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Nov 9, 2021, at 12:28 PM, Noriega, Heather via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hello,
> > I have a quick question. I am running the solvate command before the
> minimization, equilibrium, and production run in Chimera. I click the start
> solvate tool and put my water box size and apply. This gives me my box and
> in the command line it says created...with however many water molecules. I
> then go run parameters, set up everything. Once I hit run, the water box
> dissappears. I just want to make sure that the solvation did occur even
> though the water box dissappears from the screen. Everything else ran
> smoothly to show simulation. I just want to be certain and have
> confirmation that the solvation does occur as long as I use apply and do
> not close out of the window. Thanks in advance for your help.
> > Thank you,
> > Heather Noriega
>
>
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From meng at cgl.ucsf.edu  Tue Nov  9 14:37:14 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 9 Nov 2021 14:37:14 -0800
Subject: [Chimera-users] Solvation question
In-Reply-To: <CA+YTS9UB=JbUWD42v6Pw5Cup2Wttv_edGuhY2S1yFQa3QVH1Ug@mail.gmail.com>
References: <CA+YTS9Xy09vP=cTyL=6J61jLendLCmfDxXBc1rXRHm6tdN6iyQ@mail.gmail.com>
 <E75FEFE3-D6BE-477A-A4CF-4DBA7791482A@cgl.ucsf.edu>
 <CA+YTS9UB=JbUWD42v6Pw5Cup2Wttv_edGuhY2S1yFQa3QVH1Ug@mail.gmail.com>
Message-ID: <A095F566-CDD0-41C5-9576-5FFEE877FB39@cgl.ucsf.edu>

Hello Heather,
No I do not, sorry.

As mentioned in the tool caveats, the tool was developed in large part by another group for small-molecule dynamics, and may not be generally robust for macromolecular calculations.  

You might need to use a dedicated dynamics package like AMBER or GROMACS instead of Chimera for your application.
Elaine

> On Nov 9, 2021, at 2:05 PM, Noriega, Heather via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello, Elaine,
> 
> No, not on my capsid model. I am working on am example monomer. Ok, so in the Molecular Dynamics Simulation box. I have dock prepped, created my solvation box, have all the default settings for minimization, equilibrium, and production. Added a number for the trajectories so they save where I want them to. Now, the screen goes black around the 8th frame. Do you know why? 
> 
> Thank you,
> 
> Heather Noriega
> PhD-Pharmaceutical Science student
> College of Pharmacy
> Howard University
> heather.noriega at bison.howard.edu 
> 520-203-1883
> 
> On Tue, Nov 9, 2021, 4:07 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hello Heather,
> It may be a quick question but not that quick of an answer...
> 
> It sounds like you are using the separate solvation command or tool instead of the Solvation tab in the Molecular Dynamics tool.  Instead, you need to use only the tabs in that tool: first Prep Structure, then Solvation, then Run Parameters. 
> 
> The problem is if you solvate separately first, then the Molecular Dynamics tool sees that prepping still needs to be done and calls Dock Prep, which automatically deletes the waters.
> 
> I really hope you aren't trying to run this on your capsid model!!  That is waaaay too huge and Chimera's MD calculations way too slow to give any meaningful results.  Please see the gray box with the caveats to this tool in the Molecular Dynamics Simulation documentation:
> 
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Nov 9, 2021, at 12:28 PM, Noriega, Heather via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > 
> > Hello,
> > I have a quick question. I am running the solvate command before the minimization, equilibrium, and production run in Chimera. I click the start solvate tool and put my water box size and apply. This gives me my box and in the command line it says created...with however many water molecules. I then go run parameters, set up everything. Once I hit run, the water box dissappears. I just want to make sure that the solvation did occur even though the water box dissappears from the screen. Everything else ran smoothly to show simulation. I just want to be certain and have confirmation that the solvation does occur as long as I use apply and do not close out of the window. Thanks in advance for your help. 
> > Thank you,
> > Heather Noriega
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From pett at cgl.ucsf.edu  Tue Nov  9 16:00:04 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 9 Nov 2021 16:00:04 -0800
Subject: [Chimera-users] Solvation question
In-Reply-To: <A095F566-CDD0-41C5-9576-5FFEE877FB39@cgl.ucsf.edu>
References: <CA+YTS9Xy09vP=cTyL=6J61jLendLCmfDxXBc1rXRHm6tdN6iyQ@mail.gmail.com>
 <E75FEFE3-D6BE-477A-A4CF-4DBA7791482A@cgl.ucsf.edu>
 <CA+YTS9UB=JbUWD42v6Pw5Cup2Wttv_edGuhY2S1yFQa3QVH1Ug@mail.gmail.com>
 <A095F566-CDD0-41C5-9576-5FFEE877FB39@cgl.ucsf.edu>
Message-ID: <7410D531-F08A-4D33-A7DC-D67748BA4B43@cgl.ucsf.edu>

It has been my experience that the screen going black means that the simulation failed.  Specifically, some of the energies went to infinity and the molecule "exploded".  This typically means that some atoms/bonds/angles in your system were not properly parameterized.  There should be messages in the Reply Log (Favorites?Reply Log) about missing parameters/radii/masses/charges.  Proper parameterization is a pretty advanced topic and requires a bit of expertise.  It would also require more control over the simulation than Chimera offers, i.e. using one of the packages that Elaine mentions.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Nov 9, 2021, at 2:37 PM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello Heather,
> No I do not, sorry.
> 
> As mentioned in the tool caveats, the tool was developed in large part by another group for small-molecule dynamics, and may not be generally robust for macromolecular calculations.  
> 
> You might need to use a dedicated dynamics package like AMBER or GROMACS instead of Chimera for your application.
> Elaine
> 
>> On Nov 9, 2021, at 2:05 PM, Noriega, Heather via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Hello, Elaine,
>> 
>> No, not on my capsid model. I am working on am example monomer. Ok, so in the Molecular Dynamics Simulation box. I have dock prepped, created my solvation box, have all the default settings for minimization, equilibrium, and production. Added a number for the trajectories so they save where I want them to. Now, the screen goes black around the 8th frame. Do you know why? 
>> 
>> Thank you,
>> 
>> Heather Noriega
>> PhD-Pharmaceutical Science student
>> College of Pharmacy
>> Howard University
>> heather.noriega at bison.howard.edu 
>> 520-203-1883
>> 
>> On Tue, Nov 9, 2021, 4:07 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hello Heather,
>> It may be a quick question but not that quick of an answer...
>> 
>> It sounds like you are using the separate solvation command or tool instead of the Solvation tab in the Molecular Dynamics tool.  Instead, you need to use only the tabs in that tool: first Prep Structure, then Solvation, then Run Parameters. 
>> 
>> The problem is if you solvate separately first, then the Molecular Dynamics tool sees that prepping still needs to be done and calls Dock Prep, which automatically deletes the waters.
>> 
>> I really hope you aren't trying to run this on your capsid model!!  That is waaaay too huge and Chimera's MD calculations way too slow to give any meaningful results.  Please see the gray box with the caveats to this tool in the Molecular Dynamics Simulation documentation:
>> 
>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
>> 
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Nov 9, 2021, at 12:28 PM, Noriega, Heather via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hello,
>>> I have a quick question. I am running the solvate command before the minimization, equilibrium, and production run in Chimera. I click the start solvate tool and put my water box size and apply. This gives me my box and in the command line it says created...with however many water molecules. I then go run parameters, set up everything. Once I hit run, the water box dissappears. I just want to make sure that the solvation did occur even though the water box dissappears from the screen. Everything else ran smoothly to show simulation. I just want to be certain and have confirmation that the solvation does occur as long as I use apply and do not close out of the window. Thanks in advance for your help. 
>>> Thank you,
>>> Heather Noriega
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From kavyapandya.phd2020 at iar.ac.in  Tue Nov  9 21:43:36 2021
From: kavyapandya.phd2020 at iar.ac.in (Kavya Pandya)
Date: Wed, 10 Nov 2021 11:13:36 +0530
Subject: [Chimera-users] Regarding publication using Chimera.
Message-ID: <CANqK+pAgUBOHO3_7=WFaJ+7kYswadnwBzBuOAd2KoJ=DEhUhkA@mail.gmail.com>

Dear Sir/Ma'am,

I am a PhD scholar at the Institute of Advanced Research, India. I have
been using the free version of Chimera for the last few days. I wanted to
ask if I could publish the images created in Chimera using that free
version by citing it appropriately using the citation provided on the
website or do I need to buy the license to publish?

 Would you please guide me for the same.

