From ztmaldonado at icloud.com  Sat Feb  1 09:01:39 2020
From: ztmaldonado at icloud.com (Zachary Maldonado)
Date: Sat, 1 Feb 2020 11:01:39 -0600
Subject: [Chimera-users] Chimera Download issue
Message-ID: <B8CDDD50-EFD5-4F4F-9032-F2144F05F4AD@icloud.com>

To whom it may concern, 

My name is Zachary Maldonado and I am a college student at the University of Missouri-Columbia. I need this program for one of my classes I am taking this semester. I can not seem to open the program and when I try to open it, I get a message from my computer saying that I need to update the application before I can open it. My computer says it is unable to search for "malicious software". If you could assist me that would be greatly appreciated. Thank you! 

Sincerely, 

Zachary Maldonado 

From pett at cgl.ucsf.edu  Mon Feb  3 10:40:55 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 3 Feb 2020 10:40:55 -0800
Subject: [Chimera-users] Chimera Download issue
In-Reply-To: <B8CDDD50-EFD5-4F4F-9032-F2144F05F4AD@icloud.com>
References: <B8CDDD50-EFD5-4F4F-9032-F2144F05F4AD@icloud.com>
Message-ID: <861E9095-16E2-40DD-A9B8-8DB0D469CDBD@cgl.ucsf.edu>

Hi Zachary,
	Apple has imposed some new security requirements on apps that are somewhat difficult to comply with. We are working on getting Chimera in compliance, but until we manage that the workaround is to right-click (or control-left click) on the Chimera app icon. That will bring up a menu with "Open" as its first entry. Click "Open" and Chimera will start. After that you should be able to start Chimera normally with no popup menu shenanigans.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Feb 1, 2020, at 9:01 AM, Zachary Maldonado <ztmaldonado at icloud.com> wrote:
> 
> To whom it may concern, 
> 
> My name is Zachary Maldonado and I am a college student at the University of Missouri-Columbia. I need this program for one of my classes I am taking this semester. I can not seem to open the program and when I try to open it, I get a message from my computer saying that I need to update the application before I can open it. My computer says it is unable to search for "malicious software". If you could assist me that would be greatly appreciated. Thank you! 
> 
> Sincerely, 
> 
> Zachary Maldonado 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From martingonzalezbuitron at gmail.com  Tue Feb  4 02:34:22 2020
From: martingonzalezbuitron at gmail.com (=?UTF-8?B?TWFydMOtbiBHb256w6FsZXogQnVpdHLDs24=?=)
Date: Tue, 4 Feb 2020 11:34:22 +0100
Subject: [Chimera-users] Supporting XDG base directory - chimera
Message-ID: <CAOcbgHhxvFt+GjsPmjYhQG8HJNZNpb+Pd_XP9iQ2osDE5aMFwg@mail.gmail.com>

Dears all,

I realised that you are using a hidden folder (.chimera/) in $HOME
directory, linux's distribution.

Have you considered supporting freedesktop.org's standard specs?

References:
- http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html
- https://wiki.archlinux.org/index.php/XDG_Base_Directory

All the best,
Mart?n
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From gregc at cgl.ucsf.edu  Tue Feb  4 09:32:21 2020
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Tue, 4 Feb 2020 09:32:21 -0800
Subject: [Chimera-users] Supporting XDG base directory - chimera
In-Reply-To: <CAOcbgHhxvFt+GjsPmjYhQG8HJNZNpb+Pd_XP9iQ2osDE5aMFwg@mail.gmail.com>
References: <CAOcbgHhxvFt+GjsPmjYhQG8HJNZNpb+Pd_XP9iQ2osDE5aMFwg@mail.gmail.com>
Message-ID: <85c87c4f-a17c-13a4-2c19-2a514c1630d6@cgl.ucsf.edu>

ChimeraX, the follow on to Chimera, does what you suggest. Chimera is 
reaching the end of its life, so it will not be getting any breaking 
changes.

 ??? -- Greg

On 2/4/2020 2:34 AM, Mart?n Gonz?lez Buitr?n wrote:
> Dears all,
>
> I realised that you are using a hidden folder (.chimera/) in $HOME 
> directory, linux's distribution.
>
> Have you considered supporting freedesktop.org 
> <http://freedesktop.org>'s standard specs?
>
> References:
> - http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html
> - https://wiki.archlinux.org/index.php/XDG_Base_Directory
>
> All the best,
> Mart?n
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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From ztmaldonado at icloud.com  Tue Feb  4 13:58:44 2020
From: ztmaldonado at icloud.com (Zachary Maldonado)
Date: Tue, 4 Feb 2020 15:58:44 -0600
Subject: [Chimera-users] Chimera Download issue
In-Reply-To: <861E9095-16E2-40DD-A9B8-8DB0D469CDBD@cgl.ucsf.edu>
References: <B8CDDD50-EFD5-4F4F-9032-F2144F05F4AD@icloud.com>
 <861E9095-16E2-40DD-A9B8-8DB0D469CDBD@cgl.ucsf.edu>
Message-ID: <24BE034E-F9B8-4832-962A-9847EDB37078@icloud.com>

Eric, 

Thank you for the information! I have figured it out and am able to open and use Chimera! I appreciate the assistance. 

