From patelsmit11103 at gmail.com  Thu Apr  1 02:13:29 2021
From: patelsmit11103 at gmail.com (Smit Patel)
Date: Thu, 1 Apr 2021 14:43:29 +0530
Subject: [Chimera-users] identifying and counting selected residues
In-Reply-To: <AFD26598-CDE7-488B-8FBE-D1E340278976@cgl.ucsf.edu>
References: <C9BAACBC-0968-45C8-A417-A6C760CEFD94@hxcore.ol>
 <AFD26598-CDE7-488B-8FBE-D1E340278976@cgl.ucsf.edu>
Message-ID: <CAHE=p-HH_gjGiLZy550jpj7yzbAdqqHdKVtcMNXNJu2cepRifg@mail.gmail.com>

respected ma'am

greetings for the day!

Sorry to disturb you again. can you pls tell me the process to run this
selection inspector tool using chimera --nogui option. I tried but couldn't
find any. Also in the python 2.7 scripts, the inspect.py script is hard to
understand. Can you pls tell me to count residues without any involvement
of GUI? it would be really helpful.

thank you,
Regards

Smit, B.tech(bioinformatics)
Amity university

On Wed, Mar 31, 2021 at 8:52 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Greetings Smit,
> You can just use the "select" command with these amino acid categories,
> for example:
>
> select polar
> select nonpolar
> select hydrophobic
>
> See:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html>
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#builtin
> >
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
>
> .... and then the Selection Inspector says how many residues are
> selected.  You can open this tool from the menu (Actions... Inspect) or by
> clicking the magnifying-glass icon near the bottom right corner of the
> Chimera window,
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
>
> and just keep that tool open the whole time.  Then when you use the
> different select commands, it will say near the top of that dialog how many
> residues and atoms are selected.
>
> There are beginner tutorials for starting to use commands, for example
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html
> >
>
> ...and the "working with commands" section in:
> <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.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 Mar 31, 2021, at 12:29 AM, Smit Patel <patelsmit11103 at gmail.com>
> wrote:
> >
> > Respected sir/ma?am,
> >
> > Greetings for the day!
> > I?m new user of chimera tool and I don?t know many functions related to
> command line. So my question is how to identify and count polar, nonpolar ,
> hydrophobic residues in a given protein using command line.
> >
> > Like in gui I performed select?residue?amino acid category?polar or
> hydrophobic. So how to covert this process into the code using command line
> and get the count of the residues which are selected hydrophobic/polar?
> >
> > It would be very grateful if you could advise me how to code the command
> line.
> > Thank you,
> > Regards
> > Smit
> >
>
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From pett at cgl.ucsf.edu  Thu Apr  1 09:33:53 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 1 Apr 2021 09:33:53 -0700
Subject: [Chimera-users] identifying and counting selected residues
In-Reply-To: <CAHE=p-HH_gjGiLZy550jpj7yzbAdqqHdKVtcMNXNJu2cepRifg@mail.gmail.com>
References: <C9BAACBC-0968-45C8-A417-A6C760CEFD94@hxcore.ol>
 <AFD26598-CDE7-488B-8FBE-D1E340278976@cgl.ucsf.edu>
 <CAHE=p-HH_gjGiLZy550jpj7yzbAdqqHdKVtcMNXNJu2cepRifg@mail.gmail.com>
Message-ID: <71D14470-5A50-4BD6-8389-1BD4609FDF13@cgl.ucsf.edu>

These questions are oddly similar, and have the same answer.  To get the selected residues in Python, and how many, you:

	from chimera.selection import currentResidues
	sel_residues = currentResidues()
	num_sel = len(sel_residues)

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Mar 31, 2021, at 10:03 PM, Jayashree Chittari <jayashreechittari27 at gmail.com> wrote:
> 
> Respected sir/ma'am
> 
> Greetings for the day!
> I want to use chimera commands in shell scripting or python. So, my problem is how to count the residues using Chimera? in gui we know that there is a magnifying icon at the lower right portion of the window, but while running in linux terminal I'm unable to generate the same results.
> 
> Here is the attached ss of inspect selection, so if I want to print this in linux terminal what steps should I follow to get to this result?
> 
> I'm trying my best to search in the tutorials but  unable to create a command related to inspect selection.
> Kindly help me in this issue, it would be very grateful if you suggest the code.
> 
> thank you,
> 
> Regards
> Chittari Jaya Shree


> On Apr 1, 2021, at 2:13 AM, Smit Patel <patelsmit11103 at gmail.com> wrote:
> 
> respected ma'am
> 
> greetings for the day!
> 
> Sorry to disturb you again. can you pls tell me the process to run this selection inspector tool using chimera --nogui option. I tried but couldn't find any. Also in the python 2.7 scripts, the inspect.py script is hard to understand. Can you pls tell me to count residues without any involvement of GUI? it would be really helpful.
> 
> thank you,
> Regards
> 
> Smit, B.tech(bioinformatics)
> Amity university
> 
> On Wed, Mar 31, 2021 at 8:52 PM Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
> Greetings Smit,
> You can just use the "select" command with these amino acid categories, for example:
> 
> select polar
> select nonpolar
> select hydrophobic
> 
> See:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html>>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#builtin <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#builtin>>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>>
> 
> .... and then the Selection Inspector says how many residues are selected.  You can open this tool from the menu (Actions... Inspect) or by clicking the magnifying-glass icon near the bottom right corner of the Chimera window, 
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>>
> 
> and just keep that tool open the whole time.  Then when you use the different select commands, it will say near the top of that dialog how many residues and atoms are selected.
> 
> There are beginner tutorials for starting to use commands, for example 
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>>
> 
> ...and the "working with commands" section in:
> <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.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 Mar 31, 2021, at 12:29 AM, Smit Patel <patelsmit11103 at gmail.com <mailto:patelsmit11103 at gmail.com>> wrote:
> > 
> > Respected sir/ma?am,
> >  
> > Greetings for the day!
> > I?m new user of chimera tool and I don?t know many functions related to command line. So my question is how to identify and count polar, nonpolar , hydrophobic residues in a given protein using command line.
> >  
> > Like in gui I performed select?residue?amino acid category?polar or hydrophobic. So how to covert this process into the code using command line and get the count of the residues which are selected hydrophobic/polar?
> >  
> > It would be very grateful if you could advise me how to code the command line. 
> > Thank you,
> > Regards 
> > Smit  
> >  
> _______________________________________________
> 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 Ashok.Nayak at vcuhealth.org  Thu Apr  1 15:46:02 2021
From: Ashok.Nayak at vcuhealth.org (Ashok Nayak)
Date: Thu, 1 Apr 2021 22:46:02 +0000
Subject: [Chimera-users] translation along x,y and z
Message-ID: <BY5PR08MB6245AB0B30E282CB0DFE0763FE7B9@BY5PR08MB6245.namprd08.prod.outlook.com>

HI Elaine,
I want to know the rotation and translation components along x,y and z separately from the rotation matrix obtained from chimera reply log upon fitting a model into a map. Will it be possible to know?

Matrix rotation and translation
     1.00000000  -0.00000000  -0.00000000   1.83458738
    -0.00000000   1.00000000  -0.00000000   1.15016978
    -0.00000000  -0.00000000   1.00000000  -0.53835221
  Axis   0.00000000   0.00000000   1.00000000
  Axis point   0.00000000   0.00000000   0.00000000
  Rotation angle (degrees)   0.00000000
  Shift along axis  -0.53835221

thanks,
Ashok
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From meng at cgl.ucsf.edu  Thu Apr  1 17:02:05 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 1 Apr 2021 17:02:05 -0700
Subject: [Chimera-users] translation along x,y and z
In-Reply-To: <BY5PR08MB6245AB0B30E282CB0DFE0763FE7B9@BY5PR08MB6245.namprd08.prod.outlook.com>
References: <BY5PR08MB6245AB0B30E282CB0DFE0763FE7B9@BY5PR08MB6245.namprd08.prod.outlook.com>
Message-ID: <BD62A46A-0CBB-40F9-9DD6-6B6D2BE4B674@cgl.ucsf.edu>

Hey, I'm not the only one who answers these questions!  :-)

It is explained in the "Fit in Map" manual page:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html#matrices>

"The transformation matrix of the fit model relative to the reference map is reported in the Reply Log. The first three columns of the matrix describe a rotation and the fourth describes a translation (performed after the rotation)."

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

> On Apr 1, 2021, at 3:46 PM, Ashok Nayak <Ashok.Nayak at vcuhealth.org> wrote:
> 
> HI Elaine,
> I want to know the rotation and translation components along x,y and z separately from the rotation matrix obtained from chimera reply log upon fitting a model into a map. Will it be possible to know?
> 
> Matrix rotation and translation
>      1.00000000  -0.00000000  -0.00000000   1.83458738
>     -0.00000000   1.00000000  -0.00000000   1.15016978
>     -0.00000000  -0.00000000   1.00000000  -0.53835221
>   Axis   0.00000000   0.00000000   1.00000000
>   Axis point   0.00000000   0.00000000   0.00000000
>   Rotation angle (degrees)   0.00000000
>   Shift along axis  -0.53835221
> 
> thanks,
> Ashok



From Ashok.Nayak at vcuhealth.org  Thu Apr  1 17:07:05 2021
From: Ashok.Nayak at vcuhealth.org (Ashok Nayak)
Date: Fri, 2 Apr 2021 00:07:05 +0000
Subject: [Chimera-users] [EXTERNAL] Re: translation along x,y and z
In-Reply-To: <BD62A46A-0CBB-40F9-9DD6-6B6D2BE4B674@cgl.ucsf.edu>
References: <BY5PR08MB6245AB0B30E282CB0DFE0763FE7B9@BY5PR08MB6245.namprd08.prod.outlook.com>
 <BD62A46A-0CBB-40F9-9DD6-6B6D2BE4B674@cgl.ucsf.edu>
Message-ID: <736ef864-cf5d-4b6b-82bd-59fc5f94da03@Ashoks-Iphone>

Thanks Elaine!  Well you answered well before others in the team. ?



On Apr 1, 2021 at 8:02 PM, <Elaine Meng<mailto:meng at cgl.ucsf.edu>> wrote:


Hey, I'm not the only one who answers these questions!  :-)

It is explained in the "Fit in Map" manual page:
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html*matrices__;Iw!!JqxBPMk!xxVnA8H7hYuofVFeoHwHPo-TJhHwl52Ro3yS2YPnrup56wIKqpeuq-rtH-PilKRZ3g$ >

"The transformation matrix of the fit model relative to the reference map is reported in the Reply Log. The first three columns of the matrix describe a rotation and the fourth describes a translation (performed after the rotation)."

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

> On Apr 1, 2021, at 3:46 PM, Ashok Nayak <Ashok.Nayak at vcuhealth.org<mailto:Ashok.Nayak at vcuhealth.org>> wrote:
>
> HI Elaine,
> I want to know the rotation and translation components along x,y and z separately from the rotation matrix obtained from chimera reply log upon fitting a model into a map. Will it be possible to know?
>
> Matrix rotation and translation
>      1.00000000  -0.00000000  -0.00000000   1.83458738
>     -0.00000000   1.00000000  -0.00000000   1.15016978
>     -0.00000000  -0.00000000   1.00000000  -0.53835221
>   Axis   0.00000000   0.00000000   1.00000000
>   Axis point   0.00000000   0.00000000   0.00000000
>   Rotation angle (degrees)   0.00000000
>   Shift along axis  -0.53835221
>
> thanks,
> Ashok


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From meng at cgl.ucsf.edu  Mon Apr  5 09:42:30 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 Apr 2021 09:42:30 -0700
Subject: [Chimera-users] ResProp Python code
In-Reply-To: <CAB-P8-k12YOQZ8mFfQBHd3_OGoTW5DEVeR=kijkUgN0kLFAx9g@mail.gmail.com>
References: <CAB-P8-k12YOQZ8mFfQBHd3_OGoTW5DEVeR=kijkUgN0kLFAx9g@mail.gmail.com>
Message-ID: <B96168D7-34B6-4D46-A731-D82ED9D18A93@cgl.ucsf.edu>

Dear Chittari Jaya Shree,
I can't answer about python, but maybe you didn't know about the related feature that you can simply assign names to whatever you want.   There is no need to use the ResProp tool if this is all going to be in a script anyway. For example, command:

alias neutral :ile,val,leu,phe,cys,met,ala,gly,thr,ser,trp,tyr,pro,gln,asn

... will then let you use "neutral" in other commands, e.g.

select neutral

"alias" command
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.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 Apr 5, 2021, at 4:54 AM, Jayashree Chittari <jayashreechittari27 at gmail.com> wrote:
> 
> Respected sir/ma'am
> 
> Greetings for the day!
> I want to make a new category named as neutral in which I would assign some amino acids to this category. So, in GUI we know that it could be done through tools-->structural analysis--> ResProp.
> 
>  My question is how to do the similar process in python, like how to assign certain amino acids to a new category and then perform the selection("select neutral")?
> 
> Here is the attached ss of Residue category definition. I want to use this process in python where the new category contains assigned amino acids.
> 
> Kindly help me in this issue, it would be very grateful if you suggest the code.
> thank you,
> 
> Regards
> Chittari Jaya Shree
> 
> <Capture.PNG>



From divita.mathur.ctr.in at nrl.navy.mil  Mon Apr  5 09:38:30 2021
From: divita.mathur.ctr.in at nrl.navy.mil (Divita Mathur, Contractor Code 6910, FN)
Date: Mon, 5 Apr 2021 16:38:30 +0000
Subject: [Chimera-users] rna model
Message-ID: <4A769698-FC41-43FF-81ED-15DC6F196E66@contoso.com>

Hello Chimera community

I am trying to run the ?rna model sequence  #0? code but it is returning the following error:
IndexError: list index out of range

File ??path/RNALayout/rna_layout.py?, line 393, in place_residues
  rprev = rlist[0]

See reply log for Python traceback.


Anything elementary that I am missing? My fasta file is very simple and it is stored in the Documents folder.

Regards,

--
Divita Mathur, PhD
Research Assistant Professor
George Mason University &
Center for Bio/Molecular Science and Engineering
Naval Research Laboratory
(202) 767-0687 (Office)
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From meng at cgl.ucsf.edu  Mon Apr  5 17:26:09 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 Apr 2021 17:26:09 -0700
Subject: [Chimera-users] rna model
In-Reply-To: <4A769698-FC41-43FF-81ED-15DC6F196E66@contoso.com>
References: <4A769698-FC41-43FF-81ED-15DC6F196E66@contoso.com>
Message-ID: <75CB1C01-3F99-4416-A461-D996BCFF5018@cgl.ucsf.edu>

Hi Divita,
Is ?rna model sequence  #0? actually the command you gave?  In the command usage, the word "sequence" (shown in italics) is supposed to be pathname of the file with the sequence in it (not literally the word "sequence"), and you are also required to either give the "path" option or the "pairs" option.  You cannot omit both.

"rna model" help
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>

how to read command usage in help pages
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>

So if you had  the path markers as #0 then your command could be something like

rna model /Users/divita/Documents/blahblah.fasta path #0

(of course, change the pathname as appropriate for the detailed location and filename of your fasta file.)

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

> On Apr 5, 2021, at 9:38 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
> 
> Hello Chimera community
> I am trying to run the ?rna model sequence  #0? code but it is returning the following error:
> IndexError: list index out of range
>  
> File ??path/RNALayout/rna_layout.py?, line 393, in place_residues
>   rprev = rlist[0]
>  
> See reply log for Python traceback.
>  
> Anything elementary that I am missing? My fasta file is very simple and it is stored in the Documents folder.
> Regards,



From blessedogo2000 at yahoo.com  Mon Apr  5 23:29:19 2021
From: blessedogo2000 at yahoo.com (ogochukwu ngozi)
Date: Tue, 6 Apr 2021 06:29:19 +0000 (UTC)
Subject: [Chimera-users] Chimera calculating RMSD
In-Reply-To: <75A4B1F4-56D9-435D-98CE-CA3EA1CDD603@cgl.ucsf.edu>
References: <1839288619.1228100.1616912407065.ref@mail.yahoo.com>
 <1839288619.1228100.1616912407065@mail.yahoo.com>
 <75A4B1F4-56D9-435D-98CE-CA3EA1CDD603@cgl.ucsf.edu>
Message-ID: <613883093.223244.1617690559367@mail.yahoo.com>

 Thanks so much Elaine.
    On Monday, March 29, 2021, 12:08:37 AM GMT+8, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 
 Dear Ogochukwu Nwaefulu,
There is a User Guide with explanations of just about every feature.? You can use the menu: "Help... Search Documentation" to search for terms, for example: RMSD.? That will give you links to parts of the User Guide.

As for your question, there are several related features for superimposing structures, and they also report the resulting RMSD value.? See this page for a summary, wth links to the detailed information on each, including "MatchMaker" and "Ensemble Match" tools and "match" command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

There is also an "rmsd" command for if you do NOT want to superimpose structures on top of each other, but instead calculate the RMSD in their current positions.? That would be used, for example, to compare different positions of the same ligand but docked in different places on a receptor.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>

Finally, there are several tutorials with examples of using these features.