Thank You
Kavya
PhD Scholar

-- 
Disclaimer :

This e-mail and any files transmitted with it are for the 
sole use of the intended recipient(s) /addressee and may contain 
confidential and privileged information. If you are not the intended 
recipient/addressee, please contact the sender by reply e-mail and destroy 
all copies and the original message. Any unauthorized review, use, 
disclosure, dissemination, forwarding, printing or copying of this email or 
any action taken in reliance on this?email?is strictly prohibited and may 
be unlawful. The recipient /addressee acknowledges that Institute of 
Advanced Research (IAR) are unable to exercise control or ensure or 
guarantee the integrity of/over the contents of the information contained 
in e-mail transmissions and further acknowledges that any views expressed 
in this message are those of the individual sender and no binding nature of 
the message shall be implied or assumed unless the sender does so expressly 
with due authority of Institute of Advanced Research (IAR). Internet 
communications cannot be guaranteed to be timely, secure, error or 
virus-free, thus the sender does not accept liability for any errors or 
omissions. Before opening any attachments please check them for viruses and 
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From meng at cgl.ucsf.edu  Wed Nov 10 09:14:55 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 10 Nov 2021 09:14:55 -0800
Subject: [Chimera-users] Regarding publication using Chimera.
In-Reply-To: <CANqK+pAgUBOHO3_7=WFaJ+7kYswadnwBzBuOAd2KoJ=DEhUhkA@mail.gmail.com>
References: <CANqK+pAgUBOHO3_7=WFaJ+7kYswadnwBzBuOAd2KoJ=DEhUhkA@mail.gmail.com>
Message-ID: <1131DE68-96E1-4382-B1F0-40DF7885BD41@cgl.ucsf.edu>

Dear Kavya,
Chimera is free for noncommercial (academic, educational, nonprofit) use, including making figures for presentations and publications.  In the publication, please cite any use of the program, whether for calculations and/or figures, as described here:
<https://www.rbvi.ucsf.edu/chimera/docs/credits.html>

Commercial use, i.e. by a for-profit company, requires purchasing a license, as described here:
<https://www.rbvi.ucsf.edu/chimera/commercial_license.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 9, 2021, at 9:43 PM, Kavya Pandya via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Sir/Ma'am,
> I am a PhD scholar at the Institute of Advanced Research, India. I have been using the free version of Chimera for the last few days. I wanted to ask if I could publish the images created in Chimera using that free version by citing it appropriately using the citation provided on the website or do I need to buy the license to publish?
>  Would you please guide me for the same. 
> Thank You
> Kavya
> PhD Scholar



From kavyapandya.phd2020 at iar.ac.in  Thu Nov 11 01:38:47 2021
From: kavyapandya.phd2020 at iar.ac.in (Kavya Pandya)
Date: Thu, 11 Nov 2021 15:08:47 +0530
Subject: [Chimera-users] Regarding publication using Chimera.
In-Reply-To: <1131DE68-96E1-4382-B1F0-40DF7885BD41@cgl.ucsf.edu>
References: <CANqK+pAgUBOHO3_7=WFaJ+7kYswadnwBzBuOAd2KoJ=DEhUhkA@mail.gmail.com>
 <1131DE68-96E1-4382-B1F0-40DF7885BD41@cgl.ucsf.edu>
Message-ID: <CANqK+pB77_R5Hz6ZepJpTjUDCvkORghDVYBiyhQLOSxL-S=JWw@mail.gmail.com>

Dear Elaine Meng,

Thank you so much for the information. I will surely cite the reference as
mentioned on the website.

Thank you

On Wed, Nov 10, 2021 at 10:44 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Kavya,
> Chimera is free for noncommercial (academic, educational, nonprofit) use,
> including making figures for presentations and publications.  In the
> publication, please cite any use of the program, whether for calculations
> and/or figures, as described here:
> <https://www.rbvi.ucsf.edu/chimera/docs/credits.html>
>
> Commercial use, i.e. by a for-profit company, requires purchasing a
> license, as described here:
> <https://www.rbvi.ucsf.edu/chimera/commercial_license.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Nov 9, 2021, at 9:43 PM, Kavya Pandya via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Sir/Ma'am,
> > I am a PhD scholar at the Institute of Advanced Research, India. I have
> been using the free version of Chimera for the last few days. I wanted to
> ask if I could publish the images created in Chimera using that free
> version by citing it appropriately using the citation provided on the
> website or do I need to buy the license to publish?
> >  Would you please guide me for the same.
> > Thank You
> > Kavya
> > PhD Scholar
>
>

-- 
Disclaimer :

This e-mail and any files transmitted with it are for the 
sole use of the intended recipient(s) /addressee and may contain 
confidential and privileged information. If you are not the intended 
recipient/addressee, please contact the sender by reply e-mail and destroy 
all copies and the original message. Any unauthorized review, use, 
disclosure, dissemination, forwarding, printing or copying of this email or 
any action taken in reliance on this?email?is strictly prohibited and may 
be unlawful. The recipient /addressee acknowledges that Institute of 
Advanced Research (IAR) are unable to exercise control or ensure or 
guarantee the integrity of/over the contents of the information contained 
in e-mail transmissions and further acknowledges that any views expressed 
in this message are those of the individual sender and no binding nature of 
the message shall be implied or assumed unless the sender does so expressly 
with due authority of Institute of Advanced Research (IAR). Internet 
communications cannot be guaranteed to be timely, secure, error or 
virus-free, thus the sender does not accept liability for any errors or 
omissions. Before opening any attachments please check them for viruses and 
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From terre031 at r.umn.edu  Thu Nov 11 08:58:06 2021
From: terre031 at r.umn.edu (Cassidy Terrell)
Date: Thu, 11 Nov 2021 10:58:06 -0600
Subject: [Chimera-users] Chimera Launch Error
Message-ID: <CALzePbkKEkDURwQyTTBu_8G4+zTXGCSGyTwR9n-WfTXnYgHniQ@mail.gmail.com>

Hello,

A student in my course (cced here) is trying to open Chimera 1.15 and this
is the error message that appears:

"chimera exited abnormally; the exit code was -1073741819. Use the --debug
command line option for the full error message."

We cannot open the program, which mean we cannot get to the command line.

Thoughts about how to proceed? We have already removed/uninstalled previous
version and re-downloaded new one. The same messages appears each time.

Best
Cassidy

-- 
Cassidy R. Terrell, Ph.D. (she/her/hers)

Assistant Professor, Biochemistry
Center for Learning Innovation | University of Minnesota | Rochester
300 University Square | Rochester, MN 55904

*Always believe something wonderful is about to happen*
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From gregc at cgl.ucsf.edu  Thu Nov 11 10:34:47 2021
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 11 Nov 2021 10:34:47 -0800
Subject: [Chimera-users] Chimera Launch Error
In-Reply-To: <CALzePbkKEkDURwQyTTBu_8G4+zTXGCSGyTwR9n-WfTXnYgHniQ@mail.gmail.com>
References: <CALzePbkKEkDURwQyTTBu_8G4+zTXGCSGyTwR9n-WfTXnYgHniQ@mail.gmail.com>
Message-ID: <28cf5e14-772e-5b0a-de03-2c63cee54a80@cgl.ucsf.edu>

You don't say which platform this is on.? I'm going to assume it's on 
Microsoft Windows.? You can get the debug messages by using the Start 
menu and opening "UCSF Chimera 1.15 / Chimera - Debug".

That said, the typical cause of this problem is an outdated graphics 
driver.? Please update the system to the latest and greatest version.? 
This is especially true right now if you have AMD Radeon graphics, but 
also applies if you have Intel or NVidia graphics.

 ??? Regards,

 ??? Greg

On 11/11/2021 8:58 AM, Cassidy Terrell via Chimera-users wrote:
> Hello,
>
> A student in my course (cced here) is trying to open Chimera 1.15 and 
> this is the error message that appears:
>
> "chimera exited abnormally; the exit code was -1073741819. Use the 
> --debug command line option for the full error message."
>
> We cannot open the program, which mean we cannot get to the command line.
>
> Thoughts about how to proceed? We have already removed/uninstalled 
> previous version and re-downloaded new one. The same messages appears 
> each time.
>
> Best
> Cassidy
>
> -- 
> Cassidy R. Terrell, Ph.D. (she/her/hers)
>
> Assistant Professor, Biochemistry
> Center for Learning Innovation?|?University of Minnesota?|?Rochester
> 300 University Square | Rochester, MN 55904
>
> /Always believe something wonderful is about to happen/
>
>
> _______________________________________________
> Chimera-users mailing list:Chimera-users at cgl.ucsf.edu
> Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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From terre031 at r.umn.edu  Fri Nov 12 07:42:42 2021
From: terre031 at r.umn.edu (Cassidy Terrell)
Date: Fri, 12 Nov 2021 09:42:42 -0600
Subject: [Chimera-users] Chimera Launch Error
In-Reply-To: <28cf5e14-772e-5b0a-de03-2c63cee54a80@cgl.ucsf.edu>
References: <CALzePbkKEkDURwQyTTBu_8G4+zTXGCSGyTwR9n-WfTXnYgHniQ@mail.gmail.com>
 <28cf5e14-772e-5b0a-de03-2c63cee54a80@cgl.ucsf.edu>
Message-ID: <CALzePb=QDCMJr_GbfFHORDETFd+qG5NrrBBmPOp-A4eB3-J3vg@mail.gmail.com>

Yes this is for a laptop with Microsoft Windows. How do I update the
system?