This one includes MatchMaker:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html>

This one has examples of using the "match" command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html>

This one includes Ensemble Match:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.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 Mar 27, 2021, at 11:20 PM, ogochukwu ngozi <blessedogo2000 at yahoo.com> wrote:
> 
> Dear Concerned,
> I am a PHD student from University Putra Malaysia. This is my first time using Chimera, please I need your assistance. I want to use chimera to calculate RMSD values, could you direct me on steps to take please? Thanks as I await your kind reply.
> Ogochukwu Nwaefulu
> _______________________________________________
> 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 divita.mathur.ctr.in at nrl.navy.mil  Tue Apr  6 05:33:26 2021
From: divita.mathur.ctr.in at nrl.navy.mil (Divita Mathur, Contractor Code 6910, FN)
Date: Tue, 6 Apr 2021 12:33:26 +0000
Subject: [Chimera-users] rna model
In-Reply-To: <75CB1C01-3F99-4416-A461-D996BCFF5018@cgl.ucsf.edu>
References: <4A769698-FC41-43FF-81ED-15DC6F196E66@contoso.com>
 <75CB1C01-3F99-4416-A461-D996BCFF5018@cgl.ucsf.edu>
Message-ID: <5DD7F426-5D40-4265-8F31-226FAB1DBD18@nrl.navy.mil>

Hi Elaine

Sorry, I should have been clearer. This was my command:
rna model /Users/dmathur/Documents/gapB-sfGFP-mRNA.fasta path #0
and
rna model /Users/dmathur/Documents/gapB-sfGFP-mRNA.fasta path #0 start 40 length 8

Both return the same error.

-- 
Divita Mathur, PhD

Research Assistant Professor
George Mason University &
Center for Bio/Molecular Science and Engineering

Naval Research Laboratory
(202) 767-0687 (Office)

?On 4/5/21, 8:26 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

    Hi Divita,
    Is ?rna model sequence  #0? actually the command you gave?  In the command usage, the word "sequence" (shown in italics) is supposed to be pathname of the file with the sequence in it (not literally the word "sequence"), and you are also required to either give the "path" option or the "pairs" option.  You cannot omit both.

    "rna model" help
    <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>

    how to read command usage in help pages
    <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>

    So if you had  the path markers as #0 then your command could be something like

    rna model /Users/divita/Documents/blahblah.fasta path #0

    (of course, change the pathname as appropriate for the detailed location and filename of your fasta file.)

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

    > On Apr 5, 2021, at 9:38 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
    > 
    > Hello Chimera community
    > I am trying to run the ?rna model sequence  #0? code but it is returning the following error:
    > IndexError: list index out of range
    >  
    > File ??path/RNALayout/rna_layout.py?, line 393, in place_residues
    >   rprev = rlist[0]
    >  
    > See reply log for Python traceback.
    >  
    > Anything elementary that I am missing? My fasta file is very simple and it is stored in the Documents folder.
    > Regards,




From meng at cgl.ucsf.edu  Tue Apr  6 08:51:42 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 6 Apr 2021 08:51:42 -0700
Subject: [Chimera-users] rna model
In-Reply-To: <5DD7F426-5D40-4265-8F31-226FAB1DBD18@nrl.navy.mil>
References: <4A769698-FC41-43FF-81ED-15DC6F196E66@contoso.com>
 <75CB1C01-3F99-4416-A461-D996BCFF5018@cgl.ucsf.edu>
 <5DD7F426-5D40-4265-8F31-226FAB1DBD18@nrl.navy.mil>
Message-ID: <285835F2-C5C1-4147-A737-3BBB3BBF9DE4@cgl.ucsf.edu>

Hi Divita,
It is not possible to tell what is happening without the data.  Instead of sending e-mail here, please use menu: Help... Report a Bug, attach a session file, and enter a description of steps needed to reproduce the problem.  Also include your email address for feedback.  I guess the bugreport form only allows attaching one thing, but somebody may ask for your fasta file later.

Only other thoughts are that maybe the path model doesn't have the right number of markers in it for your sequence, or maybe your fasta file isn't plain text.
Best,
Elaine

> On Apr 6, 2021, at 5:33 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
> 
> Hi Elaine
> 
> Sorry, I should have been clearer. This was my command:
> rna model /Users/dmathur/Documents/gapB-sfGFP-mRNA.fasta path #0
> and
> rna model /Users/dmathur/Documents/gapB-sfGFP-mRNA.fasta path #0 start 40 length 8
> 
> Both return the same error.
> 
> -- 
> Divita Mathur, PhD
> 
> Research Assistant Professor
> George Mason University &
> Center for Bio/Molecular Science and Engineering
> 
> Naval Research Laboratory
> (202) 767-0687 (Office)
> 
> ?On 4/5/21, 8:26 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
> 
>    Hi Divita,
>    Is ?rna model sequence  #0? actually the command you gave?  In the command usage, the word "sequence" (shown in italics) is supposed to be pathname of the file with the sequence in it (not literally the word "sequence"), and you are also required to either give the "path" option or the "pairs" option.  You cannot omit both.
> 
>    "rna model" help
>    <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>
> 
>    how to read command usage in help pages
>    <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>
> 
>    So if you had  the path markers as #0 then your command could be something like
> 
>    rna model /Users/divita/Documents/blahblah.fasta path #0
> 
>    (of course, change the pathname as appropriate for the detailed location and filename of your fasta file.)
> 
>    I hope this helps,
>    Elaine
>    -----
>    Elaine C. Meng, Ph.D.                       
>    UCSF Chimera(X) team
>    Department of Pharmaceutical Chemistry
>    University of California, San Francisco
> 
>> On Apr 5, 2021, at 9:38 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
>> 
>> Hello Chimera community
>> I am trying to run the ?rna model sequence  #0? code but it is returning the following error:
>> IndexError: list index out of range
>> 
>> File ??path/RNALayout/rna_layout.py?, line 393, in place_residues
>>  rprev = rlist[0]
>> 
>> See reply log for Python traceback.
>> 
>> Anything elementary that I am missing? My fasta file is very simple and it is stored in the Documents folder.
>> Regards,



From goddard at sonic.net  Tue Apr  6 11:04:51 2021
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 6 Apr 2021 11:04:51 -0700
Subject: [Chimera-users] rna model
In-Reply-To: <5DD7F426-5D40-4265-8F31-226FAB1DBD18@nrl.navy.mil>
References: <4A769698-FC41-43FF-81ED-15DC6F196E66@contoso.com>
 <75CB1C01-3F99-4416-A461-D996BCFF5018@cgl.ucsf.edu>
 <5DD7F426-5D40-4265-8F31-226FAB1DBD18@nrl.navy.mil>
Message-ID: <51262047-11D8-49E9-BAB3-CF553D2D2C74@sonic.net>

The rna error message is because the command was not able to construct any nucleotides.  The reason why is very likely because your input data has a problem.  As Elaine says we can't determine what is wrong with your input data without seeing it.  So use Help / Report a Bug... as Elaine suggests if you want help figuring it out.

	Tom


> On Apr 6, 2021, at 5:33 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
> 
> Hi Elaine
> 
> Sorry, I should have been clearer. This was my command:
> rna model /Users/dmathur/Documents/gapB-sfGFP-mRNA.fasta path #0
> and
> rna model /Users/dmathur/Documents/gapB-sfGFP-mRNA.fasta path #0 start 40 length 8
> 
> Both return the same error.
> 
> -- 
> Divita Mathur, PhD
> 
> Research Assistant Professor
> George Mason University &
> Center for Bio/Molecular Science and Engineering
> 
> Naval Research Laboratory
> (202) 767-0687 (Office)
> 
> ?On 4/5/21, 8:26 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
> 
>    Hi Divita,
>    Is ?rna model sequence  #0? actually the command you gave?  In the command usage, the word "sequence" (shown in italics) is supposed to be pathname of the file with the sequence in it (not literally the word "sequence"), and you are also required to either give the "path" option or the "pairs" option.  You cannot omit both.
> 
>    "rna model" help
>    <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>
> 
>    how to read command usage in help pages
>    <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>
> 
>    So if you had  the path markers as #0 then your command could be something like
> 
>    rna model /Users/divita/Documents/blahblah.fasta path #0
> 
>    (of course, change the pathname as appropriate for the detailed location and filename of your fasta file.)
> 
>    I hope this helps,
>    Elaine
>    -----
>    Elaine C. Meng, Ph.D.                       
>    UCSF Chimera(X) team
>    Department of Pharmaceutical Chemistry
>    University of California, San Francisco
> 
>> On Apr 5, 2021, at 9:38 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
>> 
>> Hello Chimera community
>> I am trying to run the ?rna model sequence  #0? code but it is returning the following error:
>> IndexError: list index out of range
>> 
>> File ??path/RNALayout/rna_layout.py?, line 393, in place_residues
>>  rprev = rlist[0]
>> 
>> See reply log for Python traceback.
>> 
>> Anything elementary that I am missing? My fasta file is very simple and it is stored in the Documents folder.
>> Regards,
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From martti.tolvanen at utu.fi  Thu Apr  8 05:43:55 2021
From: martti.tolvanen at utu.fi (Martti Tolvanen)
Date: Thu, 8 Apr 2021 12:43:55 +0000
Subject: [Chimera-users] Where does Chimera copy command save images?
Message-ID: <609c336f83fc45169241fd61a851f6c0@utu.fi>

I have tried to use the command copy on command line to save images, with a goal to do that in a script. The messages of rendering a high-res image and image saved come up, but the file is nowhere to be found. My guess is that the default save location is in the Chimera program folder, which would not be permitted, but Chimera just doesn't see it as a failed attempt. I do have a workaround of including the full path in a filename, but I'm just curious where the file would be going by default, and whether there is some command to change the working folder by a command. FYI it's Chimera 1.15 in Windows 10. 

Martti Tolvanen
University Lecturer in Bioinformatics
U of Turku, Finland


From nirban.dey2019 at vitstudent.ac.in  Thu Apr  8 04:38:12 2021
From: nirban.dey2019 at vitstudent.ac.in (Nirban Dey 19MSM0098)
Date: Thu, 8 Apr 2021 17:08:12 +0530
Subject: [Chimera-users] Query about adding charge to ligand
Message-ID: <CAPbB81yYA71ti__8=h3McK9QQ7UjEa17NoYf_+DHpNwNQqGAfQ@mail.gmail.com>

Hello, I am a Masters student of VIT University India. I am using chimera
to prepare my ligand. In the add charge option I noticed that if my ligand
has negative or positive charge and I try to add AM1-BCC it gives error but
I can add Gasteiger charge. Even if I set charge to +0 for the ligands that
have charge like -1 or +1  and try to add  AM1-BCC it gives error. I want
to know what is the reason that Gasteiger charge can be added but AM1-BCC
cannot be added..Kindly help me in this regard.

Thanking You
Nirban
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From meng at cgl.ucsf.edu  Thu Apr  8 08:36:12 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 8 Apr 2021 08:36:12 -0700
Subject: [Chimera-users] Query about adding charge to ligand
In-Reply-To: <CAPbB81yYA71ti__8=h3McK9QQ7UjEa17NoYf_+DHpNwNQqGAfQ@mail.gmail.com>
References: <CAPbB81yYA71ti__8=h3McK9QQ7UjEa17NoYf_+DHpNwNQqGAfQ@mail.gmail.com>
Message-ID: <2071CDE3-21DF-46E3-8157-F71DDB73EC35@cgl.ucsf.edu>

Hello Nirban,
The Gasteiger and AM1-BCC charge calculations are completely different and so it is not a surprise that one method "works" on a molecule and the other does not.  The Gasteiger method is more simplistic and faster.  The AM1-BCC method is more intensive but will more often fail, especially on larger or more highly charged molecules.  We (the Chimera developers) did not create these methods.

If you really want to know how they work, read the original publications...

	? AM1-BCC - semi-empirical (AM1) with bond charge correction (BCC)

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.
Jakalian A, Jack DB, Bayly CI. J Comput Chem. 2002 Dec;23(16):1623-41. <https://pubmed.ncbi.nlm.nih.gov/12395429/>

	? Gasteiger - faster method based on atom types and connectivity

Iterative partial equalization of orbital electronegativity?a rapid access to atomic charges. Johann Gasteiger, Mario Marsili. Tetrahedron. Volume 36, Issue 22, 1980, Pages 3219-3228
<https://www.sciencedirect.com/science/article/pii/0040402080801682>

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

> On Apr 8, 2021, at 4:38 AM, Nirban Dey 19MSM0098 <nirban.dey2019 at vitstudent.ac.in> wrote:
> 
> Hello, I am a Masters student of VIT University India. I am using chimera to prepare my ligand. In the add charge option I noticed that if my ligand has negative or positive charge and I try to add AM1-BCC it gives error but I can add Gasteiger charge. Even if I set charge to +0 for the ligands that have charge like -1 or +1  and try to add  AM1-BCC it gives error. I want to know what is the reason that Gasteiger charge can be added but AM1-BCC cannot be added..Kindly help me in this regard.
> Thanking You
> Nirban



From meng at cgl.ucsf.edu  Thu Apr  8 08:41:27 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 8 Apr 2021 08:41:27 -0700
Subject: [Chimera-users] Where does Chimera copy command save images?
In-Reply-To: <609c336f83fc45169241fd61a851f6c0@utu.fi>
References: <609c336f83fc45169241fd61a851f6c0@utu.fi>
Message-ID: <B3685747-8F8A-43F6-917C-60748D4FF663@cgl.ucsf.edu>

Hi Martti,
I don't know the answer, but another thing you can do is use the Chimera "cd" command to change the working directory so that later in the same session, you no longer have to specify it in the filenames of files to open or save.  (Alas, there is no Chimera "pwd" command to tell you what it thinks is the current working directory, however.)

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/cd.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 Apr 8, 2021, at 5:43 AM, Martti Tolvanen <martti.tolvanen at utu.fi> wrote:
> 
> I have tried to use the command copy on command line to save images, with a goal to do that in a script. The messages of rendering a high-res image and image saved come up, but the file is nowhere to be found. My guess is that the default save location is in the Chimera program folder, which would not be permitted, but Chimera just doesn't see it as a failed attempt. I do have a workaround of including the full path in a filename, but I'm just curious where the file would be going by default, and whether there is some command to change the working folder by a command. FYI it's Chimera 1.15 in Windows 10. 
> 
> Martti Tolvanen
> University Lecturer in Bioinformatics
> U of Turku, Finland



From anfimk357 at gmail.com  Thu Apr  8 09:44:58 2021
From: anfimk357 at gmail.com (Susan)
Date: Thu, 8 Apr 2021 16:44:58 +0000
Subject: [Chimera-users] Chimera-users Where does Chimera copy command
	save images?
Message-ID: <CAF+LMcpSz8r889iVf3jhmdKk7LM5A4pDWHRd3=b16A+x5UvkJQ@mail.gmail.com>

Hi there honey!

I'm a 30 years old lonely housewife looking for an affair.
I'm ready to try anything


You can see my photos, you can see them right here
<http://gallery.prince-ss.com?n=frfya&s=687474703a2f2f646174696e6773722e636f6d2f6e65772f3f733d393026263430373336303537313330313534322664693d37672d3139352665643d63676c26693d61646d696e39302c32313333302c6368696d6572612d75736572734063676c2e756373662e6564752c4368696d6572612674733d3136313738393530333926393034373730303432363538373834&>



On Thu, Apr 8, 2021, at 5:41 PM, Chimera wrote:

>Hi Martti,
>I don't know the answer, but another thing you can do is use the Chimera
cd command to change the working directory so that later in the same
session, you no longer have to specify it in the filenames of files to open
or save. (Alas, there is no Chimera pwd command to tell you what it thinks
is the current working directory, however.)
>
>
>I hope this helps,
>Elaine
>-----
>Elaine C. Meng, Ph.D.
>UCSF Chimera(X) team
>Depa
>
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From pett at cgl.ucsf.edu  Thu Apr  8 09:51:57 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 8 Apr 2021 09:51:57 -0700
Subject: [Chimera-users] Chimera-users Where does Chimera copy command
 save images?
In-Reply-To: <CAF+LMcpSz8r889iVf3jhmdKk7LM5A4pDWHRd3=b16A+x5UvkJQ@mail.gmail.com>
References: <CAF+LMcpSz8r889iVf3jhmdKk7LM5A4pDWHRd3=b16A+x5UvkJQ@mail.gmail.com>
Message-ID: <81D6E6E9-DC6D-4FC1-81A5-80315979C1B8@cgl.ucsf.edu>

It looks like someone's account got hacked.  This user has been removed from the list.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Apr 8, 2021, at 9:44 AM, Susan <anfimk357 at gmail.com> wrote:
> 
> Hi there honey! 
> 
> I'm a 30 years old lonely housewife looking for an affair.
> I'm ready to try anything
> 
> 
> You can see my photos, you can see them right here <http://gallery.prince-ss.com/?n=frfya&s=687474703a2f2f646174696e6773722e636f6d2f6e65772f3f733d393026263430373336303537313330313534322664693d37672d3139352665643d63676c26693d61646d696e39302c32313333302c6368696d6572612d75736572734063676c2e756373662e6564752c4368696d6572612674733d3136313738393530333926393034373730303432363538373834&>
> 
> 
> 
> On Thu, Apr 8, 2021, at 5:41 PM, Chimera wrote:
> 
> >Hi Martti,
> >I don't know the answer, but another thing you can do is use the Chimera cd command to change the working directory so that later in the same session, you no longer have to specify it in the filenames of files to open or save. (Alas, there is no Chimera pwd command to tell you what it thinks is the current working directory, however.)
> >
> >
> >I hope this helps,
> >Elaine
> >-----
> >Elaine C. Meng, Ph.D.
> >UCSF Chimera(X) team
> >Depa
> >
> _______________________________________________
> 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 nirban.dey2019 at vitstudent.ac.in  Thu Apr  8 21:47:26 2021
From: nirban.dey2019 at vitstudent.ac.in (Nirban Dey 19MSM0098)
Date: Fri, 9 Apr 2021 10:17:26 +0530
Subject: [Chimera-users] Query about adding charge to ligand
In-Reply-To: <2071CDE3-21DF-46E3-8157-F71DDB73EC35@cgl.ucsf.edu>
References: <CAPbB81yYA71ti__8=h3McK9QQ7UjEa17NoYf_+DHpNwNQqGAfQ@mail.gmail.com>
 <2071CDE3-21DF-46E3-8157-F71DDB73EC35@cgl.ucsf.edu>
Message-ID: <CAPbB81xUG6OnSaC9GSOrOVyFHAQzooR-xg-gp0z_oJB51ij61A@mail.gmail.com>

Thanks a lot.

On Thu, Apr 8, 2021 at 9:06 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Nirban,
> The Gasteiger and AM1-BCC charge calculations are completely different and
> so it is not a surprise that one method "works" on a molecule and the other
> does not.  The Gasteiger method is more simplistic and faster.  The AM1-BCC
> method is more intensive but will more often fail, especially on larger or
> more highly charged molecules.  We (the Chimera developers) did not create
> these methods.
>
> If you really want to know how they work, read the original publications...
>
>         ? AM1-BCC - semi-empirical (AM1) with bond charge correction (BCC)
>
> Fast, efficient generation of high-quality atomic charges. AM1-BCC model:
> II. Parameterization and validation.
> Jakalian A, Jack DB, Bayly CI. J Comput Chem. 2002 Dec;23(16):1623-41. <
> https://pubmed.ncbi.nlm.nih.gov/12395429/>
>
>         ? Gasteiger - faster method based on atom types and connectivity
>
> Iterative partial equalization of orbital electronegativity?a rapid access
> to atomic charges. Johann Gasteiger, Mario Marsili. Tetrahedron. Volume 36,
> Issue 22, 1980, Pages 3219-3228
> <https://www.sciencedirect.com/science/article/pii/0040402080801682>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Apr 8, 2021, at 4:38 AM, Nirban Dey 19MSM0098 <
> nirban.dey2019 at vitstudent.ac.in> wrote:
> >
> > Hello, I am a Masters student of VIT University India. I am using
> chimera to prepare my ligand. In the add charge option I noticed that if my
> ligand has negative or positive charge and I try to add AM1-BCC it gives
> error but I can add Gasteiger charge. Even if I set charge to +0 for the
> ligands that have charge like -1 or +1  and try to add  AM1-BCC it gives
> error. I want to know what is the reason that Gasteiger charge can be added
> but AM1-BCC cannot be added..Kindly help me in this regard.
> > Thanking You
> > Nirban
>
>
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From kajihara at chem.sci.osaka-u.ac.jp  Thu Apr  8 22:26:20 2021
From: kajihara at chem.sci.osaka-u.ac.jp (kajihara)
Date: Fri, 9 Apr 2021 14:26:20 +0900
Subject: [Chimera-users] greeting and acknowledgement
Message-ID: <D4E8714B-B01A-4B85-84E8-CE633ABB3F08@chem.sci.osaka-u.ac.jp>

Dear Prof. Ferrin, Dear stuff of Chimera,

I am prof Yasuhiro Kajihara, Department of chemistry, Osaka University.
Last April, Corona pandemic suddenly attack us, and our university closed in-person style classes.

I needed to do online class of biochemistry.  I recommended students to download UCSF Chimera for understanding protein structure and behavior.
The Chimera soft wear was great help for us under the terrible Corona Pandemic and all students enjoy to deal with Chimera.  They got unbelievable knowledge through the Chimera.
I could not find a suitable word to express my thank.
I thank you again for your great support and kindness to deliver it as free.

Within a week 80 students will start download chimera.  So, I need to send greeting e-mail to give my thanks.

Sincerely

Yasuhiro Kajihara, Ph. D.
Department of Chemistry
Osaka University
Machikaneyama, 1-1, Toyonaka,
560-0043 Japan
kajihara at chem.sci.osaka-u.ac.jp




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From martti.tolvanen at utu.fi  Fri Apr  9 03:53:14 2021
From: martti.tolvanen at utu.fi (Martti Tolvanen)
Date: Fri, 9 Apr 2021 10:53:14 +0000
Subject: [Chimera-users] Where does Chimera copy command save images?
In-Reply-To: <B3685747-8F8A-43F6-917C-60748D4FF663@cgl.ucsf.edu>
References: <609c336f83fc45169241fd61a851f6c0@utu.fi>
 <B3685747-8F8A-43F6-917C-60748D4FF663@cgl.ucsf.edu>
Message-ID: <8892a42a8b984b59a4babea5309e7386@utu.fi>

Thanks Elaine,

Command cd had been too short in the left sidebar command index to come into my attention! This works perfectly.

Cheers,
-Martti

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: 8. huhtikuutata 2021 18:41
To: Martti Tolvanen <martti.tolvanen at utu.fi>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Where does Chimera copy command save images?

Hi Martti,
I don't know the answer, but another thing you can do is use the Chimera "cd" command to change the working directory so that later in the same session, you no longer have to specify it in the filenames of files to open or save.  (Alas, there is no Chimera "pwd" command to tell you what it thinks is the current working directory, however.)

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/cd.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 Apr 8, 2021, at 5:43 AM, Martti Tolvanen <martti.tolvanen at utu.fi> wrote:
> 
> I have tried to use the command copy on command line to save images, with a goal to do that in a script. The messages of rendering a high-res image and image saved come up, but the file is nowhere to be found. My guess is that the default save location is in the Chimera program folder, which would not be permitted, but Chimera just doesn't see it as a failed attempt. I do have a workaround of including the full path in a filename, but I'm just curious where the file would be going by default, and whether there is some command to change the working folder by a command. FYI it's Chimera 1.15 in Windows 10. 
> 
> Martti Tolvanen
> University Lecturer in Bioinformatics
> U of Turku, Finland



From meng at cgl.ucsf.edu  Fri Apr  9 08:34:23 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 9 Apr 2021 08:34:23 -0700
Subject: [Chimera-users] greeting and acknowledgement
In-Reply-To: <D4E8714B-B01A-4B85-84E8-CE633ABB3F08@chem.sci.osaka-u.ac.jp>
References: <D4E8714B-B01A-4B85-84E8-CE633ABB3F08@chem.sci.osaka-u.ac.jp>
Message-ID: <3535E583-7505-4098-87CC-14E23B94184A@cgl.ucsf.edu>

Dear Prof. Kajihara,
Thank you so much for the kind words!

We are very happy to hear that Chimera has been helpful for your class.

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


> On Apr 8, 2021, at 10:26 PM, kajihara <kajihara at chem.sci.osaka-u.ac.jp> wrote:
> 
> Dear Prof. Ferrin, Dear stuff of Chimera,
> 
> I am prof Yasuhiro Kajihara, Department of chemistry, Osaka University.
> Last April, Corona pandemic suddenly attack us, and our university closed in-person style classes.
> 
> I needed to do online class of biochemistry.  I recommended students to download UCSF Chimera for understanding protein structure and behavior.
> The Chimera soft wear was great help for us under the terrible Corona Pandemic and all students enjoy to deal with Chimera.  They got unbelievable knowledge through the Chimera.
> I could not find a suitable word to express my thank.
> I thank you again for your great support and kindness to deliver it as free.
> 
> Within a week 80 students will start download chimera.  So, I need to send greeting e-mail to give my thanks.
> 
> Sincerely
> 
> Yasuhiro Kajihara, Ph. D.
> Department of Chemistry
> Osaka University
> Machikaneyama, 1-1, Toyonaka,
> 560-0043 Japan
> kajihara at chem.sci.osaka-u.ac.jp



From chiendarret at gmail.com  Sat Apr 10 09:45:12 2021
From: chiendarret at gmail.com (Francesco Pietra)
Date: Sat, 10 Apr 2021 18:45:12 +0200
Subject: [Chimera-users] combine models
Message-ID: <CAEv0nmvncAfj6n96ZdvVPsJ06-aOo6Vz7EH_uiwAy1sRZd55jw@mail.gmail.com>

Hi
(1) I am faced by the coordinates for a nucleics/protein assembly being
given in several bundle.pdb, while I need a sequential, continuous pdb file
that comprises all nucleotides and proteins, not made of models

(2) If I load all the bundles to chimera, I see all expected ligands around
the small molecule.

(3) With all models selected, copy/combine (adopting default first model as
reference and allowing renaming chains) generates a new model. The new
model laks some proteins that should lie near the ligand, as described at
(2).

I feel that I am missing something.

Thanks for advice
francesco pietra
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From chiendarret at gmail.com  Sat Apr 10 10:37:52 2021
From: chiendarret at gmail.com (Francesco Pietra)
Date: Sat, 10 Apr 2021 19:37:52 +0200
Subject: [Chimera-users] Fwd: combine models
In-Reply-To: <CAEv0nmvncAfj6n96ZdvVPsJ06-aOo6Vz7EH_uiwAy1sRZd55jw@mail.gmail.com>
References: <CAEv0nmvncAfj6n96ZdvVPsJ06-aOo6Vz7EH_uiwAy1sRZd55jw@mail.gmail.com>
Message-ID: <CAEv0nmva4j2cY9EXW9R+qvaBhB_0h9BZEQfbupNENUEqCnhQ0A@mail.gmail.com>

Of course I tried to open the corresponding mmCIF, but CHIMERA candidate
1.15 build 42258 linux64 answered that the cif file [line 3] appears in tag
name entry.id and it was not opened

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Sat, Apr 10, 2021 at 6:45 PM
Subject: combine models
To: chimera <chimera-users at cgl.ucsf.edu>


Hi
(1) I am faced by the coordinates for a nucleics/protein assembly being
given in several bundle.pdb, while I need a sequential, continuous pdb file
that comprises all nucleotides and proteins, not made of models

(2) If I load all the bundles to chimera, I see all expected ligands around
the small molecule.

(3) With all models selected, copy/combine (adopting default first model as
reference and allowing renaming chains) generates a new model. The new
model laks some proteins that should lie near the ligand, as described at
(2).

I feel that I am missing something.

Thanks for advice
francesco pietra
-------------- next part --------------
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From meng at cgl.ucsf.edu  Sat Apr 10 16:31:23 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 10 Apr 2021 16:31:23 -0700
Subject: [Chimera-users] combine models
In-Reply-To: <CAEv0nmva4j2cY9EXW9R+qvaBhB_0h9BZEQfbupNENUEqCnhQ0A@mail.gmail.com>
References: <CAEv0nmvncAfj6n96ZdvVPsJ06-aOo6Vz7EH_uiwAy1sRZd55jw@mail.gmail.com>
 <CAEv0nmva4j2cY9EXW9R+qvaBhB_0h9BZEQfbupNENUEqCnhQ0A@mail.gmail.com>
Message-ID: <DBE604BC-2340-4C70-99B8-847281E3E1E1@cgl.ucsf.edu>

Hi Francesco,
It's not possible to identify the problem without the specific data.  If this is a PDB entry, what is the ID so we can try opening the mmCIF?  

Or, if this is not in the public database, please use Help... Report a Bug and attach a session that has all the bundle.pdb loaded into Chimera, and then in the description say how you combined them and what the problem is with the combined result.

Before you do that, make sure that you are displaying everything in the combined result.  Maybe the parts that seem to be missing were just hidden.

I should mention that ChimeraX is much better with mmCIF and very large complexes than Chimera, but maybe you are planning to use analysis features that are only in Chimera (not yet in ChimeraX).
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Apr 10, 2021, at 10:37 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 
> Of course I tried to open the corresponding mmCIF, but CHIMERA candidate 1.15 build 42258 linux64 answered that the cif file [line 3] appears in tag name entry.id and it was not opened
> 
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret at gmail.com>
> Date: Sat, Apr 10, 2021 at 6:45 PM
> Subject: combine models
> To: chimera <chimera-users at cgl.ucsf.edu>
> 
> 
> Hi
> (1) I am faced by the coordinates for a nucleics/protein assembly being given in several bundle.pdb, while I need a sequential, continuous pdb file that comprises all nucleotides and proteins, not made of models
> 
> (2) If I load all the bundles to chimera, I see all expected ligands around the small molecule. 
> 
> (3) With all models selected, copy/combine (adopting default first model as reference and allowing renaming chains) generates a new model. The new  model laks some proteins that should lie near the ligand, as described at (2).
> 
> I feel that I am missing something.
> 
> Thanks for advice
> francesco pietra



From meng at cgl.ucsf.edu  Sat Apr 10 16:44:33 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 10 Apr 2021 16:44:33 -0700
Subject: [Chimera-users] combine models
In-Reply-To: <DBE604BC-2340-4C70-99B8-847281E3E1E1@cgl.ucsf.edu>
References: <CAEv0nmvncAfj6n96ZdvVPsJ06-aOo6Vz7EH_uiwAy1sRZd55jw@mail.gmail.com>
 <CAEv0nmva4j2cY9EXW9R+qvaBhB_0h9BZEQfbupNENUEqCnhQ0A@mail.gmail.com>
 <DBE604BC-2340-4C70-99B8-847281E3E1E1@cgl.ucsf.edu>
Message-ID: <01041B15-48B1-4D13-A7C8-57ED82D871FB@cgl.ucsf.edu>

Actually, let me revise that answer: I realized that if there are too many chains for the PDB to put them into one PDB file, there may also be too many chains for combine to make them into one model in Chimera (it will also run out of valid chain IDs).  That is likely the problem, for which I don't have a solution.

Elaine

> On Apr 10, 2021, at 4:31 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Francesco,
> It's not possible to identify the problem without the specific data.  If this is a PDB entry, what is the ID so we can try opening the mmCIF?  
> 
> Or, if this is not in the public database, please use Help... Report a Bug and attach a session that has all the bundle.pdb loaded into Chimera, and then in the description say how you combined them and what the problem is with the combined result.
> 
> Before you do that, make sure that you are displaying everything in the combined result.  Maybe the parts that seem to be missing were just hidden.
> 
> I should mention that ChimeraX is much better with mmCIF and very large complexes than Chimera, but maybe you are planning to use analysis features that are only in Chimera (not yet in ChimeraX).
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Apr 10, 2021, at 10:37 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
>> 
>> Of course I tried to open the corresponding mmCIF, but CHIMERA candidate 1.15 build 42258 linux64 answered that the cif file [line 3] appears in tag name entry.id and it was not opened
>> 
>> ---------- Forwarded message ---------
>> From: Francesco Pietra <chiendarret at gmail.com>
>> Date: Sat, Apr 10, 2021 at 6:45 PM
>> Subject: combine models
>> To: chimera <chimera-users at cgl.ucsf.edu>
>> 
>> 
>> Hi
>> (1) I am faced by the coordinates for a nucleics/protein assembly being given in several bundle.pdb, while I need a sequential, continuous pdb file that comprises all nucleotides and proteins, not made of models
>> 
>> (2) If I load all the bundles to chimera, I see all expected ligands around the small molecule. 
>> 
>> (3) With all models selected, copy/combine (adopting default first model as reference and allowing renaming chains) generates a new model. The new  model laks some proteins that should lie near the ligand, as described at (2).
>> 
>> I feel that I am missing something.
>> 
>> Thanks for advice
>> francesco pietra
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From chiendarret at gmail.com  Sun Apr 11 06:50:26 2021
From: chiendarret at gmail.com (Francesco Pietra)
Date: Sun, 11 Apr 2021 15:50:26 +0200
Subject: [Chimera-users] combine models
In-Reply-To: <01041B15-48B1-4D13-A7C8-57ED82D871FB@cgl.ucsf.edu>
References: <CAEv0nmvncAfj6n96ZdvVPsJ06-aOo6Vz7EH_uiwAy1sRZd55jw@mail.gmail.com>
 <CAEv0nmva4j2cY9EXW9R+qvaBhB_0h9BZEQfbupNENUEqCnhQ0A@mail.gmail.com>
 <DBE604BC-2340-4C70-99B8-847281E3E1E1@cgl.ucsf.edu>
 <01041B15-48B1-4D13-A7C8-57ED82D871FB@cgl.ucsf.edu>
Message-ID: <CAEv0nmuiPmmEk+KC-_xJU9qYLM+d4aipbAexVK_ZoXtfApRswA@mail.gmail.com>

Hi Elaine:
chimerax furnished me, from the mmCIF file, a clean, complete pdb, a task
that all software that I tried could not do correctly (i.e., not all
proteins were extracted from the mmCIF file).

The pdb could not be opened with chimera (for the reasons you said, I
suppose), but opened with either Jmol or vmd.
With the latter, I cut a sphere of 30A around the "small molecule" of my
interest and with this sphere.pdb I went back to chimera
to visualize (all OK).

The longest part was installing chimerax on Debian amd64, but finally it
succeeded by, step by step, installing what was lacking in the system, and
changing to a desktop because the vintage VAIO has a too old graphic card
not accepting OpenGL graphics 3.3.