On Thu, Nov 11, 2021 at 2:02 PM Greg Couch <gregc at cgl.ucsf.edu> wrote:

> You don't say which platform this is on.  I'm going to assume it's on
> Microsoft Windows.  You can get the debug messages by using the Start menu
> and opening "UCSF Chimera 1.15 / Chimera - Debug".
>
> That said, the typical cause of this problem is an outdated graphics
> driver.  Please update the system to the latest and greatest version.  This
> is especially true right now if you have AMD Radeon graphics, but also
> applies if you have Intel or NVidia graphics.
>
>     Regards,
>
>     Greg
> On 11/11/2021 8:58 AM, Cassidy Terrell via Chimera-users wrote:
>
> Hello,
>
> A student in my course (cced here) is trying to open Chimera 1.15 and this
> is the error message that appears:
>
> "chimera exited abnormally; the exit code was -1073741819. Use the --debug
> command line option for the full error message."
>
> We cannot open the program, which mean we cannot get to the command line.
>
> Thoughts about how to proceed? We have already removed/uninstalled
> previous version and re-downloaded new one. The same messages appears each
> time.
>
> Best
> Cassidy
>
> --
> Cassidy R. Terrell, Ph.D. (she/her/hers)
>
> Assistant Professor, Biochemistry
> Center for Learning Innovation | University of Minnesota | Rochester
> 300 University Square | Rochester, MN 55904
>
> *Always believe something wonderful is about to happen*
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>

-- 
Cassidy R. Terrell, Ph.D. (she/her/hers)

Assistant Professor, Biochemistry
Center for Learning Innovation | University of Minnesota | Rochester
300 University Square | Rochester, MN 55904

*Always believe something wonderful is about to happen*
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From gregc at cgl.ucsf.edu  Fri Nov 12 10:16:46 2021
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 12 Nov 2021 10:16:46 -0800
Subject: [Chimera-users] Chimera Launch Error
In-Reply-To: <CALzePb=QDCMJr_GbfFHORDETFd+qG5NrrBBmPOp-A4eB3-J3vg@mail.gmail.com>
References: <CALzePbkKEkDURwQyTTBu_8G4+zTXGCSGyTwR9n-WfTXnYgHniQ@mail.gmail.com>
 <28cf5e14-772e-5b0a-de03-2c63cee54a80@cgl.ucsf.edu>
 <CALzePb=QDCMJr_GbfFHORDETFd+qG5NrrBBmPOp-A4eB3-J3vg@mail.gmail.com>
Message-ID: <e56633e1-1c97-e744-2aac-c23baf46b59b@cgl.ucsf.edu>

You don't say what kind of graphics you have.? Or whether or not you 
have administrative access to the system.? The rest of this assumes you 
do.? If you don't have administrative access, you'll need to get the 
system administrator to update the system.

To find out what graphics you have, right-click on the background and 
select "Display Settings".? Then click on "Advanced display settings".? 
And then click on "Display adapter properties for Display 1".? And the 
Adapter Type will be what you have.

Since you have a laptop, first try going to the vendor's support web 
site and get the latest driver for your system.? If you don't have a 
laptop, or if that doesn't fix the problem, you'll need to go the 
graphics vendor's website for newer drivers.

 ??? * for AMD: www.amd.com/drivers
 ??? * for Intel: downloadcenter.intel.com
 ??? * for NVidia: www.nvidia.com/drivers

Then find the new graphics driver for? your system, and install it.? Or 
use the tool the website provides if it has one.

 ??? Regards,

 ??? Greg

On 11/12/2021 7:42 AM, Cassidy Terrell wrote:
> Yes this is for a laptop with Microsoft Windows. How do I update the 
> system?
>
> On Thu, Nov 11, 2021 at 2:02 PM Greg Couch <gregc at cgl.ucsf.edu> wrote:
>
>     You don't say which platform this is on.? I'm going to assume it's
>     on Microsoft Windows.? You can get the debug messages by using the
>     Start menu and opening "UCSF Chimera 1.15 / Chimera - Debug".
>
>     That said, the typical cause of this problem is an outdated
>     graphics driver.? Please update the system to the latest and
>     greatest version.? This is especially true right now if you have
>     AMD Radeon graphics, but also applies if you have Intel or NVidia
>     graphics.
>
>     ??? Regards,
>
>     ??? Greg
>
>     On 11/11/2021 8:58 AM, Cassidy Terrell via Chimera-users wrote:
>>     Hello,
>>
>>     A student in my course (cced here) is trying to open Chimera 1.15
>>     and this is the error message that appears:
>>
>>     "chimera exited abnormally; the exit code was -1073741819. Use
>>     the --debug command line option for the full error message."
>>
>>     We cannot open the program, which mean we cannot get to the
>>     command line.
>>
>>     Thoughts about how to proceed? We have already
>>     removed/uninstalled previous version and re-downloaded new one.
>>     The same messages appears each time.
>>
>>     Best
>>     Cassidy
>>
>>     -- 
>>     Cassidy R. Terrell, Ph.D. (she/her/hers)
>>
>>     Assistant Professor, Biochemistry
>>     Center for Learning Innovation?|?University of Minnesota?|?Rochester
>>     300 University Square | Rochester, MN 55904
>>
>>     /Always believe something wonderful is about to happen/
>>
>>
>>     _______________________________________________
>>     Chimera-users mailing list:Chimera-users at cgl.ucsf.edu
>>     Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
> -- 
> Cassidy R. Terrell, Ph.D. (she/her/hers)
>
> Assistant Professor, Biochemistry
> Center for Learning Innovation?|?University of Minnesota?|?Rochester
> 300 University Square | Rochester, MN 55904
>
> /Always believe something wonderful is about to happen/
>
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From saikatpaliitg at yahoo.com  Mon Nov 15 07:17:16 2021
From: saikatpaliitg at yahoo.com (Saikat Pal)
Date: Mon, 15 Nov 2021 15:17:16 +0000 (UTC)
Subject: [Chimera-users] How to smooth trajectory?
References: <1555842662.830278.1636989436337.ref@mail.yahoo.com>
Message-ID: <1555842662.830278.1636989436337@mail.yahoo.com>

Dear all,
I want to make a movie using chimera. So, what are the steps to smooth the trajectory?

Thanks and Regards,
Saikat Pal

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From pett at cgl.ucsf.edu  Mon Nov 15 08:26:20 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 15 Nov 2021 08:26:20 -0800
Subject: [Chimera-users] How to smooth trajectory?
In-Reply-To: <1555842662.830278.1636989436337@mail.yahoo.com>
References: <1555842662.830278.1636989436337.ref@mail.yahoo.com>
 <1555842662.830278.1636989436337@mail.yahoo.com>
Message-ID: <E5B5DBD9-A6D5-48D4-AF59-482FC1B19936@cgl.ucsf.edu>

Hi Saikat,
	Chimera has no builtin ability to perform trajectory smoothing, but it can be done with a Python script.  You can find such a script on this page: Scripts ? Chimera <https://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>.  Look for "smoothMD.py?" (not "smooth_md.py", which is the same script but for ChimeraX).  Make sure to look at the chimera-users message linked next to the script, which describes how to use the it.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Nov 15, 2021, at 7:17 AM, Saikat Pal via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear all,
> 
> I want to make a movie using chimera. So, what are the steps to smooth the trajectory?
> 
> Thanks and Regards,
> 
> Saikat Pal
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From rioxel at gmail.com  Thu Nov 18 11:37:12 2021
From: rioxel at gmail.com (Rio Aquarius)
Date: Thu, 18 Nov 2021 22:37:12 +0300
Subject: [Chimera-users] chimera, H-bonds
Message-ID: <CAFraFW52TpaxpU9rDwbLn80WGFzQNxXjN8v3DbzWyu-yi=qTbQ@mail.gmail.com>

 Dear Developer,
I have a specific task for ChimeraX. I want to show H-bonds and hide all
amino acid residues. But when I hide amino acid residues, all H-bonds I
need disappear. Is there a way to do what I want?
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From meng at cgl.ucsf.edu  Thu Nov 18 12:20:47 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 18 Nov 2021 12:20:47 -0800
Subject: [Chimera-users] chimera, H-bonds
In-Reply-To: <CAFraFW52TpaxpU9rDwbLn80WGFzQNxXjN8v3DbzWyu-yi=qTbQ@mail.gmail.com>
References: <CAFraFW52TpaxpU9rDwbLn80WGFzQNxXjN8v3DbzWyu-yi=qTbQ@mail.gmail.com>
Message-ID: <70B9C5A5-4492-4E12-9F56-313A8B8A863C@cgl.ucsf.edu>

Dear Rio,
Sorry I accidentally told you to send the message to chimera-users but now I see it is a ChimeraX question, not Chimera.  Below is the answer for Chimera (not ChimeraX), so you may want to ignore it.  I will send a separate message about ChimeraX on the chimerax-users at cgl.ucsf.edu list.

The H-bond displays are lines (pseudobonds) drawn between atoms.  When you hide those atoms, by default the H-bonds are also hidden.  I don't understand why you would want to display a bunch of lines in space without any atoms, as you won't be able to see most of the valuable information from the calculation.  However, I will explain how to do it:

You can set pseudobond display to be "on" regardless of whether their atoms are displayed, e.g. with the command:

setattr p display 1

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

That would do it for ALL pseudobonds including missing segments, metal coordination bonds, etc.

To limit it to the H-bonds only, you would need to open the Pseudobond Panel (under Tools... General Controls in the menu) and then in that panel, click "hydrogen bonds" on the left to choose that row, then click "select bonded" in the right side.

...then when all the H-bonded atoms are still selected, use command:

setattr p display 1 sel

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 18, 2021, at 11:37 AM, Rio Aquarius via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Developer,
> I have a specific task for ChimeraX. I want to show H-bonds and hide all amino acid residues. But when I hide amino acid residues, all H-bonds I need disappear. Is there a way to do what I want?



From rioxel at gmail.com  Fri Nov 19 07:30:15 2021
From: rioxel at gmail.com (Rio Aquarius)
Date: Fri, 19 Nov 2021 18:30:15 +0300
Subject: [Chimera-users] chimera, H-bonds
In-Reply-To: <70B9C5A5-4492-4E12-9F56-313A8B8A863C@cgl.ucsf.edu>
References: <CAFraFW52TpaxpU9rDwbLn80WGFzQNxXjN8v3DbzWyu-yi=qTbQ@mail.gmail.com>
 <70B9C5A5-4492-4E12-9F56-313A8B8A863C@cgl.ucsf.edu>
Message-ID: <CAFraFW6cjm8szftuCBe6XEM5RshMNqzRwcs1ceW03PgFiBte6w@mail.gmail.com>

Dear Elaine,
Now I have installed Chimera as well and used algorithm you sent. I have
got the result I need.
Thank you so much. I appreciate it.

??, 18 ????. 2021 ?. ? 23:20, Elaine Meng <meng at cgl.ucsf.edu>:

> Dear Rio,
> Sorry I accidentally told you to send the message to chimera-users but now
> I see it is a ChimeraX question, not Chimera.  Below is the answer for
> Chimera (not ChimeraX), so you may want to ignore it.  I will send a
> separate message about ChimeraX on the chimerax-users at cgl.ucsf.edu list.
>
> The H-bond displays are lines (pseudobonds) drawn between atoms.  When you
> hide those atoms, by default the H-bonds are also hidden.  I don't
> understand why you would want to display a bunch of lines in space without
> any atoms, as you won't be able to see most of the valuable information
> from the calculation.  However, I will explain how to do it:
>
> You can set pseudobond display to be "on" regardless of whether their
> atoms are displayed, e.g. with the command:
>
> setattr p display 1
>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
>
> That would do it for ALL pseudobonds including missing segments, metal
> coordination bonds, etc.
>
> To limit it to the H-bonds only, you would need to open the Pseudobond
> Panel (under Tools... General Controls in the menu) and then in that panel,
> click "hydrogen bonds" on the left to choose that row, then click "select
> bonded" in the right side.
>
> ...then when all the H-bonded atoms are still selected, use command:
>
> setattr p display 1 sel
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Nov 18, 2021, at 11:37 AM, Rio Aquarius via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Developer,
> > I have a specific task for ChimeraX. I want to show H-bonds and hide all
> amino acid residues. But when I hide amino acid residues, all H-bonds I
> need disappear. Is there a way to do what I want?
>
>
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From zehragunes at stu.comu.edu.tr  Sat Nov 20 08:59:49 2021
From: zehragunes at stu.comu.edu.tr (=?UTF-8?B?WmVocmEgR8OcTkXFng==?=)
Date: Sat, 20 Nov 2021 19:59:49 +0300
Subject: [Chimera-users] FAD Topology/Parameter Files
Message-ID: <CAM0t2OhgUa5=oAP9ZTVaPdhhShd+W2NyqTOopBc7DD+JYg8F6A@mail.gmail.com>

Dear all,

I am working on a research protein that contains FAD. I have tried to
prepare it for simulation but unfortunately I have neither trajectory nor
parameter file of FAD. Would it be possible to share with me these files if
you have?

Thanks in advance,

Zehra G?ne?
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From pett at cgl.ucsf.edu  Mon Nov 22 13:09:48 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 22 Nov 2021 13:09:48 -0800
Subject: [Chimera-users] FAD Topology/Parameter Files
In-Reply-To: <CAM0t2OhgUa5=oAP9ZTVaPdhhShd+W2NyqTOopBc7DD+JYg8F6A@mail.gmail.com>
References: <CAM0t2OhgUa5=oAP9ZTVaPdhhShd+W2NyqTOopBc7DD+JYg8F6A@mail.gmail.com>
Message-ID: <3D6AFA4A-65A0-4D2A-8490-2A2ED1CE84E3@cgl.ucsf.edu>

Hi Zehra,
	Chimera does not include any explicit parameterization of FAD.  If necessary, it estimates parameters on the fly.  If you are doing a serious simulation you would want the most accurate parameters you can obtain, so perhaps you could ask for help on the AMBER mailing list (http://ambermd.org/MailingLists.php <http://ambermd.org/MailingLists.php>).  That said, there is a parameterization for FAD at this site: AMBER parameter database <http://amber.manchester.ac.uk/>, though I don't know if its protonation state matches what you need.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Nov 20, 2021, at 8:59 AM, Zehra G?NE? via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear all,
> 
> I am working on a research protein that contains FAD. I have tried to prepare it for simulation but unfortunately I have neither trajectory nor parameter file of FAD. Would it be possible to share with me these files if you have?
> 
> Thanks in advance,
> 
> Zehra G?ne? 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From meng at cgl.ucsf.edu  Mon Nov 22 13:36:10 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 22 Nov 2021 13:36:10 -0800
Subject: [Chimera-users] FAD Topology/Parameter Files
In-Reply-To: <3D6AFA4A-65A0-4D2A-8490-2A2ED1CE84E3@cgl.ucsf.edu>
References: <CAM0t2OhgUa5=oAP9ZTVaPdhhShd+W2NyqTOopBc7DD+JYg8F6A@mail.gmail.com>
 <3D6AFA4A-65A0-4D2A-8490-2A2ED1CE84E3@cgl.ucsf.edu>
Message-ID: <1371B4B1-4366-4104-9611-E4777F2C4F0E@cgl.ucsf.edu>

Hi Zehra,
If you mean you're trying to minimize (or even do short dynamics) inside of Chimera, it might not be possible.  If you tried to minimize this structure in Chimera, it will attempt to calculate partial charges and other force field parameters it needs for the FAD using Antechamber. 

However, charge calculation may fail on residues as large as FAD especially those with high charge density like phosphates.  You could try the Gasteiger option of the charge calculation for a more quick-and-dirty calculation, but it is not recommended for detailed/quantitative simulations of any kind.  Although it is possible to manually add specific charge values to use in Chimera, it is somewhat difficult.  Details about calculating or adding charges for ligand residues here:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#nonstandard>

If you want to perform longer simulations or get quantitative results you should probably use some full-featured dynamics software like AMBER or GROMACS instead of Chimera.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 22, 2021, at 1:09 PM, Eric Pettersen via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Zehra,
> 	Chimera does not include any explicit parameterization of FAD.  If necessary, it estimates parameters on the fly.  If you are doing a serious simulation you would want the most accurate parameters you can obtain, so perhaps you could ask for help on the AMBER mailing list (http://ambermd.org/MailingLists.php).  That said, there is a parameterization for FAD at this site: AMBER parameter database, though I don't know if its protonation state matches what you need.
> 
> --Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
>> On Nov 20, 2021, at 8:59 AM, Zehra G?NE? via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Dear all,
>> 
>> I am working on a research protein that contains FAD. I have tried to prepare it for simulation but unfortunately I have neither trajectory nor parameter file of FAD. Would it be possible to share with me these files if you have?
>> 
>> Thanks in advance,
>> 
>> Zehra G?ne? 