Thanks a lot
francesco

On Sun, Apr 11, 2021 at 1:44 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Actually, let me revise that answer: I realized that if there are too many
> chains for the PDB to put them into one PDB file, there may also be too
> many chains for combine to make them into one model in Chimera (it will
> also run out of valid chain IDs).  That is likely the problem, for which I
> don't have a solution.
>
> Elaine
>
> > On Apr 10, 2021, at 4:31 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Francesco,
> > It's not possible to identify the problem without the specific data.  If
> this is a PDB entry, what is the ID so we can try opening the mmCIF?
> >
> > Or, if this is not in the public database, please use Help... Report a
> Bug and attach a session that has all the bundle.pdb loaded into Chimera,
> and then in the description say how you combined them and what the problem
> is with the combined result.
> >
> > Before you do that, make sure that you are displaying everything in the
> combined result.  Maybe the parts that seem to be missing were just hidden.
> >
> > I should mention that ChimeraX is much better with mmCIF and very large
> complexes than Chimera, but maybe you are planning to use analysis features
> that are only in Chimera (not yet in ChimeraX).
> > Best,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> >> On Apr 10, 2021, at 10:37 AM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
> >>
> >> Of course I tried to open the corresponding mmCIF, but CHIMERA
> candidate 1.15 build 42258 linux64 answered that the cif file [line 3]
> appears in tag name entry.id and it was not opened
> >>
> >> ---------- Forwarded message ---------
> >> From: Francesco Pietra <chiendarret at gmail.com>
> >> Date: Sat, Apr 10, 2021 at 6:45 PM
> >> Subject: combine models
> >> To: chimera <chimera-users at cgl.ucsf.edu>
> >>
> >>
> >> Hi
> >> (1) I am faced by the coordinates for a nucleics/protein assembly being
> given in several bundle.pdb, while I need a sequential, continuous pdb file
> that comprises all nucleotides and proteins, not made of models
> >>
> >> (2) If I load all the bundles to chimera, I see all expected ligands
> around the small molecule.
> >>
> >> (3) With all models selected, copy/combine (adopting default first
> model as reference and allowing renaming chains) generates a new model. The
> new  model laks some proteins that should lie near the ligand, as described
> at (2).
> >>
> >> I feel that I am missing something.
> >>
> >> Thanks for advice
> >> francesco pietra
> >
> >
> > _______________________________________________
> > 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 siddhartha.pradhan1 at gilead.com  Mon Apr 12 00:56:09 2021
From: siddhartha.pradhan1 at gilead.com (Siddhartha Pradhan (Contractor))
Date: Mon, 12 Apr 2021 07:56:09 +0000
Subject: [Chimera-users] Need help- Why there is network connection
Message-ID: <BYAPR16MB2949CB2ECCD740329DB3FF85D4709@BYAPR16MB2949.namprd16.prod.outlook.com>

Hi,

Before we install any  software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made.


  1.  Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu)

*             Why the network connection is being made and what is the reason behind it?
*             Is there any sorts of data transfer is being happened from the user system?
*             Is there any settings in the application to disable the network connections?
*             If users can use the software to export/import data. Is there any cloud service associated with this?

It would be of great help if you can kindly give a clarity for the above network connection ASAP.

Regards,
Siddhartha
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From pett at cgl.ucsf.edu  Mon Apr 12 11:00:50 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 12 Apr 2021 11:00:50 -0700
Subject: [Chimera-users] Need help- Why there is network connection
In-Reply-To: <BYAPR16MB2949CB2ECCD740329DB3FF85D4709@BYAPR16MB2949.namprd16.prod.outlook.com>
References: <BYAPR16MB2949CB2ECCD740329DB3FF85D4709@BYAPR16MB2949.namprd16.prod.outlook.com>
Message-ID: <87FE3980-6DC9-4B5C-88EC-19BEF5BBD2D4@cgl.ucsf.edu>

Hi Siddhartha,
	When Chimera starts up, it may contact www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/> to determine if a newer version of Chimera is available and alert the user if there is one.  The frequency of checking (including never) is controlled by the "Update check interval" preference setting (Favorites?Preferences).
	There is no setting in Chimera to disable all outbound network connections, and doing so would significantly reduce Chimera's usefulness.  It would not be able to fetch data from publicly available databases such as the PDB and UniProt, be able to convert SMILES strings to structures, and many other things.
	There are some "cloud services" (really web services) run on CGL's own servers that some Chimera tools are built on and that involve exporting user data and importing results.  They are: comparative modeling with MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega or MUSCLE.  It is possible to install local versions of all these programs and have Chimera use the locally installed version instead of the web service.  As far as SMILES strings could be considered "user data", the strings are sent to external servers to convert into 3D structures.  There may be other less-used external services I'm forgetting (Chimera is a big program and I basing this off my memory).

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com> wrote:
> 
> Hi,
>  
> Before we install any  software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made.
>  
> Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/>)
>  
> ?             Why the network connection is being made and what is the reason behind it?
> ?             Is there any sorts of data transfer is being happened from the user system?
> ?             Is there any settings in the application to disable the network connections?
> ?             If users can use the software to export/import data. Is there any cloud service associated with this?
>  
> It would be of great help if you can kindly give a clarity for the above network connection ASAP.
>  
> Regards,
> Siddhartha
> _______________________________________________
> 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 meng at cgl.ucsf.edu  Mon Apr 12 11:16:19 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 12 Apr 2021 11:16:19 -0700
Subject: [Chimera-users] Need help- Why there is network connection
In-Reply-To: <87FE3980-6DC9-4B5C-88EC-19BEF5BBD2D4@cgl.ucsf.edu>
References: <BYAPR16MB2949CB2ECCD740329DB3FF85D4709@BYAPR16MB2949.namprd16.prod.outlook.com>
 <87FE3980-6DC9-4B5C-88EC-19BEF5BBD2D4@cgl.ucsf.edu>
Message-ID: <A1A0B25A-67AC-4AD0-B29B-141138CA4D52@cgl.ucsf.edu>

Hi Siddhartha,
This page lists the web services (and databases on the web) that may be accessed by Chimera, depending on which features you use and which data you fetch:

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

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


> On Apr 12, 2021, at 11:00 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Hi Siddhartha,
> 	When Chimera starts up, it may contact www.cgl.ucsf.edu to determine if a newer version of Chimera is available and alert the user if there is one.  The frequency of checking (including never) is controlled by the "Update check interval" preference setting (Favorites?Preferences).
> 	There is no setting in Chimera to disable all outbound network connections, and doing so would significantly reduce Chimera's usefulness.  It would not be able to fetch data from publicly available databases such as the PDB and UniProt, be able to convert SMILES strings to structures, and many other things.
> 	There are some "cloud services" (really web services) run on CGL's own servers that some Chimera tools are built on and that involve exporting user data and importing results.  They are: comparative modeling with MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega or MUSCLE.  It is possible to install local versions of all these programs and have Chimera use the locally installed version instead of the web service.  As far as SMILES strings could be considered "user data", the strings are sent to external servers to convert into 3D structures.  There may be other less-used external services I'm forgetting (Chimera is a big program and I basing this off my memory).
> 
> --Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
>> On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com> wrote:
>> 
>> Hi, 
>> Before we install any  software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made.
>>  
>> 	? Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu)
>>  
>> ?             Why the network connection is being made and what is the reason behind it?
>> ?             Is there any sorts of data transfer is being happened from the user system?
>> ?             Is there any settings in the application to disable the network connections?
>> ?             If users can use the software to export/import data. Is there any cloud service associated with this?
>>  
>> It would be of great help if you can kindly give a clarity for the above network connection ASAP.
>>  
>> Regards,
>> Siddhartha



From siddhartha.pradhan1 at gilead.com  Mon Apr 12 23:44:19 2021
From: siddhartha.pradhan1 at gilead.com (Siddhartha Pradhan (Contractor))
Date: Tue, 13 Apr 2021 06:44:19 +0000
Subject: [Chimera-users] [EXTERNAL] Re: Need help- Why there is network
 connection
In-Reply-To: <A1A0B25A-67AC-4AD0-B29B-141138CA4D52@cgl.ucsf.edu>
References: <BYAPR16MB2949CB2ECCD740329DB3FF85D4709@BYAPR16MB2949.namprd16.prod.outlook.com>
 <87FE3980-6DC9-4B5C-88EC-19BEF5BBD2D4@cgl.ucsf.edu>
 <A1A0B25A-67AC-4AD0-B29B-141138CA4D52@cgl.ucsf.edu>
Message-ID: <BYAPR16MB294912756C19855CF2C84AB4D44F9@BYAPR16MB2949.namprd16.prod.outlook.com>

Hi Elaine,

Good day!!
Thanks much for sharing the details.
If we need more information, we shall connect you.

Thanks much for your help and support in advance.

Regards,
Siddhartha

-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Monday, April 12, 2021 11:46 PM
To: Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [Chimera-users] Need help- Why there is network connection

Hi Siddhartha,
This page lists the web services (and databases on the web) that may be accessed by Chimera, depending on which features you use and which data you fetch:

<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/webservices.html__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloKAxwyMw$ >

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


> On Apr 12, 2021, at 11:00 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Hi Siddhartha,
> 	When Chimera starts up, it may contact https://urldefense.com/v3/__http://www.cgl.ucsf.edu__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloM5McTW0$  to determine if a newer version of Chimera is available and alert the user if there is one.  The frequency of checking (including never) is controlled by the "Update check interval" preference setting (Favorites?Preferences).
> 	There is no setting in Chimera to disable all outbound network connections, and doing so would significantly reduce Chimera's usefulness.  It would not be able to fetch data from publicly available databases such as the PDB and UniProt, be able to convert SMILES strings to structures, and many other things.
> 	There are some "cloud services" (really web services) run on CGL's own servers that some Chimera tools are built on and that involve exporting user data and importing results.  They are: comparative modeling with MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega or MUSCLE.  It is possible to install local versions of all these programs and have Chimera use the locally installed version instead of the web service.  As far as SMILES strings could be considered "user data", the strings are sent to external servers to convert into 3D structures.  There may be other less-used external services I'm forgetting (Chimera is a big program and I basing this off my memory).
> 
> --Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
>> On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com> wrote:
>> 
>> Hi, 
>> Before we install any  software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made.
>>  
>> 	? Connection to https://urldefense.com/v3/__http://169.230.27.29__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloHTjBBII$  on tcp/80 (https://urldefense.com/v3/__http://www.cgl.ucsf.edu__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloM5McTW0$ )
>>  
>> ?             Why the network connection is being made and what is the reason behind it?
>> ?             Is there any sorts of data transfer is being happened from the user system?
>> ?             Is there any settings in the application to disable the network connections?
>> ?             If users can use the software to export/import data. Is there any cloud service associated with this?
>>  
>> It would be of great help if you can kindly give a clarity for the above network connection ASAP.
>>  
>> Regards,
>> Siddhartha



From siddhartha.pradhan1 at gilead.com  Mon Apr 12 23:46:22 2021
From: siddhartha.pradhan1 at gilead.com (Siddhartha Pradhan (Contractor))
Date: Tue, 13 Apr 2021 06:46:22 +0000
Subject: [Chimera-users] [EXTERNAL] Re: Need help- Why there is network
 connection
In-Reply-To: <87FE3980-6DC9-4B5C-88EC-19BEF5BBD2D4@cgl.ucsf.edu>
References: <BYAPR16MB2949CB2ECCD740329DB3FF85D4709@BYAPR16MB2949.namprd16.prod.outlook.com>
 <87FE3980-6DC9-4B5C-88EC-19BEF5BBD2D4@cgl.ucsf.edu>
Message-ID: <BYAPR16MB2949EC1D66EB9FA5AE9049D1D44F9@BYAPR16MB2949.namprd16.prod.outlook.com>

Hi Eric,

Good day!!
Thanks much for sharing the details.
If we need more information we shall connect you.

Thanks you in advance for your help and support.

Regards,
Siddhartha

From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Monday, April 12, 2021 11:31 PM
To: Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com>
Cc: chimera-users at cgl.ucsf.edu
Subject: [EXTERNAL] Re: [Chimera-users] Need help- Why there is network connection

Hi Siddhartha,
                When Chimera starts up, it may contact www.cgl.ucsf.edu<https://urldefense.com/v3/__http:/www.cgl.ucsf.edu__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaN_idOu24$> to determine if a newer version of Chimera is available and alert the user if there is one.  The frequency of checking (including never) is controlled by the "Update check interval" preference setting (Favorites?Preferences).
                There is no setting in Chimera to disable all outbound network connections, and doing so would significantly reduce Chimera's usefulness.  It would not be able to fetch data from publicly available databases such as the PDB and UniProt, be able to convert SMILES strings to structures, and many other things.
                There are some "cloud services" (really web services) run on CGL's own servers that some Chimera tools are built on and that involve exporting user data and importing results.  They are: comparative modeling with MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega or MUSCLE.  It is possible to install local versions of all these programs and have Chimera use the locally installed version instead of the web service.  As far as SMILES strings could be considered "user data", the strings are sent to external servers to convert into 3D structures.  There may be other less-used external services I'm forgetting (Chimera is a big program and I basing this off my memory).

--Eric

                Eric Pettersen
                UCSF Computer Graphics Lab



On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com<mailto:siddhartha.pradhan1 at gilead.com>> wrote:

Hi,

Before we install any  software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made.


  1.  Connection to 169.230.27.29<https://urldefense.com/v3/__http:/169.230.27.29__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaNSBeZYQY$> on tcp/80 (www.cgl.ucsf.edu<https://urldefense.com/v3/__http:/www.cgl.ucsf.edu/__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaNhFT045w$>)

?             Why the network connection is being made and what is the reason behind it?
?             Is there any sorts of data transfer is being happened from the user system?
?             Is there any settings in the application to disable the network connections?
?             If users can use the software to export/import data. Is there any cloud service associated with this?

It would be of great help if you can kindly give a clarity for the above network connection ASAP.

Regards,
Siddhartha
_______________________________________________
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://urldefense.com/v3/__https:/plato.cgl.ucsf.edu/mailman/listinfo/chimera-users__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaNxBkYCHg$>

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From siddhartha.pradhan1 at gilead.com  Tue Apr 13 06:54:08 2021
From: siddhartha.pradhan1 at gilead.com (Siddhartha Pradhan (Contractor))
Date: Tue, 13 Apr 2021 13:54:08 +0000
Subject: [Chimera-users] Need help- Why there is network connection
Message-ID: <BYAPR16MB2949CB8BA2247FE754B44A21D44F9@BYAPR16MB2949.namprd16.prod.outlook.com>

Hi,

Before we install any  software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF ChimeraX v1.1", we found below external network connection is being made.


  1.  Connection to 13.107.4.52 on tcp/80 (www.msftconnecttest.com)

*             Why the network connection is being made and what is the reason behind it?
*             Is there any sorts of data transfer is being happened from the user system, if yes then what kind of data are being transferred?
*             Is there any settings in the application to disable the network connections?
*             If users can use the software to export/import data. Is there any cloud service associated with this?

It would be of great help if you can kindly give a clarity for the above network connection ASAP.

Regards,
Siddhartha

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From dylanramirez123 at gmail.com  Tue Apr 13 07:44:45 2021
From: dylanramirez123 at gmail.com (Dylan Ramir)
Date: Tue, 13 Apr 2021 10:44:45 -0400
Subject: [Chimera-users] [EXTERNAL] Re: Need help- Why there is network
	connection
In-Reply-To: <BYAPR16MB294912756C19855CF2C84AB4D44F9@BYAPR16MB2949.namprd16.prod.outlook.com>
References: <BYAPR16MB2949CB2ECCD740329DB3FF85D4709@BYAPR16MB2949.namprd16.prod.outlook.com>
 <87FE3980-6DC9-4B5C-88EC-19BEF5BBD2D4@cgl.ucsf.edu>
 <A1A0B25A-67AC-4AD0-B29B-141138CA4D52@cgl.ucsf.edu>
 <BYAPR16MB294912756C19855CF2C84AB4D44F9@BYAPR16MB2949.namprd16.prod.outlook.com>
Message-ID: <CAPO5Bu37JWrgJw8WLGxr7=xfC-Lvrt8QGg83tVRv=uDHZfeytg@mail.gmail.com>

Thank you for the explanation,
That as really insightful and helped me gain a better understanding of data
transfer, blasting, and where/how processing of certain tasks are done.
Everyone in the Chimera program is doing great work and your support is top
notch! You are all deeply appreciated.
Warmly,
Dylan Ramirez

On Tue, Apr 13, 2021, 10:35 AM Siddhartha Pradhan (Contractor) <
siddhartha.pradhan1 at gilead.com> wrote:

> Hi Elaine,
>
> Good day!!
> Thanks much for sharing the details.
> If we need more information, we shall connect you.
>
> Thanks much for your help and support in advance.
>
> Regards,
> Siddhartha
>
> -----Original Message-----
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Monday, April 12, 2021 11:46 PM
> To: Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com>
> Cc: Chimera <chimera-users at cgl.ucsf.edu>
> Subject: [EXTERNAL] Re: [Chimera-users] Need help- Why there is network
> connection
>
> Hi Siddhartha,
> This page lists the web services (and databases on the web) that may be
> accessed by Chimera, depending on which features you use and which data you
> fetch:
>
> <
> https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/webservices.html__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloKAxwyMw$
> >
>
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Apr 12, 2021, at 11:00 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> >
> > Hi Siddhartha,
> >       When Chimera starts up, it may contact
> https://urldefense.com/v3/__http://www.cgl.ucsf.edu__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloM5McTW0$
> to determine if a newer version of Chimera is available and alert the user
> if there is one.  The frequency of checking (including never) is controlled
> by the "Update check interval" preference setting (Favorites?Preferences).
> >       There is no setting in Chimera to disable all outbound network
> connections, and doing so would significantly reduce Chimera's usefulness.
> It would not be able to fetch data from publicly available databases such
> as the PDB and UniProt, be able to convert SMILES strings to structures,
> and many other things.
> >       There are some "cloud services" (really web services) run on CGL's
> own servers that some Chimera tools are built on and that involve exporting
> user data and importing results.  They are: comparative modeling with
> MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega
> or MUSCLE.  It is possible to install local versions of all these programs
> and have Chimera use the locally installed version instead of the web
> service.  As far as SMILES strings could be considered "user data", the
> strings are sent to external servers to convert into 3D structures.  There
> may be other less-used external services I'm forgetting (Chimera is a big
> program and I basing this off my memory).
> >
> > --Eric
> >
> >       Eric Pettersen
> >       UCSF Computer Graphics Lab
> >
> >
> >> On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <
> siddhartha.pradhan1 at gilead.com> wrote:
> >>
> >> Hi,
> >> Before we install any  software in our system within Gilead
> organization, we do the software security assessment. During our assessment
> for " UCSF Chimera v1.15", we found below external network connection is
> being made.
> >>
> >>      ? Connection to
> https://urldefense.com/v3/__http://169.230.27.29__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloHTjBBII$
> on tcp/80 (
> https://urldefense.com/v3/__http://www.cgl.ucsf.edu__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloM5McTW0$
> )
> >>
> >> ?             Why the network connection is being made and what is the
> reason behind it?
> >> ?             Is there any sorts of data transfer is being happened
> from the user system?
> >> ?             Is there any settings in the application to disable the
> network connections?
> >> ?             If users can use the software to export/import data. Is
> there any cloud service associated with this?
> >>
> >> It would be of great help if you can kindly give a clarity for the
> above network connection ASAP.
> >>
> >> Regards,
> >> Siddhartha
>
>
> _______________________________________________
> 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  Tue Apr 13 08:38:02 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 13 Apr 2021 08:38:02 -0700
Subject: [Chimera-users] Need help- Why there is network connection
In-Reply-To: <BYAPR16MB2949CB8BA2247FE754B44A21D44F9@BYAPR16MB2949.namprd16.prod.outlook.com>
References: <BYAPR16MB2949CB8BA2247FE754B44A21D44F9@BYAPR16MB2949.namprd16.prod.outlook.com>
Message-ID: <76010E27-BFFC-491F-ACDE-42DEBB931398@cgl.ucsf.edu>

AFAIK, Chimera does not connect to that URL.  You would have to provide details about what you were doing in Chimera when this connection occurred for me to help any further.

--Eric

> On Apr 13, 2021, at 6:54 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com> wrote:
> 
> Hi,
>  
> Before we install any  software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF ChimeraX v1.1", we found below external network connection is being made.
>  
> Connection to 13.107.4.52 on tcp/80 (www.msftconnecttest.com <http://www.msftconnecttest.com/>)
>  
> ?             Why the network connection is being made and what is the reason behind it?
> ?             Is there any sorts of data transfer is being happened from the user system, if yes then what kind of data are being transferred?
> ?             Is there any settings in the application to disable the network connections?
> ?             If users can use the software to export/import data. Is there any cloud service associated with this?
>  
> It would be of great help if you can kindly give a clarity for the above network connection ASAP.
>  
> Regards,
> Siddhartha
>  
> _______________________________________________
> 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 pett at cgl.ucsf.edu  Tue Apr 13 08:44:21 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 13 Apr 2021 08:44:21 -0700
Subject: [Chimera-users] Need help- Why there is network connection
In-Reply-To: <76010E27-BFFC-491F-ACDE-42DEBB931398@cgl.ucsf.edu>
References: <BYAPR16MB2949CB8BA2247FE754B44A21D44F9@BYAPR16MB2949.namprd16.prod.outlook.com>
 <76010E27-BFFC-491F-ACDE-42DEBB931398@cgl.ucsf.edu>
Message-ID: <C87A2BCC-260A-40E0-9E54-BB01DC081F06@cgl.ucsf.edu>

I see now that this question pertains to ChimeraX.  There is a "chimerax-users" list for questions pertaining to ChimeraX.  At any rate, the answer is the same:  AFAIK ChimeraX does not connect to that URL.  Were you simply starting ChimeraX when this connection occurred?

--Eric

> On Apr 13, 2021, at 8:38 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> AFAIK, Chimera does not connect to that URL.  You would have to provide details about what you were doing in Chimera when this connection occurred for me to help any further.
> 
> --Eric
> 
>> On Apr 13, 2021, at 6:54 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com <mailto:siddhartha.pradhan1 at gilead.com>> wrote:
>> 
>> Hi,
>>  
>> Before we install any  software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF ChimeraX v1.1", we found below external network connection is being made.
>>  
>> Connection to 13.107.4.52 on tcp/80 (www.msftconnecttest.com <http://www.msftconnecttest.com/>)
>>  
>> ?             Why the network connection is being made and what is the reason behind it?
>> ?             Is there any sorts of data transfer is being happened from the user system, if yes then what kind of data are being transferred?
>> ?             Is there any settings in the application to disable the network connections?
>> ?             If users can use the software to export/import data. Is there any cloud service associated with this?
>>  
>> It would be of great help if you can kindly give a clarity for the above network connection ASAP.
>>  
>> Regards,
>> Siddhartha
>>  
>> _______________________________________________
>> 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>
> _______________________________________________
> 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 siddhartha.pradhan1 at gilead.com  Tue Apr 13 23:22:13 2021
From: siddhartha.pradhan1 at gilead.com (Siddhartha Pradhan (Contractor))
Date: Wed, 14 Apr 2021 06:22:13 +0000
Subject: [Chimera-users] [EXTERNAL] Re: Need help- Why there is network
 connection
In-Reply-To: <76010E27-BFFC-491F-ACDE-42DEBB931398@cgl.ucsf.edu>
References: <BYAPR16MB2949CB8BA2247FE754B44A21D44F9@BYAPR16MB2949.namprd16.prod.outlook.com>
 <76010E27-BFFC-491F-ACDE-42DEBB931398@cgl.ucsf.edu>
Message-ID: <BYAPR16MB2949B44AE37435252152BCC8D44E9@BYAPR16MB2949.namprd16.prod.outlook.com>

Hi Eric,

Good day!!
Thanks much for the email.

We use ?Carbon Black? tool to find the network connections of particular application.

We got this connection from ?werfault.exe? which is a child process of chimera.exe.

Please find the attached screenshot for your reference.

Hope this helps.

Let us know in case any queries.

Regards,
Siddhartha


From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Tuesday, April 13, 2021 9:08 PM
To: Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [Chimera-users] Need help- Why there is network connection

AFAIK, Chimera does not connect to that URL.  You would have to provide details about what you were doing in Chimera when this connection occurred for me to help any further.

--Eric


On Apr 13, 2021, at 6:54 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com<mailto:siddhartha.pradhan1 at gilead.com>> wrote:

Hi,

Before we install any  software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF ChimeraX v1.1", we found below external network connection is being made.


  1.  Connection to 13.107.4.52<https://urldefense.com/v3/__http:/13.107.4.52__;!!Dq7g1IpY!zXmXqV_hu8JQE3MNrgYdN4nMu05GdFqoHmwl8ebTLusxtjEk9L0OrhbfrAUDPwpwf1WF0NY$> on tcp/80 (www.msftconnecttest.com<https://urldefense.com/v3/__http:/www.msftconnecttest.com/__;!!Dq7g1IpY!zXmXqV_hu8JQE3MNrgYdN4nMu05GdFqoHmwl8ebTLusxtjEk9L0OrhbfrAUDPwpwhsZZNHo$>)

?             Why the network connection is being made and what is the reason behind it?
?             Is there any sorts of data transfer is being happened from the user system, if yes then what kind of data are being transferred?
?             Is there any settings in the application to disable the network connections?
?             If users can use the software to export/import data. Is there any cloud service associated with this?

It would be of great help if you can kindly give a clarity for the above network connection ASAP.

Regards,
Siddhartha

_______________________________________________
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://urldefense.com/v3/__https:/plato.cgl.ucsf.edu/mailman/listinfo/chimera-users__;!!Dq7g1IpY!zXmXqV_hu8JQE3MNrgYdN4nMu05GdFqoHmwl8ebTLusxtjEk9L0OrhbfrAUDPwpwAARZCow$>

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From pett at cgl.ucsf.edu  Wed Apr 14 08:40:51 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 14 Apr 2021 08:40:51 -0700
Subject: [Chimera-users] [EXTERNAL] Need help- Why there is network
 connection
In-Reply-To: <BYAPR16MB2949B44AE37435252152BCC8D44E9@BYAPR16MB2949.namprd16.prod.outlook.com>
References: <BYAPR16MB2949CB8BA2247FE754B44A21D44F9@BYAPR16MB2949.namprd16.prod.outlook.com>
 <76010E27-BFFC-491F-ACDE-42DEBB931398@cgl.ucsf.edu>
 <BYAPR16MB2949B44AE37435252152BCC8D44E9@BYAPR16MB2949.namprd16.prod.outlook.com>
Message-ID: <F4ADFF63-0140-4AEB-A1E0-40E081F7955E@cgl.ucsf.edu>

Hi Siddhartha,
	Any cursory amount of googling would have revealed that werfault.exe is Windows Error Reporting and has nothing to do with Chimera per se: About WER - Win32 apps | Microsoft Docs <https://docs.microsoft.com/en-us/windows/win32/wer/about-wer>

--Eric

> On Apr 13, 2021, at 11:22 PM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com> wrote:
> 
> Hi Eric,
>  
> Good day!!
> Thanks much for the email.
>  
> We use ?Carbon Black? tool to find the network connections of particular application.
>  
> We got this connection from ?werfault.exe? which is a child process of chimera.exe.
>  
> Please find the attached screenshot for your reference.
>  
> Hope this helps.
>  
> Let us know in case any queries.
>  
> Regards,
> Siddhartha
>  
>  
> From: Eric Pettersen <pett at cgl.ucsf.edu> 
> Sent: Tuesday, April 13, 2021 9:08 PM
> To: Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com>
> Cc: Chimera <chimera-users at cgl.ucsf.edu>
> Subject: [EXTERNAL] Re: [Chimera-users] Need help- Why there is network connection
>  
> AFAIK, Chimera does not connect to that URL.  You would have to provide details about what you were doing in Chimera when this connection occurred for me to help any further.
>  
> --Eric
> 
> 
> On Apr 13, 2021, at 6:54 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com <mailto:siddhartha.pradhan1 at gilead.com>> wrote:
>  
> Hi,
>  
> Before we install any  software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF ChimeraX v1.1", we found below external network connection is being made.
>  
> Connection to 13.107.4.52 <https://urldefense.com/v3/__http:/13.107.4.52__;!!Dq7g1IpY!zXmXqV_hu8JQE3MNrgYdN4nMu05GdFqoHmwl8ebTLusxtjEk9L0OrhbfrAUDPwpwf1WF0NY$> on tcp/80 (www.msftconnecttest.com <https://urldefense.com/v3/__http:/www.msftconnecttest.com/__;!!Dq7g1IpY!zXmXqV_hu8JQE3MNrgYdN4nMu05GdFqoHmwl8ebTLusxtjEk9L0OrhbfrAUDPwpwhsZZNHo$>)
>  
> ?             Why the network connection is being made and what is the reason behind it?
> ?             Is there any sorts of data transfer is being happened from the user system, if yes then what kind of data are being transferred?
> ?             Is there any settings in the application to disable the network connections?
> ?             If users can use the software to export/import data. Is there any cloud service associated with this?
>  
> It would be of great help if you can kindly give a clarity for the above network connection ASAP.
>  
> Regards,
> Siddhartha
>  
> _______________________________________________
> 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://urldefense.com/v3/__https:/plato.cgl.ucsf.edu/mailman/listinfo/chimera-users__;!!Dq7g1IpY!zXmXqV_hu8JQE3MNrgYdN4nMu05GdFqoHmwl8ebTLusxtjEk9L0OrhbfrAUDPwpwAARZCow$>
>  
> <Werfault.PNG>

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From cynthia.page at colorado.edu  Wed Apr 14 13:15:46 2021
From: cynthia.page at colorado.edu (Cynthia Lee Page)
Date: Wed, 14 Apr 2021 20:15:46 +0000
Subject: [Chimera-users] Pixel size/box size and map display
Message-ID: <C82F1AFA-84DC-416B-9FD3-F675C2D3463A@colorado.edu>

Hi,

I have three maps to be used in Relion for reference models. All of these maps are different in pixel size and box size, however they display as the same size in Chimera, with the same size outline box. The voxel size in volume viewer is correct according to the pixel size I designated in Relion_image_handler. I assumed that these maps would be different in size since they have different pixel sizes and box sizes. 

Can someone set me straight on this?

Many thanks,

Cynthia

From meng at cgl.ucsf.edu  Wed Apr 14 13:23:24 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 14 Apr 2021 13:23:24 -0700
Subject: [Chimera-users] Pixel size/box size and map display
In-Reply-To: <C82F1AFA-84DC-416B-9FD3-F675C2D3463A@colorado.edu>
References: <C82F1AFA-84DC-416B-9FD3-F675C2D3463A@colorado.edu>
Message-ID: <AC6C7B45-F913-449A-AB0D-8D235479F84A@cgl.ucsf.edu>

Hi Cynthia,
The question is:  does Chimera know they have different pixel sizes?  

(How do you know that they have different pixel sizes.... is it set or reported in Relion?)

To check or adjust pixel size of maps in Chimera, use Volume Viewer menu "Features... Coordinates" to show map Coordinates settings in the Volume Viewer dialog.  These include Voxel size.  You can see the current values and optionally enter different ones to change them.

Volume Viewer
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

...and its Coordinates settings:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>

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

> On Apr 14, 2021, at 1:15 PM, Cynthia Lee Page <cynthia.page at colorado.edu> wrote:
> 
> Hi,
> I have three maps to be used in Relion for reference models. All of these maps are different in pixel size and box size, however they display as the same size in Chimera, with the same size outline box. The voxel size in volume viewer is correct according to the pixel size I designated in Relion_image_handler. I assumed that these maps would be different in size since they have different pixel sizes and box sizes. 
> 
> Can someone set me straight on this?
> Many thanks,
> Cynthia



From meng at cgl.ucsf.edu  Wed Apr 14 13:34:10 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 14 Apr 2021 13:34:10 -0700
Subject: [Chimera-users] Pixel size/box size and map display
In-Reply-To: <AC6C7B45-F913-449A-AB0D-8D235479F84A@cgl.ucsf.edu>
References: <C82F1AFA-84DC-416B-9FD3-F675C2D3463A@colorado.edu>
 <AC6C7B45-F913-449A-AB0D-8D235479F84A@cgl.ucsf.edu>
Message-ID: <40B0162C-A733-46DC-984D-EFFECF7FAD43@cgl.ucsf.edu>

Sorry. I failed to read everything you wrote...  including that you already checked the voxel size in Chimera.  The outline box for a map should reflect grid size (number of points in each dimension) multiplied by the voxel size (physical distance per grid point in each dimension).  If it does not, you could try using Help... Report a Bug and attaching your session with an explanation of what is not matching up.  Include your email address if you would like a response.

My only other ideas:  (1) Make sure you are really showing the outline boxes of all the different maps, not just that for a single map.  E.g. commands

volume all show
volume all showOutlineBox true

 (2) Make sure you are showing the full data, not after cropping.  E.g.

volume all region all

Thanks,
Elaine

> On Apr 14, 2021, at 1:23 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Cynthia,
> The question is:  does Chimera know they have different pixel sizes?  
> 
> (How do you know that they have different pixel sizes.... is it set or reported in Relion?)
> 
> To check or adjust pixel size of maps in Chimera, use Volume Viewer menu "Features... Coordinates" to show map Coordinates settings in the Volume Viewer dialog.  These include Voxel size.  You can see the current values and optionally enter different ones to change them.
> 
> Volume Viewer
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
> 
> ...and its Coordinates settings:
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Apr 14, 2021, at 1:15 PM, Cynthia Lee Page <cynthia.page at colorado.edu> wrote:
>> 
>> Hi,
>> I have three maps to be used in Relion for reference models. All of these maps are different in pixel size and box size, however they display as the same size in Chimera, with the same size outline box. The voxel size in volume viewer is correct according to the pixel size I designated in Relion_image_handler. I assumed that these maps would be different in size since they have different pixel sizes and box sizes. 
>> 
>> Can someone set me straight on this?
>> Many thanks,
>> Cynthia



From pett at cgl.ucsf.edu  Wed Apr 14 13:34:45 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 14 Apr 2021 13:34:45 -0700
Subject: [Chimera-users] ADP EM Chimera plugin
Message-ID: <D35BF1CB-32C7-4E6B-BB3B-90B81B5AC3C7@cgl.ucsf.edu>

Hi Vilde,
	Since ADP EM is a third-party plugin, I don't know that I know that much more than you about how it works.  Hopefully the plugin developers will get back to you.  Nonetheless, I can offer some generic advice about seeing/finding the fitted structure.  First, check the Model Panel (Favorites?Model Panel) to ensure that the structure model is shown (the "Shown" column for the structure model is checked).  Second, type the 'window' command (Favorites?Command Line) to ensure the view is large enough to show the position of the structure.  Third, click on the color well in the Volume Viewer panel (the square next to "Color") and adjust the 'A' component of the color (A = alpha, or opacity) so the the contour surface is semi-transparent, in case the structure is completely within a contour.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> Hello, 
>  
> I?m trying to use the ADP EM molecular fitting tool (Chimera Plugin) to fit my PDB-models into a low resolution map. The plugin works as it should, but I?m having trouble visualizing the solutions. Once the fitting is finished (the table with all the coordinates is produced) and I chose for example solution 1, the PDB structure disappears in the Chimera Window. The EM map is still showing. If I click on the ?Back to initial?-button, the PDB structure comes back, but in the initial position, of course. I have tried to save the solutions, but they are still not showing (the solutions are selected as ?show? as a cartoon in the model panel). According to the description of the plugin developers, the solutions/fits should be visualized just by selecting one, no extra steps needed. 
> I?m doing something wrong in Chimera or is there a bug?
> I have tried with the two latest versions of Chimera for Windows (1.14 and 1.15), with the same result.
>  
> Any help or advice would be much appreciated! I have also tried to contact the developers of the plugin, but no response so far.
>  
> Best regards, 
> Vilde Leipart
> PhD-student,
>  
> Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences
> H?gskoleveien 12, 1430 ?s, Norway
>  
> Honey Bee Research Lab, Arizona Sate University
> 427 East Tyler Mall, Tempe, AZ 85287
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From cynthia.page at colorado.edu  Wed Apr 14 14:03:42 2021
From: cynthia.page at colorado.edu (Cynthia Lee Page)
Date: Wed, 14 Apr 2021 21:03:42 +0000
Subject: [Chimera-users] Pixel size/box size and map display
In-Reply-To: <AC6C7B45-F913-449A-AB0D-8D235479F84A@cgl.ucsf.edu>
References: <C82F1AFA-84DC-416B-9FD3-F675C2D3463A@colorado.edu>
 <AC6C7B45-F913-449A-AB0D-8D235479F84A@cgl.ucsf.edu>
Message-ID: <9D1268D0-FB74-418F-89CB-731C965725DF@colorado.edu>

Thanks Elaine!