From dr.hknajmee at gmail.com  Mon Nov 22 23:32:01 2021
From: dr.hknajmee at gmail.com (HK Haris)
Date: Tue, 23 Nov 2021 01:32:01 -0600
Subject: [Chimera-users] Chimera compatibility with Window 11
Message-ID: <CAAZ25uwugzi99sFjeaoqx0J++9QqKkHm9+JZv_uUX+9eorN2aw@mail.gmail.com>

Hi,

Please confirm can I download the following version of Chimera on my laptop
which is operating on Windows 11.
Microsoft Windows 64-bit chimera-1.15-win64.exe
<https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/chimera-1.15-win64.exe>
Size: 152310162 bytes
MD5: 6a68ab33f35a298059b9ef89f6372cfc Dec 18, 2020 Instructions
<https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/win64.html>
Documentation <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/docs/>
Runs on Windows 7 or later.


*Best Regards,Dr. HIRA KHALID*
Associate Professor Chemistry
Forman Christian College University
(A Chartered University)
Lahore, Pakistan.54600
Ph: 042-99231581-88 x: 562
www.fccollege.edu.pk
........................
HEC APPROVED Supervisor
Advisor ACS Punjab
Associate member RSC
Member & Ambassador Chemistry ACS
Member AOCS
Life-time CSP Member
IUPAC Young Fellow
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From olibclarke at gmail.com  Tue Nov 23 08:13:51 2021
From: olibclarke at gmail.com (Oliver Clarke)
Date: Tue, 23 Nov 2021 11:13:51 -0500
Subject: [Chimera-users] Color volume series by per voxel variance?
Message-ID: <A09C41DC-56F6-4D0D-AB65-93D8EB7C8791@gmail.com>

Hi all,

Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?

When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. 

Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.

Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?

Cheers
Oli

From meng at cgl.ucsf.edu  Tue Nov 23 08:33:06 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 23 Nov 2021 08:33:06 -0800
Subject: [Chimera-users] [chimerax-users] Color volume series by per
	voxel variance?
In-Reply-To: <A09C41DC-56F6-4D0D-AB65-93D8EB7C8791@gmail.com>
References: <A09C41DC-56F6-4D0D-AB65-93D8EB7C8791@gmail.com>
Message-ID: <F50DE24A-1C8F-418C-A0CD-0AFE460E44AC@cgl.ucsf.edu>

Hi Oli,
Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation>

ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi all,
> 
> Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
> 
> When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. 
> 
> Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
> 
> Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
> 
> Cheers
> Oli



From olibclarke at gmail.com  Tue Nov 23 08:40:29 2021
From: olibclarke at gmail.com (Oliver Clarke)
Date: Tue, 23 Nov 2021 11:40:29 -0500
Subject: [Chimera-users] [chimerax-users] Color volume series by per
	voxel variance?
In-Reply-To: <F50DE24A-1C8F-418C-A0CD-0AFE460E44AC@cgl.ucsf.edu>
References: <A09C41DC-56F6-4D0D-AB65-93D8EB7C8791@gmail.com>
 <F50DE24A-1C8F-418C-A0CD-0AFE460E44AC@cgl.ucsf.edu>
Message-ID: <9D78C206-4193-4736-A089-B9BABFA2027F@gmail.com>

Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!

Cheers
Oli

> On Nov 23, 2021, at 11:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Oli,
> Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation>
> 
> ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure>
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hi all,
>> 
>> Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
>> 
>> When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. 
>> 
>> Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
>> 
>> Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
>> 
>> Cheers
>> Oli
> 



From goddard at sonic.net  Tue Nov 23 10:00:53 2021
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 23 Nov 2021 10:00:53 -0800
Subject: [Chimera-users] [chimerax-users] Color volume series by per
 voxel variance?
In-Reply-To: <9D78C206-4193-4736-A089-B9BABFA2027F@gmail.com>
References: <A09C41DC-56F6-4D0D-AB65-93D8EB7C8791@gmail.com>
 <F50DE24A-1C8F-418C-A0CD-0AFE460E44AC@cgl.ucsf.edu>
 <9D78C206-4193-4736-A089-B9BABFA2027F@gmail.com>
Message-ID: <6353887F-5F34-4BF7-9520-88283C31EB0B@sonic.net>

Hi Oli,

  Here is something similar I tried to see the motion in lightsheet microscopy of neutrophil-like cells crawling in collagen.

	https://www.cgl.ucsf.edu/chimera/data/mullins/cactus-oct2014/cactus.html <https://www.cgl.ucsf.edu/chimera/data/mullins/cactus-oct2014/cactus.html>


Done with the ChimeraX (or Chimera) measure motion command

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#motion <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#motion>

   Tom



> On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
> 
> Cheers
> Oli
> 
>> On Nov 23, 2021, at 11:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Oli,
>> Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series:
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation>
>> 
>> ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability.
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure>
>> 
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hi all,
>>> 
>>> Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
>>> 
>>> When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. 
>>> 
>>> Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
>>> 
>>> Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
>>> 
>>> Cheers
>>> Oli
>> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From goddard at sonic.net  Tue Nov 23 10:06:31 2021
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 23 Nov 2021 10:06:31 -0800
Subject: [Chimera-users] [chimerax-users] Color volume series by per
 voxel variance?
In-Reply-To: <9D78C206-4193-4736-A089-B9BABFA2027F@gmail.com>
References: <A09C41DC-56F6-4D0D-AB65-93D8EB7C8791@gmail.com>
 <F50DE24A-1C8F-418C-A0CD-0AFE460E44AC@cgl.ucsf.edu>
 <9D78C206-4193-4736-A089-B9BABFA2027F@gmail.com>
Message-ID: <808D3569-D113-4F72-B5E9-80CC69C2EAE4@sonic.net>

It would not be hard for ChimeraX to compute the per-pixel variance map with a little Python script.  Then you could use that to color your movie map surface by variance map value.

	Tom


> On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
> 
> Cheers
> Oli
> 
>> On Nov 23, 2021, at 11:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Oli,
>> Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series:
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation>
>> 
>> ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability.
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure>
>> 
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hi all,
>>> 
>>> Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
>>> 
>>> When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. 
>>> 
>>> Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
>>> 
>>> Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
>>> 
>>> Cheers
>>> Oli
>> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From goddard at sonic.net  Tue Nov 23 12:08:22 2021
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 23 Nov 2021 12:08:22 -0800
Subject: [Chimera-users] Chimera compatibility with Window 11
In-Reply-To: <CAAZ25uwugzi99sFjeaoqx0J++9QqKkHm9+JZv_uUX+9eorN2aw@mail.gmail.com>
References: <CAAZ25uwugzi99sFjeaoqx0J++9QqKkHm9+JZv_uUX+9eorN2aw@mail.gmail.com>
Message-ID: <43E359B9-AB26-44F2-A567-9667D3828AEB@sonic.net>

Yes Chimera 1.15 and the Chimera daily build both work on Windows 11.

	Tom


> On Nov 22, 2021, at 11:32 PM, HK Haris via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> 
> Please confirm can I download the following version of Chimera on my laptop which is operating on Windows 11.
> Microsoft Windows 64-bit	chimera-1.15-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/chimera-1.15-win64.exe>
> Size: 152310162 bytes
> MD5: 6a68ab33f35a298059b9ef89f6372cfc	Dec 18, 2020	Instructions <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/win64.html>
> Documentation <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/docs/>
> Runs on Windows 7 or later.
> 
> Best Regards,
> Dr. HIRA KHALID
> Associate Professor Chemistry
> Forman Christian College University
> (A Chartered University)
> Lahore, Pakistan.54600
> Ph: 042-99231581-88 x: 562
> www.fccollege.edu.pk <http://www.fccollege.edu.pk/>
> ........................
> HEC APPROVED Supervisor
> Advisor ACS Punjab
> Associate member RSC
> Member & Ambassador Chemistry ACS 
> Member AOCS
> Life-time CSP Member
> IUPAC Young Fellow
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From olibclarke at gmail.com  Tue Nov 23 15:08:48 2021
From: olibclarke at gmail.com (Oliver Clarke)
Date: Tue, 23 Nov 2021 18:08:48 -0500
Subject: [Chimera-users] [chimerax-users] Color volume series by per
 voxel variance?
In-Reply-To: <808D3569-D113-4F72-B5E9-80CC69C2EAE4@sonic.net>
References: <A09C41DC-56F6-4D0D-AB65-93D8EB7C8791@gmail.com>
 <F50DE24A-1C8F-418C-A0CD-0AFE460E44AC@cgl.ucsf.edu>
 <9D78C206-4193-4736-A089-B9BABFA2027F@gmail.com>
 <808D3569-D113-4F72-B5E9-80CC69C2EAE4@sonic.net>
Message-ID: <855FD15D-9593-4BF4-84CE-55D488B9CEA2@gmail.com>