These files were all mol maps that were made originally using 15 res, so the voxel size was 5. Then resized using a script from Relion, relion_image_handler , with options --rescale_angpix and ?new_box.

This suggests my relion script did not work, however as you say the voxel size is what I would have expected if the script did the job. I believe the box outlines are fine, I "turn them on" one at a time with check box (used three different colors, white, yellow, aqua), or with your command line, and in both cases here they are right on top of each other.

Here?s a picture. I will do as you have suggested to report a potential bug, but honestly it is probably me :)

Cheers,

Cynthia

[cid:CFDC301F-1AF7-46CA-BA58-CBC8C8A6946F at colorado.edu]



On Apr 14, 2021, at 2:23 PM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Cynthia,
The question is:  does Chimera know they have different pixel sizes?

(How do you know that they have different pixel sizes.... is it set or reported in Relion?)

To check or adjust pixel size of maps in Chimera, use Volume Viewer menu "Features... Coordinates" to show map Coordinates settings in the Volume Viewer dialog.  These include Voxel size.  You can see the current values and optionally enter different ones to change them.

Volume Viewer
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

...and its Coordinates settings:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>

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

On Apr 14, 2021, at 1:15 PM, Cynthia Lee Page <cynthia.page at colorado.edu<mailto:cynthia.page at colorado.edu>> wrote:

Hi,
I have three maps to be used in Relion for reference models. All of these maps are different in pixel size and box size, however they display as the same size in Chimera, with the same size outline box. The voxel size in volume viewer is correct according to the pixel size I designated in Relion_image_handler. I assumed that these maps would be different in size since they have different pixel sizes and box sizes.

Can someone set me straight on this?
Many thanks,
Cynthia


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From goddard at sonic.net  Wed Apr 14 14:31:27 2021
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 14 Apr 2021 14:31:27 -0700
Subject: [Chimera-users] Pixel size/box size and map display
In-Reply-To: <9D1268D0-FB74-418F-89CB-731C965725DF@colorado.edu>
References: <C82F1AFA-84DC-416B-9FD3-F675C2D3463A@colorado.edu>
 <AC6C7B45-F913-449A-AB0D-8D235479F84A@cgl.ucsf.edu>
 <9D1268D0-FB74-418F-89CB-731C965725DF@colorado.edu>
Message-ID: <5B26DB44-C48C-44C0-8C28-204C1C82EA9F@sonic.net>

Hi Cynthia,

  This does not seem like a bug.  I would expect the box size to stay the same when Relion changes the pixel size.  For instance if you change the pixel size from 2 Angstroms to 1 Angstrom it probably doubles the number of grid points so the overall size of the map remains the same.

	Tom


> On Apr 14, 2021, at 2:03 PM, Cynthia Lee Page <cynthia.page at colorado.edu> wrote:
> 
> Thanks Elaine!  
> 
> These files were all mol maps that were made originally using 15 res, so the voxel size was 5. Then resized using a script from Relion, relion_image_handler , with options --rescale_angpix and ?new_box. 
> 
> This suggests my relion script did not work, however as you say the voxel size is what I would have expected if the script did the job. I believe the box outlines are fine, I "turn them on" one at a time with check box (used three different colors, white, yellow, aqua), or with your command line, and in both cases here they are right on top of each other.
> 
> Here?s a picture. I will do as you have suggested to report a potential bug, but honestly it is probably me :)
> 
> Cheers,
> 
> Cynthia
> 
> 
> 
> 
> 
>> On Apr 14, 2021, at 2:23 PM, Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
>> 
>> Hi Cynthia,
>> The question is:  does Chimera know they have different pixel sizes?  
>> 
>> (How do you know that they have different pixel sizes.... is it set or reported in Relion?)
>> 
>> To check or adjust pixel size of maps in Chimera, use Volume Viewer menu "Features... Coordinates" to show map Coordinates settings in the Volume Viewer dialog.  These include Voxel size.  You can see the current values and optionally enter different ones to change them.
>> 
>> Volume Viewer
>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>>
>> 
>> ...and its Coordinates settings:
>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Apr 14, 2021, at 1:15 PM, Cynthia Lee Page <cynthia.page at colorado.edu <mailto:cynthia.page at colorado.edu>> wrote:
>>> 
>>> Hi,
>>> I have three maps to be used in Relion for reference models. All of these maps are different in pixel size and box size, however they display as the same size in Chimera, with the same size outline box. The voxel size in volume viewer is correct according to the pixel size I designated in Relion_image_handler. I assumed that these maps would be different in size since they have different pixel sizes and box sizes. 
>>> 
>>> Can someone set me straight on this?
>>> Many thanks,
>>> Cynthia
>> 
> 
> _______________________________________________
> 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 vilde.leipart at nmbu.no  Thu Apr 15 00:36:58 2021
From: vilde.leipart at nmbu.no (Vilde Leipart)
Date: Thu, 15 Apr 2021 07:36:58 +0000
Subject: [Chimera-users] ADP EM Chimera plugin
In-Reply-To: <D35BF1CB-32C7-4E6B-BB3B-90B81B5AC3C7@cgl.ucsf.edu>
References: <D35BF1CB-32C7-4E6B-BB3B-90B81B5AC3C7@cgl.ucsf.edu>
Message-ID: <OL1P279MB004915B7D6D5A171093770B6EA4D9@OL1P279MB0049.NORP279.PROD.OUTLOOK.COM>

Hi Eric,
Thank you for the quick response, and it was vey helpful, as the ?window? command helped me find the structure (I?m not that familiar with Chimera, so thank for teaching me this command). I was thinking the solution might have been placed somewhere far away from the map, but it turns out it was sent out to space, as the EM map and structure can been seen as two small dots after using the command. Anyway, that?s another problem.
Thank you!!
Vilde
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: onsdag 14. april 2021 22:35
To: Vilde Leipart <vilde.leipart at nmbu.no>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: ADP EM Chimera plugin

Hi Vilde,
              Since ADP EM is a third-party plugin, I don't know that I know that much more than you about how it works.  Hopefully the plugin developers will get back to you.  Nonetheless, I can offer some generic advice about seeing/finding the fitted structure.  First, check the Model Panel (Favorites?Model Panel) to ensure that the structure model is shown (the "Shown" column for the structure model is checked).  Second, type the 'window' command (Favorites?Command Line) to ensure the view is large enough to show the position of the structure.  Third, click on the color well in the Volume Viewer panel (the square next to "Color") and adjust the 'A' component of the color (A = alpha, or opacity) so the the contour surface is semi-transparent, in case the structure is completely within a contour.

--Eric

              Eric Pettersen
              UCSF Computer Graphics Lab

Hello,

I?m trying to use the ADP EM molecular fitting tool (Chimera Plugin) to fit my PDB-models into a low resolution map. The plugin works as it should, but I?m having trouble visualizing the solutions. Once the fitting is finished (the table with all the coordinates is produced) and I chose for example solution 1, the PDB structure disappears in the Chimera Window. The EM map is still showing. If I click on the ?Back to initial?-button, the PDB structure comes back, but in the initial position, of course. I have tried to save the solutions, but they are still not showing (the solutions are selected as ?show? as a cartoon in the model panel). According to the description of the plugin developers, the solutions/fits should be visualized just by selecting one, no extra steps needed.
I?m doing something wrong in Chimera or is there a bug?
I have tried with the two latest versions of Chimera for Windows (1.14 and 1.15), with the same result.

Any help or advice would be much appreciated! I have also tried to contact the developers of the plugin, but no response so far.

Best regards,
Vilde Leipart
PhD-student,

Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences
H?gskoleveien 12, 1430 ?s, Norway

Honey Bee Research Lab, Arizona Sate University
427 East Tyler Mall, Tempe, AZ 85287
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From pett at cgl.ucsf.edu  Thu Apr 15 09:08:54 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 15 Apr 2021 09:08:54 -0700
Subject: [Chimera-users] ADP EM Chimera plugin
In-Reply-To: <OL1P279MB004915B7D6D5A171093770B6EA4D9@OL1P279MB0049.NORP279.PROD.OUTLOOK.COM>
References: <D35BF1CB-32C7-4E6B-BB3B-90B81B5AC3C7@cgl.ucsf.edu>
 <OL1P279MB004915B7D6D5A171093770B6EA4D9@OL1P279MB0049.NORP279.PROD.OUTLOOK.COM>
Message-ID: <FCBBD74B-1073-4276-BE41-F27CDFCD3A9E@cgl.ucsf.edu>

Happy to help!

--Eric

> On Apr 15, 2021, at 12:36 AM, Vilde Leipart <vilde.leipart at nmbu.no> wrote:
> 
> Hi Eric, 
> Thank you for the quick response, and it was vey helpful, as the ?window? command helped me find the structure (I?m not that familiar with Chimera, so thank for teaching me this command). I was thinking the solution might have been placed somewhere far away from the map, but it turns out it was sent out to space, as the EM map and structure can been seen as two small dots after using the command. Anyway, that?s another problem.
> Thank you!!
> Vilde
> From: Eric Pettersen <pett at cgl.ucsf.edu> 
> Sent: onsdag 14. april 2021 22:35
> To: Vilde Leipart <vilde.leipart at nmbu.no>
> Cc: Chimera <chimera-users at cgl.ucsf.edu>
> Subject: ADP EM Chimera plugin
>  
> Hi Vilde,
>               Since ADP EM is a third-party plugin, I don't know that I know that much more than you about how it works.  Hopefully the plugin developers will get back to you.  Nonetheless, I can offer some generic advice about seeing/finding the fitted structure.  First, check the Model Panel (Favorites?Model Panel) to ensure that the structure model is shown (the "Shown" column for the structure model is checked).  Second, type the 'window' command (Favorites?Command Line) to ensure the view is large enough to show the position of the structure.  Third, click on the color well in the Volume Viewer panel (the square next to "Color") and adjust the 'A' component of the color (A = alpha, or opacity) so the the contour surface is semi-transparent, in case the structure is completely within a contour.
>  
> --Eric
>  
>               Eric Pettersen
>               UCSF Computer Graphics Lab
>  
> Hello, 
>  
> I?m trying to use the ADP EM molecular fitting tool (Chimera Plugin) to fit my PDB-models into a low resolution map. The plugin works as it should, but I?m having trouble visualizing the solutions. Once the fitting is finished (the table with all the coordinates is produced) and I chose for example solution 1, the PDB structure disappears in the Chimera Window. The EM map is still showing. If I click on the ?Back to initial?-button, the PDB structure comes back, but in the initial position, of course. I have tried to save the solutions, but they are still not showing (the solutions are selected as ?show? as a cartoon in the model panel). According to the description of the plugin developers, the solutions/fits should be visualized just by selecting one, no extra steps needed. 
> I?m doing something wrong in Chimera or is there a bug?
> I have tried with the two latest versions of Chimera for Windows (1.14 and 1.15), with the same result.
>  
> Any help or advice would be much appreciated! I have also tried to contact the developers of the plugin, but no response so far.
>  
> Best regards, 
> Vilde Leipart
> PhD-student,
>  
> Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences
> H?gskoleveien 12, 1430 ?s, Norway
>  
> Honey Bee Research Lab, Arizona Sate University
> 427 East Tyler Mall, Tempe, AZ 85287
> _______________________________________________
> 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 henry.w.shook at gmail.com  Sun Apr 18 08:36:19 2021
From: henry.w.shook at gmail.com (Henry Shook)
Date: Sun, 18 Apr 2021 11:36:19 -0400
Subject: [Chimera-users] Chimera Errors
Message-ID: <CAN=xPG6H-MVGZODF+YXvp7KsU=FsjoDSsPp5q+0y+dBj-wE-hQ@mail.gmail.com>

Chimera Team,

I have been using Chimera to test several Sialic Acid isomers on the
Sars-CoV-2 spike protein over the past couple of months and a couple of
days ago, I have been getting this error telling me that there was an
"application stderr" and "application stdout". Previously to a couple of
days ago, anytime I tried to run it during the day, this message would show
up, however, I was able to run the docks from 9-12 pm at night without any
problem, so I just worked on the docking during that time. Now, no matter
what time I run the docks at, this message shows up. I have not changed any
procedures from when I started until now. Is there a way I can fix this
problem? I attached a screen recording of my procedures and how I arrived
at the problem. Here is a link
<https://drive.google.com/file/d/1QkQakaG7QnY_pjJsbdlK0HWNEuupnJqJ/view?usp=sharing>
if the video does not load.

Thanks!

Henry Shook
 Screen Recording 2021-04-18 at 11.19.06 AM.mov
<https://drive.google.com/file/d/1QkQakaG7QnY_pjJsbdlK0HWNEuupnJqJ/view?usp=drive_web>
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From meng at cgl.ucsf.edu  Sun Apr 18 09:28:30 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sun, 18 Apr 2021 09:28:30 -0700
Subject: [Chimera-users] Chimera Errors
In-Reply-To: <CAN=xPG6H-MVGZODF+YXvp7KsU=FsjoDSsPp5q+0y+dBj-wE-hQ@mail.gmail.com>
References: <CAN=xPG6H-MVGZODF+YXvp7KsU=FsjoDSsPp5q+0y+dBj-wE-hQ@mail.gmail.com>
Message-ID: <37CEC2FA-206A-4EB3-B443-E5F13805A963@cgl.ucsf.edu>

Hi Henry,
I see you are running a local copy of Autodock Vina and that some error appears in the Reply Log after you try to run it... you could just say that, instead of sending a 5-minute movie, since it's not possible to read the Reply Log in the movie (too blurry). That's still really not enough information, so instead of sending e-mail here, right after you get the error,  please use menu: Help... Report a Bug which would automaticaly send us the Reply Log contents and other information.  In the bug report, please include a short description of what you did... it would also be useful to attach a session file to the report, and your email address if you want updates on what we find.

However, see also the warning in the help page for this tool in Chimera:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

"this tool only allows docking a single ligand with very limited sampling. For a more intensive sampling of space, as needed for most research applications, or access to other options such as ligand database search, we recommend running the locally installed copy of AutoDock Vina directly (not using Chimera). Chimera can still be used to view the output."

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

> On Apr 18, 2021, at 8:36 AM, Henry Shook <henry.w.shook at gmail.com> wrote:
> 
> Chimera Team, 
> 
> I have been using Chimera to test several Sialic Acid isomers on the Sars-CoV-2 spike protein over the past couple of months and a couple of days ago, I have been getting this error telling me that there was an "application stderr" and "application stdout". Previously to a couple of days ago, anytime I tried to run it during the day, this message would show up, however, I was able to run the docks from 9-12 pm at night without any problem, so I just worked on the docking during that time. Now, no matter what time I run the docks at, this message shows up. I have not changed any procedures from when I started until now. Is there a way I can fix this problem? I attached a screen recording of my procedures and how I arrived at the problem. Here is a link if the video does not load.  
> 
> Thanks!
> 
> Henry Shook



From chiendarret at gmail.com  Wed Apr 21 07:17:42 2021
From: chiendarret at gmail.com (Francesco Pietra)
Date: Wed, 21 Apr 2021 16:17:42 +0200
Subject: [Chimera-users] Four letter residue names
Message-ID: <CAEv0nmuaaW4E2Bk8=OtGHa3vgCpkr6+OaH9qsa6w7q0CoDBkNg@mail.gmail.com>

Hi all
A pdb file deriving from a mmCIF file (with chimerax) and comprising both
nucleotides and proteins, shows the protein residue names with four
characters (i.e., using also column 21), such as ALAM in one subunit, or
GLNm in another subunit.

I read on passing somewhere (and I am unable to trace that back) that
chimera accepts such four character names but was unable to find a
description from chimera help. I also got lost in deciphering the
intricacies of mmCIF files.  What is the scope of the column 21 character?
Could that simply be ignored, or deleted, for use with the CHARMM FF?

Thanks for advice

francesco pietra
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From meng at cgl.ucsf.edu  Wed Apr 21 08:22:00 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 21 Apr 2021 08:22:00 -0700
Subject: [Chimera-users] Four letter residue names
In-Reply-To: <CAEv0nmuaaW4E2Bk8=OtGHa3vgCpkr6+OaH9qsa6w7q0CoDBkNg@mail.gmail.com>
References: <CAEv0nmuaaW4E2Bk8=OtGHa3vgCpkr6+OaH9qsa6w7q0CoDBkNg@mail.gmail.com>
Message-ID: <73CE94B2-B8FD-45AE-A176-908E8D81012E@cgl.ucsf.edu>

Hi Francesco,
Short answer since I'm theoretically not at work today, but yes Chimera reads and allows 4-character residue names, even though the PDB standard format description is only for 3-character names.  

This is mentioned in the "intro to PDB format" in the Chimera User Guide:

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note5>  

Not much else to say about it though.  I don't know what you mean by the "scope" or how to modify the file for CHARMM or other programs.

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


> On Apr 21, 2021, at 7:17 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 
> Hi all
> A pdb file deriving from a mmCIF file (with chimerax) and comprising both nucleotides and proteins, shows the protein residue names with four characters (i.e., using also column 21), such as ALAM in one subunit, or GLNm in another subunit.
> 
> I read on passing somewhere (and I am unable to trace that back) that chimera accepts such four character names but was unable to find a description from chimera help. I also got lost in deciphering the intricacies of mmCIF files.  What is the scope of the column 21 character? Could that simply be ignored, or deleted, for use with the CHARMM FF?
> 
> Thanks for advice
> 
> francesco pietra



From ichrakbenamri at gmail.com  Thu Apr 22 17:04:00 2021
From: ichrakbenamri at gmail.com (Ichrak Benamri)
Date: Fri, 23 Apr 2021 00:04:00 +0000
Subject: [Chimera-users] problem (exit code -1073741819)
Message-ID: <CAGTH2ge7fC25XWFVMRP5Om8ZvhW9h=aS9GwOMN7u13uUkSeLqw@mail.gmail.com>

Hello,
I hope you are doing well.
I have problem launching the chimera tool (error code: -1073741819), I
don't know exactly where the problem is.
Please, can you help me?
Thank you

[image: image.png]


-- 

*Ichrak BENAMRI*

PhD Student in Bioinfomatics

*+212648548583*

ichrakbenamri at gmail.com

Systems and Data Engineering Team, National School of Applied Sciences,

Abdelmalek Essa?di University, BP1818 Route Ziaten, 90 000, Tangier, Morocco

Chlamydiae and Mycoplasma Laboratory, Institut Pasteur du Maroc,
Casablanca, Morocco
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From gregc at cgl.ucsf.edu  Fri Apr 23 11:25:26 2021
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 23 Apr 2021 11:25:26 -0700
Subject: [Chimera-users] problem (exit code -1073741819)
In-Reply-To: <CAGTH2ge7fC25XWFVMRP5Om8ZvhW9h=aS9GwOMN7u13uUkSeLqw@mail.gmail.com>
References: <CAGTH2ge7fC25XWFVMRP5Om8ZvhW9h=aS9GwOMN7u13uUkSeLqw@mail.gmail.com>
Message-ID: <388c12a2-babd-c803-561f-9243d32b1ae7@cgl.ucsf.edu>

Generally weird start up errors are usually due to bugs with the 
graphics driver.? So the recommendation is to upgrade your graphics 
driver.? That said, sometimes the newer graphics drivers introduce bugs, 
and you need to revert to an earlier version.

In your case, please prepare the following information and sent it to 
chimera-bugs at cgl.ucsf.edu:

 ??? (1) Run "Chimera - Debug" from the start menu.? That will pop up a 
window that shows more about the startup process.? Ideally, you will 
copy and paste the text from that window for the bug report.? A 
screenshot of the window is okay, but not preferred.

 ??? (2) Run the dxdiag program.? Click on "Save All Information" to 
save the information into a file, and attach that file to the bug report.

With that bug report, we will be able to give you specific 
recommendations on how to fix your problem.

 ??? HTH,

 ??? Greg

On 4/22/2021 5:04 PM, Ichrak Benamri wrote:
> Hello,
> I hope you are doing well.
> I have problem?launching the chimera tool (error code: -1073741819), I 
> don't know exactly where the problem is.
> Please, can you help me?
> Thank you
>
> image.png
>
>
> -- 
>
> *Ichrak BENAMRI*
>
> PhD Student in Bioinfomatics*
> *
>
> /+212648548583/
>
> ichrakbenamri at gmail.com <mailto:ichrakbenamri at gmail.com>
>
> Systems and Data Engineering Team, National School of Applied Sciences,
>
> Abdelmalek Essa?di University, BP1818 Route Ziaten, 90 000, Tangier, 
> Morocco
>
> Chlamydiae and Mycoplasma Laboratory, Institut Pasteur du Maroc, 
> Casablanca, Morocco
>
>
>
> _______________________________________________
> 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 s.molnar at sbcglobal.net  Sat Apr 24 05:42:52 2021
From: s.molnar at sbcglobal.net (Stephen P. Molnar)
Date: Sat, 24 Apr 2021 08:42:52 -0400
Subject: [Chimera-users] Problem Saava9ng merged PDB Files
References: <6084124C.3060707.ref@sbcglobal.net>
Message-ID: <6084124C.3060707@sbcglobal.net>

I am using Chimera v-1.14 (build 42094) on my Debian Buster Linux 
computer and have run into a problem saving a pdb file containing two 
pdb files.

The files are attached to this email.This is a portion of the combined 
flies:



The structure of the D21.pdb file isthe ball image.

I followed the instructions in the Building Structures, Modifying and 
Saving Data in the Help pages.

However, when I open DD21Mod1 in LigPlot to identify the docked ligand I 
get:



Clearly, this is not the ligand docked int the active site. I have used 
LigPlot on a number of pdb files with good results and am forced to 
conclude that there is a problem with D21Mod1.pdb.

I would appreciate help in solving this problem.

Thanks in advance.

-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1

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From meng at cgl.ucsf.edu  Sat Apr 24 15:41:14 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 24 Apr 2021 15:41:14 -0700
Subject: [Chimera-users] Problem Saava9ng merged PDB Files
In-Reply-To: <6084124C.3060707@sbcglobal.net>
References: <6084124C.3060707.ref@sbcglobal.net>
 <6084124C.3060707@sbcglobal.net>
Message-ID: <65154B98-0607-4DDA-B13A-F0C0D159ED7C@cgl.ucsf.edu>

Hi Stephen,
Probably you just need to combine the ligand and receptor into a single model before saving to a PDB file, instead of saving the two models to a single multimodel PDB file.  This is usually the problem when you want to use some other program afterward for ligand-receptor analysis, and I see that your file has two models in it instead of a single model with both receptor and ligand.

For example, see instructions in this recent post on how to combine the models before saving:
<https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-March/017672.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 Apr 24, 2021, at 5:42 AM, Stephen P. Molnar <s.molnar at sbcglobal.net> wrote:
> 
> I am using Chimera v-1.14 (build 42094) on my Debian Buster Linux computer and have run into a problem saving a pdb file containing two pdb files.
> 
> The files are attached to this email.This is a portion of the combined flies:
> 
> <Screenshot_2021-04-24_08-29-16.png>
> 
> The structure of the D21.pdb file isthe ball image.
> 
> I followed the instructions in the Building Structures, Modifying and Saving Data in the Help pages.
> 
> However, when I open DD21Mod1 in LigPlot to identify the docked ligand I get:
> 
> <Screenshot_2021-04-24_08-30-37.png>
> 
> Clearly, this is not the ligand docked int the active site. I have used LigPlot on a number of pdb files with good results and am forced to conclude that there is a problem with D21Mod1.pdb.
> 
> I would appreciate help in solving this problem.
> 
> Thanks in advance.
> -- 
> Stephen P. Molnar, Ph.D.
> 
> www.molecular-modeling.net
> 
> 614.312.7528 (c)
> Skype:  smolnar1
> 
> 
> <D21.pdb><D21Mod1.pdb><Mod1.pdb>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From susanne.kandolf at imp.ac.at  Tue Apr 27 22:55:39 2021
From: susanne.kandolf at imp.ac.at (Kandolf,Susanne)
Date: Wed, 28 Apr 2021 05:55:39 +0000
Subject: [Chimera-users] 2D panorama view of a 3D model
Message-ID: <176954E9-3E83-4469-BA98-035EFDF3284C@imp.ac.at>

Hello,

I was wondering if it is possible to display a 3D model as a 2D panorama view?
I would like to show all sides of a holoenzyme and instead of taking several pictures of each view,
I thought it would be more convenient to have one picture displayed as panorama showing all sides at the same time.

Thank you for your help,

Susanne

??????????????????????????..
Susanne Kandolf
Research Technician at Haselbach Lab
Mobile: +43 699 17250493
susanne.kandolf at imp.ac.at<mailto:susanne.kandolf at imp.ac.at>
www.imp.ac.at<http://www.imp.ac.at>

IMP
Research Institute of Molecular Pathology
Campus-Vienna-BioCenter 1
1030 Vienna, Austria

Part of Vienna BioCenter
www.viennabiocenter.org<http://www.viennabiocenter.org>

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From meng at cgl.ucsf.edu  Wed Apr 28 07:50:35 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 28 Apr 2021 07:50:35 -0700
Subject: [Chimera-users] 2D panorama view of a 3D model
In-Reply-To: <176954E9-3E83-4469-BA98-035EFDF3284C@imp.ac.at>
References: <176954E9-3E83-4469-BA98-035EFDF3284C@imp.ac.at>
Message-ID: <29081E8A-7733-4A19-8CAB-463C1C81E3ED@cgl.ucsf.edu>

Hi Susanne,
I'm not too familiar with panorama views.  There is a "horizontal field of view" angle parameter in the Camera tool (menu: Tools... Viewing Controls... Camera) but it only allows going up to 179 degrees.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#camera>

If you use ChimeraX instead of Chimera, there are some 360-degree modes, e.g. ChimeraX command "camera 360".  ChimeraX also allows setting the field-of-view parameter mentioned above.

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

As I understand it, however, these 360-degree views are mainly for recording movies to play back in virtual reality headsets.  An example of recording a 360-degree movie in ChimeraX is given here:
<https://rbvi.ucsf.edu/chimerax/docs/user/vrphone.html>

So, maybe neither of these things (360-degree view or setting wider field-of-view angle) is the same as the panorama view you had in mind.  If none of the settings in the Camera tool in Chimera give what you want, then as far as I know it is not possible to make a 2D panorama view directly in Chimera.
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 27, 2021, at 10:55 PM, Kandolf,Susanne <susanne.kandolf at imp.ac.at> wrote:
> 
> Hello, 
>  
> I was wondering if it is possible to display a 3D model as a 2D panorama view?
> I would like to show all sides of a holoenzyme and instead of taking several pictures of each view,
> I thought it would be more convenient to have one picture displayed as panorama showing all sides at the same time.
>  
> Thank you for your help, 
> Susanne



From s.molnar at sbcglobal.net  Fri Apr 30 05:22:06 2021
From: s.molnar at sbcglobal.net (Stephen P. Molnar)
Date: Fri, 30 Apr 2021 08:22:06 -0400
Subject: [Chimera-users] Problem Saava9ng merged PDB Files
In-Reply-To: <65154B98-0607-4DDA-B13A-F0C0D159ED7C@cgl.ucsf.edu>
References: <6084124C.3060707.ref@sbcglobal.net>
 <6084124C.3060707@sbcglobal.net>
 <65154B98-0607-4DDA-B13A-F0C0D159ED7C@cgl.ucsf.edu>
Message-ID: <608BF66E.8070508@sbcglobal.net>

Elaine

Ran into a problem.

I need to combine a Ligand and a Protein n in order to use LigPlot+ to 
characterize the bound ligand in the active site of the protein. Both 
pdb files are attached.

Following the steps in the URL you referenced:

Open Chimera
Open Ligand
Open Protein
Open favorites --> Model Pane
     at this point the only active choice is 'activate all'
Click on Ligand
     copy/combine is now active
Right click Protein
Copy/Combine
     2 combination is now aticve
Save 2.pdb

Edit 2.pdb to conform with LigPlus+ pdb file format (2edited.pdb)

Open 2.pdb in  LigPlot+

Oops - and other not printable comments. Not exactly the expected 
result.  Just what is the problem?

HETATM   25  H  UNLD     1     -25.457  -6.079 183.671  0.00 
0.00           H
MDL
ATOM      1  N   SER A  13     -59.051  40.339 226.398  0.00 0.00      
AS1  N
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Misaligned fields! (Unfortunately, I didn't know this was the problem., 
but the author of LigPlot+ did)

What did I do/fail to do in Chimera?

Thanks in advance.

         Steve



On 04/24/2021 06:41 PM, Elaine Meng wrote:
> Hi Stephen,
> Probably you just need to combine the ligand and receptor into a single model before saving to a PDB file, instead of saving the two models to a single multimodel PDB file.  This is usually the problem when you want to use some other program afterward for ligand-receptor analysis, and I see that your file has two models in it instead of a single model with both receptor and ligand.
>
> For example, see instructions in this recent post on how to combine the models before saving:
> <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-March/017672.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 Apr 24, 2021, at 5:42 AM, Stephen P. Molnar <s.molnar at sbcglobal.net> wrote:
>>
>> I am using Chimera v-1.14 (build 42094) on my Debian Buster Linux computer and have run into a problem saving a pdb file containing two pdb files.
>>
>> The files are attached to this email.This is a portion of the combined flies:
>>
>> <Screenshot_2021-04-24_08-29-16.png>
>>
>> The structure of the D21.pdb file isthe ball image.
>>
>> I followed the instructions in the Building Structures, Modifying and Saving Data in the Help pages.
>>
>> However, when I open DD21Mod1 in LigPlot to identify the docked ligand I get:
>>
>> <Screenshot_2021-04-24_08-30-37.png>
>>
>> Clearly, this is not the ligand docked int the active site. I have used LigPlot on a number of pdb files with good results and am forced to conclude that there is a problem with D21Mod1.pdb.
>>
>> I would appreciate help in solving this problem.
>>
>> Thanks in advance.
>> -- 
>> Stephen P. Molnar, Ph.D.
>>
>> www.molecular-modeling.net
>>
>> 614.312.7528 (c)
>> Skype:  smolnar1
>>
>>
>> <D21.pdb><D21Mod1.pdb><Mod1.pdb>_______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1

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From meng at cgl.ucsf.edu  Fri Apr 30 08:36:32 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 30 Apr 2021 08:36:32 -0700
Subject: [Chimera-users] Problem Saava9ng merged PDB Files
In-Reply-To: <608BF66E.8070508@sbcglobal.net>
References: <6084124C.3060707.ref@sbcglobal.net>
 <6084124C.3060707@sbcglobal.net>
 <65154B98-0607-4DDA-B13A-F0C0D159ED7C@cgl.ucsf.edu>
 <608BF66E.8070508@sbcglobal.net>
Message-ID: <B70B3AD7-0AE8-48AC-AE98-04A1EA06DF7D@cgl.ucsf.edu>

HI Stephen,
I do not use LigPlot+ but as far as I know Chimera writes correct PDB format no matter which steps you use.

Your message (see below) has lots of unreadable characters and is nearly impossible to decipher.  Also whenever you have a problem with a specific file it is not useful to merely describe it in e-mail.  Instead you should attach the file to the message so we can actually take a look at it.  (Or, for future reference, if you believe it's a bug, don't send e-mail here but instead use menu: Help... Report a Bug, fill out the form, and attach any file needed to reproduce the problem to the bug report form.)