Thanks Tom for the cactus idea I will give that a go! Not sure where to start with computing the per pixel variance but will do some digging into the docs

Cheers
Oli

> On Nov 23, 2021, at 1:06 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> It would not be hard for ChimeraX to compute the per-pixel variance map with a little Python script.  Then you could use that to color your movie map surface by variance map value.
> 
> 	Tom
> 
> 
>> On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
>> 
>> Cheers
>> Oli
>> 
>>> On Nov 23, 2021, at 11:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Oli,
>>> Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series:
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation>
>>> 
>>> ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability.
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure>
>>> 
>>> Best,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>> 
>>>> On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>>> 
>>>> Hi all,
>>>> 
>>>> Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
>>>> 
>>>> When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. 
>>>> 
>>>> Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
>>>> 
>>>> Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
>>>> 
>>>> Cheers
>>>> Oli
>>> 
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 



From goddard at sonic.net  Wed Nov 24 00:27:36 2021
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 24 Nov 2021 00:27:36 -0800
Subject: [Chimera-users] [chimerax-users] Color volume series by per
 voxel variance?
In-Reply-To: <855FD15D-9593-4BF4-84CE-55D488B9CEA2@gmail.com>
References: <A09C41DC-56F6-4D0D-AB65-93D8EB7C8791@gmail.com>
 <F50DE24A-1C8F-418C-A0CD-0AFE460E44AC@cgl.ucsf.edu>
 <9D78C206-4193-4736-A089-B9BABFA2027F@gmail.com>
 <808D3569-D113-4F72-B5E9-80CC69C2EAE4@sonic.net>
 <855FD15D-9593-4BF4-84CE-55D488B9CEA2@gmail.com>
Message-ID: <07A833AC-747D-45E0-899F-3BEB82A7B165@sonic.net>

Here is an example Python script to add a "volume variance" command to ChimeraX.

	https://rbvi.github.io/chimerax-recipes/variance/variance.html <https://rbvi.github.io/chimerax-recipes/variance/variance.html>

  Tom



> On Nov 23, 2021, at 3:08 PM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Thanks Tom for the cactus idea I will give that a go! Not sure where to start with computing the per pixel variance but will do some digging into the docs
> 
> Cheers
> Oli
> 
>> On Nov 23, 2021, at 1:06 PM, Tom Goddard <goddard at sonic.net> wrote:
>> 
>> It would not be hard for ChimeraX to compute the per-pixel variance map with a little Python script.  Then you could use that to color your movie map surface by variance map value.
>> 
>> 	Tom
>> 
>> 
>>> On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>> 
>>> Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
>>> 
>>> Cheers
>>> Oli
>>> 
>>>> On Nov 23, 2021, at 11:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>>> 
>>>> Hi Oli,
>>>> Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series:
>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation>
>>>> 
>>>> ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability.
>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure>
>>>> 
>>>> Best,
>>>> Elaine
>>>> -----
>>>> Elaine C. Meng, Ph.D.                       
>>>> UCSF Chimera(X) team
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>> 
>>>> 
>>>>> On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>>>> 
>>>>> Hi all,
>>>>> 
>>>>> Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
>>>>> 
>>>>> When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. 
>>>>> 
>>>>> Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
>>>>> 
>>>>> Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
>>>>> 
>>>>> Cheers
>>>>> Oli
>>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From olibclarke at gmail.com  Wed Nov 24 03:39:24 2021
From: olibclarke at gmail.com (Oliver Clarke)
Date: Wed, 24 Nov 2021 06:39:24 -0500
Subject: [Chimera-users] [chimerax-users] Color volume series by per
	voxel variance?
In-Reply-To: <07A833AC-747D-45E0-899F-3BEB82A7B165@sonic.net>
References: <07A833AC-747D-45E0-899F-3BEB82A7B165@sonic.net>
Message-ID: <C42D32BA-6FA6-412A-B516-6679DFCE83B6@gmail.com>

Nice this exactly what I was looking for, thank you Tom!!

Cheers
Oli

> On Nov 24, 2021, at 3:27 AM, Tom Goddard <goddard at sonic.net> wrote:
> 
> ?Here is an example Python script to add a "volume variance" command to ChimeraX.
> 
> 	https://rbvi.github.io/chimerax-recipes/variance/variance.html
> 
>   Tom
> 
> 
> 
>> On Nov 23, 2021, at 3:08 PM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Thanks Tom for the cactus idea I will give that a go! Not sure where to start with computing the per pixel variance but will do some digging into the docs
>> 
>> Cheers
>> Oli
>> 
>>> On Nov 23, 2021, at 1:06 PM, Tom Goddard <goddard at sonic.net> wrote:
>>> 
>>> It would not be hard for ChimeraX to compute the per-pixel variance map with a little Python script.  Then you could use that to color your movie map surface by variance map value.
>>> 
>>> 	Tom
>>> 
>>> 
>>>> On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>>> 
>>>> Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
>>>> 
>>>> Cheers
>>>> Oli
>>>> 
>>>>> On Nov 23, 2021, at 11:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>>>> 
>>>>> Hi Oli,
>>>>> Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series:
>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation>
>>>>> 
>>>>> ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability.
>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure>
>>>>> 
>>>>> Best,
>>>>> Elaine
>>>>> -----
>>>>> Elaine C. Meng, Ph.D.                       
>>>>> UCSF Chimera(X) team
>>>>> Department of Pharmaceutical Chemistry
>>>>> University of California, San Francisco
>>>>> 
>>>>> 
>>>>>> On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>>>>> 
>>>>>> Hi all,
>>>>>> 
>>>>>> Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
>>>>>> 
>>>>>> When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. 
>>>>>> 
>>>>>> Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
>>>>>> 
>>>>>> Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
>>>>>> 
>>>>>> Cheers
>>>>>> Oli
>>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>> 
>>> 
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 
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From smritisingh at mnnit.ac.in  Tue Nov 23 21:39:14 2021
From: smritisingh at mnnit.ac.in (Smriti Singh 2018RBT01)
Date: Wed, 24 Nov 2021 11:09:14 +0530
Subject: [Chimera-users] how to rectify error No MMTK name for atom
Message-ID: <CALHHkNa-PtCN+NXdHOUOrXgMwOyj540VYRknLptnsPu+Lzn=5g@mail.gmail.com>

hello administrator,

I am trying to minimize the Nucleotide sequence (DNA aptamer) through
chimera.
While performing energy minimisation steps, Chimera error  "No MMTK name
for atom 'HO5' in standard residue 'DA' showed. Please let me know how to
rectify this issue.

With warm regards

Smriti Singh
Research Scholar
Department of Biotechnology
MNNIT Allahabad
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From pett at cgl.ucsf.edu  Wed Nov 24 13:49:14 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 24 Nov 2021 13:49:14 -0800
Subject: [Chimera-users] how to rectify error No MMTK name for atom
In-Reply-To: <CALHHkNa-PtCN+NXdHOUOrXgMwOyj540VYRknLptnsPu+Lzn=5g@mail.gmail.com>
References: <CALHHkNa-PtCN+NXdHOUOrXgMwOyj540VYRknLptnsPu+Lzn=5g@mail.gmail.com>
Message-ID: <DBA63201-9C13-422B-9726-7B20D5AAFDD1@cgl.ucsf.edu>

Hi Smriti,
	It is likely something unusual about your structure file.  You should use Chimera's Help?Report A Bug menu item to file a bug report and then attach your structure file and then we can investigate and get back to you.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Nov 23, 2021, at 9:39 PM, Smriti Singh 2018RBT01 via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> hello administrator,
> 
> I am trying to minimize the Nucleotide sequence (DNA aptamer) through chimera. 
> While performing energy minimisation steps, Chimera error  "No MMTK name for atom 'HO5' in standard residue 'DA' showed. Please let me know how to rectify this issue.
>  
> With warm regards
> 
> Smriti Singh
> Research Scholar 
> Department of Biotechnology
> MNNIT Allahabad
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From laddhadi at iitk.ac.in  Wed Nov 24 23:59:48 2021
From: laddhadi at iitk.ac.in (Aditi Laddha)
Date: Thu, 25 Nov 2021 13:29:48 +0530
Subject: [Chimera-users] question regarding UCSF Chimera FindHBond feature
Message-ID: <ccfe2dfd3bdc8c9dfdbbe8dc81441397@iitk.ac.in>

Hello,

I have been using the FindHBond feature of Chimera for finding hydrogen 
bonds between water molecules and the polypeptide chains. I need to use 
some specific distance and angle criteria to find H-bonds, so I wanted 
to ask what is the default distance (D....A) and angle criteria 
(D-H....A) used in the software to find out the H-bonds,

-- 
Regards,
Aditi Laddha
PhD Scholar
Indian Institute of Technology,
Kanpur, Uttar Pradesh 208016
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From meng at cgl.ucsf.edu  Thu Nov 25 08:43:55 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 25 Nov 2021 08:43:55 -0800
Subject: [Chimera-users] question regarding UCSF Chimera FindHBond
	feature
In-Reply-To: <ccfe2dfd3bdc8c9dfdbbe8dc81441397@iitk.ac.in>
References: <ccfe2dfd3bdc8c9dfdbbe8dc81441397@iitk.ac.in>
Message-ID: <9C83EBE3-6CAF-4D8E-ADE3-62F22811EDE0@cgl.ucsf.edu>

Hello Aditi Laddha,
There is not one specific distance or angle, instead several different ones depending on the atom types of the acceptor and donor atoms.  This is explained in the help page:

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria>

"The geometric criteria are based on a survey of small-molecule crystal structures, as described in

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22.
<https://pubmed.ncbi.nlm.nih.gov/9007693/>

There are many different sets of geometric criteria, corresponding to the many different donor-acceptor combinations (see Tables 5-8 in the reference)."