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

> On Apr 30, 2021, at 5:22 AM, Stephen P. Molnar <s.molnar at sbcglobal.net> wrote:
> 
> Elaine
> 
> Ran into a problem.
> 
> I need to combine a Ligand and a Protein n in order to use LigPlot+ to characterize the bound ligand in the active site of the protein. Both pdb files are attached.
> 
> Following the steps in the URL you referenced:
> 
> Open Chimera
> Open Ligand
> Open Protein
> Open favorites --> Model Pane
> ????????? at this point the only active choice is 'activate all'
> Click on Ligand
> ????????? copy/combine is now active
> Right click Protein 
> Copy/Combine
> ????????? 2 combination is now aticve
> Save 2.pdb
> 
> Edit 2.pdb to conform with LigPlus+ pdb file format (2edited.pdb)
> 
> Open 2.pdb in??? LigPlot+
> <Screenshot_2021-04-30_08-15-13.png>
> Oops - and other not printable comments. Not exactly the expected result.??? Just what is the problem?
> 
> HETATM?????? 25??? H??? UNLD???????????? 1???????????? -25.457??? -6.079 183.671??? 0.00??? 0.00?????????????????????????????? H
> MDL
> ATOM??????????????? 1??? N?????? SER A??? 13???????????? -59.051??? 40.339 226.398??? 0.00??? 0.00??????????????? AS1??? N
> ????????????????????????????????????????????????????????????????????????????????????????????? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ?????? 
> Misaligned fields! (Unfortunately, I didn't know this was the problem., but the author of LigPlot+ did)
> 
> What did I do/fail to do in Chimera?
> 
> Thanks in advance.
> 
> ????????? ????????? Steve
> 
> 
> 
> On 04/24/2021 06:41 PM, Elaine Meng wrote:
>> Hi Stephen,
>> Probably you just need to combine the ligand and receptor into a single model before saving to a PDB file, instead of saving the two models to a single multimodel PDB file.  This is usually the problem when you want to use some other program afterward for ligand-receptor analysis, and I see that your file has two models in it instead of a single model with both receptor and ligand.
>> 
>> For example, see instructions in this recent post on how to combine the models before saving:
>> 
>> <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-March/017672.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 Apr 24, 2021, at 5:42 AM, Stephen P. Molnar <s.molnar at sbcglobal.net>
>>>  wrote:
>>> 
>>> I am using Chimera v-1.14 (build 42094) on my Debian Buster Linux computer and have run into a problem saving a pdb file containing two pdb files.
>>> 
>>> The files are attached to this email.This is a portion of the combined flies:
>>> 
>>> <Screenshot_2021-04-24_08-29-16.png>
>>> 
>>> The structure of the D21.pdb file isthe ball image.
>>> 
>>> I followed the instructions in the Building Structures, Modifying and Saving Data in the Help pages.
>>> 
>>> However, when I open DD21Mod1 in LigPlot to identify the docked ligand I get:
>>> 
>>> <Screenshot_2021-04-24_08-30-37.png>
>>> 
>>> Clearly, this is not the ligand docked int the active site. I have used LigPlot on a number of pdb files with good results and am forced to conclude that there is a problem with D21Mod1.pdb.
>>> 
>>> I would appreciate help in solving this problem.
>>> 
>>> Thanks in advance.
>>> -- 
>>> Stephen P. Molnar, Ph.D.
>>> 
>>> 
>>> www.molecular-modeling.net
>>> 
>>> 
>>> 614.312.7528 (c)
>>> Skype:  smolnar1
>>> 
>>> 
>>> <D21.pdb><D21Mod1.pdb><Mod1.pdb>_______________________________________________
>>> Chimera-users mailing list: 
>>> Chimera-users at cgl.ucsf.edu
>>> 
>>> Manage subscription: 
>>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 
> -- 
> Stephen P. Molnar, Ph.D.
> 
> www.molecular-modeling.net
> 
> 614.312.7528 (c)
> Skype:  smolnar1
> 
> 
> <Ligand.pdb><Protein.pdb><2edited.pdb>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From rhloring at gmail.com  Fri Apr 30 08:59:54 2021
From: rhloring at gmail.com (Ralph Loring)
Date: Fri, 30 Apr 2021 11:59:54 -0400
Subject: [Chimera-users] What do you do for comparative modeling if the pdb
 is so new it's not in UniProt?
Message-ID: <CAMDKwDKo6dfKsFjrtW2LMdnQH-jhPPVC=6X1bYRfDXOrh2+m-A@mail.gmail.com>

Hi,
I'm very new to Chimera and have been working through the tutorials,
including the Comparative Modeling Tutorial.  However I'm stumped.  I'm
interested in modeling chimeric proteins that involve the following pdbs:
PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align
with the template structure in the pdbs.  The problem is that the template
pdbs only came out in April and are not yet included in UniProt.  They are
deposited in RSCB and EMDB, but these don't appear to be alignment options
in Chimera.  Do I need to appeal to UniProt, or is there an alternative way
to make the association between the sequence and the structure?  Any
additional tutorials on using MAV would be helpful as there seem to be a
lot of editing features that are not explored in your tutorial.
Thanks for your help,

Ralph Loring
Associate Professor of Pharmacology
Department of Pharmaceutical Sciences
Northeastern University
360 Huntington Avenue
Boston, MA 02115 USA
617-373-3216 office
617-373-8886 fax
r.loring at northeastern.edu
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From meng at cgl.ucsf.edu  Fri Apr 30 09:25:21 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 30 Apr 2021 09:25:21 -0700
Subject: [Chimera-users] What do you do for comparative modeling if the
 pdb is so new it's not in UniProt?
In-Reply-To: <CAMDKwDKo6dfKsFjrtW2LMdnQH-jhPPVC=6X1bYRfDXOrh2+m-A@mail.gmail.com>
References: <CAMDKwDKo6dfKsFjrtW2LMdnQH-jhPPVC=6X1bYRfDXOrh2+m-A@mail.gmail.com>
Message-ID: <633F2083-8F8E-4E7B-A127-017767EC9277@cgl.ucsf.edu>

Hi Ralph,
I should say first that this may not be the right tool for your task, since it will only model a single chain (single subunit).  However, if that is not a problem for you, I think I can answer your question.

It doesn't matter if the template protein is in UniProt.  If I understand correctly, you have already opened a sequence of your target (the chimeric protein), and now you are trying to add the sequence from your template(s) to make an alignment?  In the Sequence window of that target sequence, choose "Edit... Add Sequence"  and then use the "From Structure" tab.  (I.e. you need to first open the structure of your template and then you can add its sequence to the existing ones in the alignment via that tab.)  You can alternatively paste in sequences "From Text" but probably the other way is easier.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit>

Another way is to just create the whole alignment in some other application (e.g. Jalview) and then save it in some sequence-alignment format that Chimera can read, then open it in Chimera.  Sequence formats:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment>

Presumably you already had to text-edit to make a fasta file or use some other application to create the sequence of your target in the first place.

There is some discussion of how to get inputs for comparative modelling in Chimera here:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>

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

> On Apr 30, 2021, at 8:59 AM, Ralph Loring <rhloring at gmail.com> wrote:
> 
> Hi,
> I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial.  However I'm stumped.  I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs.  The problem is that the template pdbs only came out in April and are not yet included in UniProt.  They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera.  Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure?  Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial.
> Thanks for your help,
> 
> Ralph Loring
> Associate Professor of Pharmacology
> Department of Pharmaceutical Sciences
> Northeastern University
> 360 Huntington Avenue 
> Boston, MA 02115 USA
> 617-373-3216 office
> 617-373-8886 fax
> r.loring at northeastern.edu
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From sette at uniroma2.it  Fri Apr 30 09:27:54 2021
From: sette at uniroma2.it (Marco Sette)
Date: Fri, 30 Apr 2021 18:27:54 +0200
Subject: [Chimera-users] What do you do for comparative modeling if the
 pdb is so new it's not in UniProt?
In-Reply-To: <CAMDKwDKo6dfKsFjrtW2LMdnQH-jhPPVC=6X1bYRfDXOrh2+m-A@mail.gmail.com>
References: <CAMDKwDKo6dfKsFjrtW2LMdnQH-jhPPVC=6X1bYRfDXOrh2+m-A@mail.gmail.com>
Message-ID: <b0285e8d-5bb7-0be0-82a6-267672e8eb1d@uniroma2.it>

If you search for the sequences the PDB Data Bank (RCSB) provides both 
the pdb file and the sequence in fasta format.

Best regards,

Marco

Il 30/04/2021 17:59, Ralph Loring ha scritto:
> Hi,
> I'm very new to Chimera and have been working through the tutorials, 
> including the Comparative Modeling Tutorial. However I'm stumped.? I'm 
> interested in modeling chimeric proteins that involve the following 
> pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my 
> chimera to align with the template structure in the pdbs.? The problem 
> is that the template pdbs only came out in April and are not yet 
> included in UniProt.? They are deposited in RSCB and EMDB, but these 
> don't appear to be alignment options in Chimera.? Do I need to appeal 
> to UniProt, or is there an alternative way to make the association 
> between the sequence and the structure?? Any additional tutorials on 
> using MAV would be helpful as there seem to be a lot of editing 
> features that are not explored in your tutorial.
> Thanks for your help,
>
> Ralph Loring
> Associate Professor of Pharmacology
> Department of Pharmaceutical Sciences
> Northeastern University
> 360 Huntington Avenue
> Boston, MA 02115 USA
> 617-373-3216 office
> 617-373-8886 fax
> r.loring at northeastern.edu <mailto:r.loring at northeastern.edu>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-- 
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette at uniroma2.it
e-mail: m77it at yahoo.it
Tel.: +39-0672594424
Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette


Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle linee guida del Garante per posta elettronica e interne (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell?amministrazione digitale) si precisa che le informazioni contenute in questo messaggio -come pure i dati esteriori delle comunicazioni e i file allegati- sono riservate e ad uso esclusivo del destinatario. Divulgazione, copia, stampa o qualunque altro uso da parte di altri non ? autorizzato. Qualora il messaggio in parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza copiarlo e di non inoltrarlo a terzi, dandocene gentilmente comunicazione al seguente indirizzo e-mail privacy at uniroma2.it.

On the basis of ?(UE) Rules 2016/679 and the codes in general guidelines of Garante for electronic and internal mail (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell?amministrazione digitale) information here contained and any attachments is confidential and intended for the recipient(s) only. Dissemination, copying, printing or use by anybody else is unauthorized. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail to privacy at uniroma2.it.

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From meng at cgl.ucsf.edu  Fri Apr 30 10:33:03 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 30 Apr 2021 10:33:03 -0700
Subject: [Chimera-users] What do you do for comparative modeling if the
 pdb is so new it's not in UniProt?
In-Reply-To: <b0285e8d-5bb7-0be0-82a6-267672e8eb1d@uniroma2.it>
References: <CAMDKwDKo6dfKsFjrtW2LMdnQH-jhPPVC=6X1bYRfDXOrh2+m-A@mail.gmail.com>
 <b0285e8d-5bb7-0be0-82a6-267672e8eb1d@uniroma2.it>
Message-ID: <4B54129F-6110-415D-B53C-E77F1A8A9CF5@cgl.ucsf.edu>

Also, if you open a structure from the PDB in Chimera, then you can just use the Chimera menu: Favorites... Sequence to show the sequence of any/all of its biopolymer chains.

Elaine


> On Apr 30, 2021, at 9:27 AM, Marco Sette <sette at uniroma2.it> wrote:
> 
> If you search for the sequences the PDB Data Bank (RCSB) provides both the pdb file and the sequence in fasta format.
> 
> Best regards,
> 
> Marco
> 
> Il 30/04/2021 17:59, Ralph Loring ha scritto:
>> Hi,
>> I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial.  However I'm stumped.  I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs.  The problem is that the template pdbs only came out in April and are not yet included in UniProt.  They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera.  Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure?  Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial.
>> Thanks for your help,
>> 
>> Ralph Loring
>> Associate Professor of Pharmacology
>> Department of Pharmaceutical Sciences
>> Northeastern University
>> 360 Huntington Avenue 
>> Boston, MA 02115 USA
>> 617-373-3216 office
>> 617-373-8886 fax
>> r.loring at northeastern.edu
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: 
>> Chimera-users at cgl.ucsf.edu
>> 
>> Manage subscription: 
>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> -- 
> Dr.Marco Sette, Ph.D.
> Department of Chemical Sciences and Technology
> University of Rome, "Tor Vergata"
> via della Ricerca Scientifica, 00133, Rome, Italy
> e-mail: 
> sette at uniroma2.it
> 
> e-mail: 
> m77it at yahoo.it
> 
> Tel.: +39-0672594424
> Fax: +39-0672594328
> 
> http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
> 
> 
> 
> Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle linee guida del Garante per posta elettronica e interne (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell?amministrazione digitale) si precisa che le informazioni contenute in questo messaggio -come pure i dati esteriori delle comunicazioni e i file allegati- sono riservate e ad uso esclusivo del destinatario. Divulgazione, copia, stampa o qualunque altro uso da parte di altri non ? autorizzato. Qualora il messaggio in parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza copiarlo e di non inoltrarlo a terzi, dandocene gentilmente comunicazione al seguente indirizzo e-mail 
> privacy at uniroma2.it
> .
> 
> On the basis of ?(UE) Rules 2016/679 and the codes in general guidelines of Garante for electronic and internal mail (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell?amministrazione digitale) information here contained and any attachments is confidential and intended for the recipient(s) only. Dissemination, copying, printing or use by anybody else is unauthorized. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail to 
> privacy at uniroma2.it.
> _______________________________________________
> 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  Fri Apr 30 11:16:00 2021
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 30 Apr 2021 11:16:00 -0700
Subject: [Chimera-users] 2D panorama view of a 3D model
In-Reply-To: <29081E8A-7733-4A19-8CAB-463C1C81E3ED@cgl.ucsf.edu>
References: <176954E9-3E83-4469-BA98-035EFDF3284C@imp.ac.at>
 <29081E8A-7733-4A19-8CAB-463C1C81E3ED@cgl.ucsf.edu>
Message-ID: <3770184D-7733-41E7-906A-8B6D3CFAC8FE@sonic.net>

Hi Susanne,

  Do you have an example image of a 360 degree molecule panorama image?  Years ago I tried to make such a thing but did not produce anything good.  If you think of a rectangular map of the world which flattens a 360 degree picture of the surface of the earth you may think it can work.  But the earth is a sphere, the surface has negligible variation in height, while a molecule has residues at all different depths.  So if you try to do the same type of image with a molecule the different parts get wildly different magnifications and it does not look useful.

	Tom


> On Apr 28, 2021, at 7:50 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Susanne,
> I'm not too familiar with panorama views.  There is a "horizontal field of view" angle parameter in the Camera tool (menu: Tools... Viewing Controls... Camera) but it only allows going up to 179 degrees.
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#camera>
> 
> If you use ChimeraX instead of Chimera, there are some 360-degree modes, e.g. ChimeraX command "camera 360".  ChimeraX also allows setting the field-of-view parameter mentioned above.
> 
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/camera.html>
> 
> As I understand it, however, these 360-degree views are mainly for recording movies to play back in virtual reality headsets.  An example of recording a 360-degree movie in ChimeraX is given here:
> <https://rbvi.ucsf.edu/chimerax/docs/user/vrphone.html>
> 
> So, maybe neither of these things (360-degree view or setting wider field-of-view angle) is the same as the panorama view you had in mind.  If none of the settings in the Camera tool in Chimera give what you want, then as far as I know it is not possible to make a 2D panorama view directly in Chimera.
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Apr 27, 2021, at 10:55 PM, Kandolf,Susanne <susanne.kandolf at imp.ac.at> wrote:
>> 
>> Hello, 
>> 
>> I was wondering if it is possible to display a 3D model as a 2D panorama view?
>> I would like to show all sides of a holoenzyme and instead of taking several pictures of each view,
>> I thought it would be more convenient to have one picture displayed as panorama showing all sides at the same time.
>> 
>> Thank you for your help, 
>> Susanne
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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> 



From rhloring at gmail.com  Fri Apr 30 12:22:28 2021
From: rhloring at gmail.com (Ralph Loring)
Date: Fri, 30 Apr 2021 15:22:28 -0400
Subject: [Chimera-users] What do you do for comparative modeling if the
 pdb is so new it's not in UniProt?
In-Reply-To: <633F2083-8F8E-4E7B-A127-017767EC9277@cgl.ucsf.edu>
References: <CAMDKwDKo6dfKsFjrtW2LMdnQH-jhPPVC=6X1bYRfDXOrh2+m-A@mail.gmail.com>
 <633F2083-8F8E-4E7B-A127-017767EC9277@cgl.ucsf.edu>
Message-ID: <CAMDKwDL+A+bS0Q82_U=c8eDB-hrYQKA0jgdA+Upnp-abyz-yWg@mail.gmail.com>

Thanks,
This is helpful


On Fri, Apr 30, 2021 at 12:25 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Ralph,
> I should say first that this may not be the right tool for your task,
> since it will only model a single chain (single subunit).  However, if that
> is not a problem for you, I think I can answer your question.
>
> It doesn't matter if the template protein is in UniProt.  If I understand
> correctly, you have already opened a sequence of your target (the chimeric
> protein), and now you are trying to add the sequence from your template(s)
> to make an alignment?  In the Sequence window of that target sequence,
> choose "Edit... Add Sequence"  and then use the "From Structure" tab.
> (I.e. you need to first open the structure of your template and then you
> can add its sequence to the existing ones in the alignment via that tab.)
> You can alternatively paste in sequences "From Text" but probably the other
> way is easier.
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html
> >
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit
> >
>
> Another way is to just create the whole alignment in some other
> application (e.g. Jalview) and then save it in some sequence-alignment
> format that Chimera can read, then open it in Chimera.  Sequence formats:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment
> >
>
> Presumably you already had to text-edit to make a fasta file or use some
> other application to create the sequence of your target in the first place.
>
> There is some discussion of how to get inputs for comparative modelling in
> Chimera here:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Apr 30, 2021, at 8:59 AM, Ralph Loring <rhloring at gmail.com> wrote:
> >
> > Hi,
> > I'm very new to Chimera and have been working through the tutorials,
> including the Comparative Modeling Tutorial.  However I'm stumped.  I'm
> interested in modeling chimeric proteins that involve the following pdbs:
> PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align
> with the template structure in the pdbs.  The problem is that the template
> pdbs only came out in April and are not yet included in UniProt.  They are
> deposited in RSCB and EMDB, but these don't appear to be alignment options
> in Chimera.  Do I need to appeal to UniProt, or is there an alternative way
> to make the association between the sequence and the structure?  Any
> additional tutorials on using MAV would be helpful as there seem to be a
> lot of editing features that are not explored in your tutorial.
> > Thanks for your help,
> >
> > Ralph Loring
> > Associate Professor of Pharmacology
> > Department of Pharmaceutical Sciences
> > Northeastern University
> > 360 Huntington Avenue
> > Boston, MA 02115 USA
> > 617-373-3216 office
> > 617-373-8886 fax
> > r.loring at northeastern.edu
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