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 24, 2021, at 11:59 PM, Aditi Laddha via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I have been using the FindHBond feature of Chimera for finding hydrogen bonds between water molecules and the polypeptide chains. I need to use some specific distance and angle criteria to find H-bonds, so I wanted to ask what is the default distance (D....A) and angle criteria (D-H....A) used in the software to find out the H-bonds, 



From l84zhao at uwaterloo.ca  Fri Nov 26 08:40:52 2021
From: l84zhao at uwaterloo.ca (Leonard Zhao)
Date: Fri, 26 Nov 2021 16:40:52 +0000
Subject: [Chimera-users] Get Minimization Energy
Message-ID: <YT2PR01MB43335C99E69AB90A1DED1509C6639@YT2PR01MB4333.CANPRD01.PROD.OUTLOOK.COM>

Hello,

I am running a Python script to perform multiple structure minimizations and I need to extract to final potential energy from each minimization. I see that the potential energy is usually reported in the Reply Log, but when IDLE is open, it is instead redirected to IDLE. Is there any way to redirect it back to the Reply Log so I can more easily extract it in my script, or is there some other method to easily extract the energy value programmatically?

Thanks,
Leonard Zhao
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From meng at cgl.ucsf.edu  Fri Nov 26 08:58:41 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 26 Nov 2021 08:58:41 -0800
Subject: [Chimera-users] Get Minimization Energy
In-Reply-To: <YT2PR01MB43335C99E69AB90A1DED1509C6639@YT2PR01MB4333.CANPRD01.PROD.OUTLOOK.COM>
References: <YT2PR01MB43335C99E69AB90A1DED1509C6639@YT2PR01MB4333.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <26DD6147-2D62-48C5-BDA9-ACBDD0E0809C@cgl.ucsf.edu>

Hi Leonard,
The values are not really meaningful except relative to one another for the same structure (e.g. minimization reduces the value), and not for comparing between different structures.  So while this does not answer your technical question per se, I don't think you can get much information by saving these values.  Some other dedicated MM/MD programs may give a more useful/valuable breakdown of terms, but this single, usually huge number doesn't tell you much of anything.  

Furthermore, minimization just gives you a local minimum, not generally the global mininum, and it's not the free energy of the system either way.  So for example if a mutated structure has a higher number than the wild type after minimization, you still don't know whether it is more or less stable than the wild type protein.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 26, 2021, at 8:40 AM, Leonard Zhao via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I am running a Python script to perform multiple structure minimizations and I need to extract to final potential energy from each minimization. I see that the potential energy is usually reported in the Reply Log, but when IDLE is open, it is instead redirected to IDLE. Is there any way to redirect it back to the Reply Log so I can more easily extract it in my script, or is there some other method to easily extract the energy value programmatically? 
> Thanks,
> Leonard Zhao



From l84zhao at uwaterloo.ca  Fri Nov 26 09:15:33 2021
From: l84zhao at uwaterloo.ca (Leonard Zhao)
Date: Fri, 26 Nov 2021 17:15:33 +0000
Subject: [Chimera-users] Get Minimization Energy
In-Reply-To: <26DD6147-2D62-48C5-BDA9-ACBDD0E0809C@cgl.ucsf.edu>
References: <YT2PR01MB43335C99E69AB90A1DED1509C6639@YT2PR01MB4333.CANPRD01.PROD.OUTLOOK.COM>
 <26DD6147-2D62-48C5-BDA9-ACBDD0E0809C@cgl.ucsf.edu>
Message-ID: <YT2PR01MB4333D4E4E90CEED6704403F4C6639@YT2PR01MB4333.CANPRD01.PROD.OUTLOOK.COM>

Hi Elaine,

I will only be using the energy value to compare with other minimizations done on the same structure, and MM/MD methods have too high of a computational cost since I will be performing thousands of minimizations on the same structure. I am hoping that, even though the energy values are only local minimums, they can still be used for comparison with repeated minimizations on the same structure with a slight perturbation each time.

Thanks,
Leonard Zhao
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, November 26, 2021 11:58 AM
To: Leonard Zhao <l84zhao at uwaterloo.ca>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Get Minimization Energy

Hi Leonard,
The values are not really meaningful except relative to one another for the same structure (e.g. minimization reduces the value), and not for comparing between different structures.  So while this does not answer your technical question per se, I don't think you can get much information by saving these values.  Some other dedicated MM/MD programs may give a more useful/valuable breakdown of terms, but this single, usually huge number doesn't tell you much of anything.

Furthermore, minimization just gives you a local minimum, not generally the global mininum, and it's not the free energy of the system either way.  So for example if a mutated structure has a higher number than the wild type after minimization, you still don't know whether it is more or less stable than the wild type protein.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 26, 2021, at 8:40 AM, Leonard Zhao via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hello,
> I am running a Python script to perform multiple structure minimizations and I need to extract to final potential energy from each minimization. I see that the potential energy is usually reported in the Reply Log, but when IDLE is open, it is instead redirected to IDLE. Is there any way to redirect it back to the Reply Log so I can more easily extract it in my script, or is there some other method to easily extract the energy value programmatically?
> Thanks,
> Leonard Zhao

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From pett at cgl.ucsf.edu  Fri Nov 26 09:42:00 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 26 Nov 2021 09:42:00 -0800
Subject: [Chimera-users] Get Minimization Energy
In-Reply-To: <YT2PR01MB4333D4E4E90CEED6704403F4C6639@YT2PR01MB4333.CANPRD01.PROD.OUTLOOK.COM>
References: <YT2PR01MB43335C99E69AB90A1DED1509C6639@YT2PR01MB4333.CANPRD01.PROD.OUTLOOK.COM>
 <26DD6147-2D62-48C5-BDA9-ACBDD0E0809C@cgl.ucsf.edu>
 <YT2PR01MB4333D4E4E90CEED6704403F4C6639@YT2PR01MB4333.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <6355DC16-96E4-4A39-8A2E-4A66714B1EA4@cgl.ucsf.edu>

Do get the replies to go back to the log, in IDLE type:

	from chimera import replyobj
	replyobj.popReply(replyobj.currentReply())

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Nov 26, 2021, at 9:15 AM, Leonard Zhao via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> I will only be using the energy value to compare with other minimizations done on the same structure, and MM/MD methods have too high of a computational cost since I will be performing thousands of minimizations on the same structure. I am hoping that, even though the energy values are only local minimums, they can still be used for comparison with repeated minimizations on the same structure with a slight perturbation each time.
> 
> Thanks,
> Leonard Zhao
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Friday, November 26, 2021 11:58 AM
> To: Leonard Zhao <l84zhao at uwaterloo.ca>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Get Minimization Energy
>  
> Hi Leonard,
> The values are not really meaningful except relative to one another for the same structure (e.g. minimization reduces the value), and not for comparing between different structures.  So while this does not answer your technical question per se, I don't think you can get much information by saving these values.  Some other dedicated MM/MD programs may give a more useful/valuable breakdown of terms, but this single, usually huge number doesn't tell you much of anything.  
> 
> Furthermore, minimization just gives you a local minimum, not generally the global mininum, and it's not the free energy of the system either way.  So for example if a mutated structure has a higher number than the wild type after minimization, you still don't know whether it is more or less stable than the wild type protein.
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Nov 26, 2021, at 8:40 AM, Leonard Zhao via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > 
> > Hello,
> > I am running a Python script to perform multiple structure minimizations and I need to extract to final potential energy from each minimization. I see that the potential energy is usually reported in the Reply Log, but when IDLE is open, it is instead redirected to IDLE. Is there any way to redirect it back to the Reply Log so I can more easily extract it in my script, or is there some other method to easily extract the energy value programmatically? 
> > Thanks,
> > Leonard Zhao
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From francesca.magarotto2 at studio.unibo.it  Sat Nov 27 01:01:54 2021
From: francesca.magarotto2 at studio.unibo.it (Francesca Magarotto - francesca.magarotto2@studio.unibo.it)
Date: Sat, 27 Nov 2021 09:01:54 +0000
Subject: [Chimera-users] Minimization on complex
Message-ID: <VI1PR0102MB32457CAB907B682F3697431D80649@VI1PR0102MB3245.eurprd01.prod.exchangelabs.com>

Hi,
I need an advice regarding minimization of complexes. I've performed a virtual screening and I've selected some molecules of interest. Now, I've looked for the possibile interactions in the binding site and I would like to perform a minimization moving only the hydrogen atoms in the binding site. However, I have to create a new file pdb complex formed by my protein and one molecule from VS results.
So, I opened the pdb file of the protein and the mol2 file of the molecule from the VS: now, do I need to save a pdb file of the complex and how to save it? I need the hydrogens to  move according to the ligand inside the protein and I don't know if it's possibile with both the type of saving (is it better individual MOLECULE sections or combined MOLECULE section?).
Moreover, I don't know if (for this kind of purpose) it's better first to save the complex in pdb file and then to use dockprep and minimization or use dockprep and minimization and only after saving the file of the complex. My main aim is to see if some hydrogens of the residues in the binding site move their places according to the presence of this ligand.
Hope someone can help me,
thanks.
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From meng at cgl.ucsf.edu  Sun Nov 28 11:22:54 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sun, 28 Nov 2021 11:22:54 -0800
Subject: [Chimera-users] Minimization on complex
In-Reply-To: <VI1PR0102MB32457CAB907B682F3697431D80649@VI1PR0102MB3245.eurprd01.prod.exchangelabs.com>
References: <VI1PR0102MB32457CAB907B682F3697431D80649@VI1PR0102MB3245.eurprd01.prod.exchangelabs.com>
Message-ID: <8BE32AFD-BEF5-49DF-8844-1EFCC74EEEDE@cgl.ucsf.edu>

Hi Francesca,
There are different ways you could do it, but personally I would:

(1) Combine ligand and receptor into one model.  

T o combine the ligand and the protein into one model, you can use the Model Panel (open from Favorites menu) "copy/combine" function.  You have to choose the two models (the ligand and the protein) on the left side of the Model Panel and then click "copy/combine" button on the right side of the Model Panel.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>

Or, instead of Model Panel, you could use the "combine" command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

(2) Close the original two models so that only the new combined model is open.  Save PDB of the new combined model.  
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

You don't absolutely have to save a PDB file at this point, but you should always save your work frequently.  Some reasons:
(A) if some later step gets messed up, you can start over by opening this PDB file again.  
(B) if  you decide to use some other program for later steps you can open the PDB file in that other program.
(C) saving a file before minimization allows you to easily compare with the structure after minimization

(3) dock prep, minimize, and probably save another PDB.  There are minimize options for only allowing selected atoms to move ("fixed atoms" cannot move), so that's how you would limit the movements to hydrogens.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 27, 2021, at 1:01 AM, Francesca Magarotto - francesca.magarotto2--- via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> I need an advice regarding minimization of complexes. I've performed a virtual screening and I've selected some molecules of interest. Now, I've looked for the possibile interactions in the binding site and I would like to perform a minimization moving only the hydrogen atoms in the binding site. However, I have to create a new file pdb complex formed by my protein and one molecule from VS results.
> So, I opened the pdb file of the protein and the mol2 file of the molecule from the VS: now, do I need to save a pdb file of the complex and how to save it? I need the hydrogens to  move according to the ligand inside the protein and I don't know if it's possibile with both the type of saving (is it better individual MOLECULE sections or combined MOLECULE section?).
> Moreover, I don't know if (for this kind of purpose) it's better first to save the complex in pdb file and then to use dockprep and minimization or use dockprep and minimization and only after saving the file of the complex. My main aim is to see if some hydrogens of the residues in the binding site move their places according to the presence of this ligand.
> Hope someone can help me,
> thanks.



From francesca.magarotto2 at studio.unibo.it  Mon Nov 29 05:52:06 2021
From: francesca.magarotto2 at studio.unibo.it (Francesca Magarotto - francesca.magarotto2@studio.unibo.it)
Date: Mon, 29 Nov 2021 13:52:06 +0000
Subject: [Chimera-users] R:  Minimization on complex
In-Reply-To: <8BE32AFD-BEF5-49DF-8844-1EFCC74EEEDE@cgl.ucsf.edu>
References: <VI1PR0102MB32457CAB907B682F3697431D80649@VI1PR0102MB3245.eurprd01.prod.exchangelabs.com>
 <8BE32AFD-BEF5-49DF-8844-1EFCC74EEEDE@cgl.ucsf.edu>
Message-ID: <VI1PR0102MB3245CB08F4927DEE0C5545AF80669@VI1PR0102MB3245.eurprd01.prod.exchangelabs.com>

Thank you really much
________________________________
Da: Elaine Meng <meng at cgl.ucsf.edu>
Inviato: domenica 28 novembre 2021 20:22
A: Francesca Magarotto - francesca.magarotto2 at studio.unibo.it <francesca.magarotto2 at studio.unibo.it>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Oggetto: Re: [Chimera-users] Minimization on complex

Hi Francesca,
There are different ways you could do it, but personally I would:

(1) Combine ligand and receptor into one model.

T o combine the ligand and the protein into one model, you can use the Model Panel (open from Favorites menu) "copy/combine" function.  You have to choose the two models (the ligand and the protein) on the left side of the Model Panel and then click "copy/combine" button on the right side of the Model Panel.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>

Or, instead of Model Panel, you could use the "combine" command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

(2) Close the original two models so that only the new combined model is open.  Save PDB of the new combined model.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

You don't absolutely have to save a PDB file at this point, but you should always save your work frequently.  Some reasons:
(A) if some later step gets messed up, you can start over by opening this PDB file again.
(B) if  you decide to use some other program for later steps you can open the PDB file in that other program.
(C) saving a file before minimization allows you to easily compare with the structure after minimization

(3) dock prep, minimize, and probably save another PDB.  There are minimize options for only allowing selected atoms to move ("fixed atoms" cannot move), so that's how you would limit the movements to hydrogens.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 27, 2021, at 1:01 AM, Francesca Magarotto - francesca.magarotto2--- via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi,
> I need an advice regarding minimization of complexes. I've performed a virtual screening and I've selected some molecules of interest. Now, I've looked for the possibile interactions in the binding site and I would like to perform a minimization moving only the hydrogen atoms in the binding site. However, I have to create a new file pdb complex formed by my protein and one molecule from VS results.
> So, I opened the pdb file of the protein and the mol2 file of the molecule from the VS: now, do I need to save a pdb file of the complex and how to save it? I need the hydrogens to  move according to the ligand inside the protein and I don't know if it's possibile with both the type of saving (is it better individual MOLECULE sections or combined MOLECULE section?).
> Moreover, I don't know if (for this kind of purpose) it's better first to save the complex in pdb file and then to use dockprep and minimization or use dockprep and minimization and only after saving the file of the complex. My main aim is to see if some hydrogens of the residues in the binding site move their places according to the presence of this ligand.
> Hope someone can help me,
> thanks.

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From kl126835 at 163.com  Tue Nov 30 01:56:32 2021
From: kl126835 at 163.com (=?UTF-8?B?5YWN5a2R?=)
Date: Tue, 30 Nov 2021 17:56:32 +0800 (GMT+08:00)
Subject: [Chimera-users] UCSF software cannot be opened normally
Message-ID: <5b1e1607.84c8.17d704642e1.Coremail.kl126835@163.com>

As shown in the attached figure, I hope you can help solve this problem. Thank you.


| |
??
|
|
kl126835 at 163.com
|
???????????
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From prathvi at iitk.ac.in  Tue Nov 30 21:50:31 2021
From: prathvi at iitk.ac.in (Prathvi Singh)
Date: Wed, 1 Dec 2021 11:20:31 +0530
Subject: [Chimera-users] Curiosity regarding amino acid category in UCSF
	chimera
Message-ID: <CAD3Hi5YqN5ELceoR2UmOByEO4_yAgL1tXdB4gy_xog6_VjzhgQ@mail.gmail.com>

Hi,

In UCSF chimera, when I go to Select > Residue > Amino Acid Category >
Hydrophobic, the LYSINE residues also get selected. However, according to
the Kyte-Dolittle scale, LYSINE is a fairly hydrophilic residue. Is there
any specific reason why chimera lists them as hydrophobic residues?

--
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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