Best, 

Zachary Maldonado 

> On Feb 3, 2020, at 12:40 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Hi Zachary,
> 	Apple has imposed some new security requirements on apps that are somewhat difficult to comply with. We are working on getting Chimera in compliance, but until we manage that the workaround is to right-click (or control-left click) on the Chimera app icon. That will bring up a menu with "Open" as its first entry. Click "Open" and Chimera will start. After that you should be able to start Chimera normally with no popup menu shenanigans.
> 
> --Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
>> On Feb 1, 2020, at 9:01 AM, Zachary Maldonado <ztmaldonado at icloud.com> wrote:
>> 
>> To whom it may concern, 
>> 
>> My name is Zachary Maldonado and I am a college student at the University of Missouri-Columbia. I need this program for one of my classes I am taking this semester. I can not seem to open the program and when I try to open it, I get a message from my computer saying that I need to update the application before I can open it. My computer says it is unable to search for "malicious software". If you could assist me that would be greatly appreciated. Thank you! 
>> 
>> Sincerely, 
>> 
>> Zachary Maldonado 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From pett at cgl.ucsf.edu  Tue Feb  4 15:22:58 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 4 Feb 2020 15:22:58 -0800
Subject: [Chimera-users] Chimera Download issue
In-Reply-To: <24BE034E-F9B8-4832-962A-9847EDB37078@icloud.com>
References: <B8CDDD50-EFD5-4F4F-9032-F2144F05F4AD@icloud.com>
 <861E9095-16E2-40DD-A9B8-8DB0D469CDBD@cgl.ucsf.edu>
 <24BE034E-F9B8-4832-962A-9847EDB37078@icloud.com>
Message-ID: <9D1EA0A8-C6AF-4BD0-B257-ADABD9757B2F@cgl.ucsf.edu>

Glad I could help!

?Eric

> On Feb 4, 2020, at 1:58 PM, Zachary Maldonado <ztmaldonado at icloud.com> wrote:
> 
> Eric, 
> 
> Thank you for the information! I have figured it out and am able to open and use Chimera! I appreciate the assistance. 
> 
> Best, 
> 
> Zachary Maldonado 
> 
>> On Feb 3, 2020, at 12:40 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> 
>> Hi Zachary,
>> 	Apple has imposed some new security requirements on apps that are somewhat difficult to comply with. We are working on getting Chimera in compliance, but until we manage that the workaround is to right-click (or control-left click) on the Chimera app icon. That will bring up a menu with "Open" as its first entry. Click "Open" and Chimera will start. After that you should be able to start Chimera normally with no popup menu shenanigans.
>> 
>> --Eric
>> 
>> 	Eric Pettersen
>> 	UCSF Computer Graphics Lab
>> 
>>> On Feb 1, 2020, at 9:01 AM, Zachary Maldonado <ztmaldonado at icloud.com> wrote:
>>> 
>>> To whom it may concern, 
>>> 
>>> My name is Zachary Maldonado and I am a college student at the University of Missouri-Columbia. I need this program for one of my classes I am taking this semester. I can not seem to open the program and when I try to open it, I get a message from my computer saying that I need to update the application before I can open it. My computer says it is unable to search for "malicious software". If you could assist me that would be greatly appreciated. Thank you! 
>>> 
>>> Sincerely, 
>>> 
>>> Zachary Maldonado 
>>> _______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From daniel.hilger at pharmazie.uni-marburg.de  Wed Feb  5 07:34:43 2020
From: daniel.hilger at pharmazie.uni-marburg.de (Daniel Hilger)
Date: Wed, 5 Feb 2020 16:34:43 +0100
Subject: [Chimera-users] Phosphorylated residues showing up as X
Message-ID: <10EB8C08-29D4-467D-98A5-2DDA402CE22D@pharmazie.uni-marburg.de>

Hi,

I modeled two phosphorylated residues in my structure. The primary sequence window in Chimera, however, is only showing a ?X? at those positions. Is there a possibility to change that to the original amino acid (S or T) or to show them as SEP or TPO in the sequence window?
Thanks,
Daniel


Daniel Hilger, Dr.
Group leader 
Philipps-University Marburg
Marbacher Weg 6
35032 Marburg
Germany
daniel.hilger at pharmazie.uni-marburg.de
Phone: +49 6421 28 25930









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From pett at cgl.ucsf.edu  Wed Feb  5 11:24:33 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 5 Feb 2020 11:24:33 -0800
Subject: [Chimera-users] Phosphorylated residues showing up as X
In-Reply-To: <10EB8C08-29D4-467D-98A5-2DDA402CE22D@pharmazie.uni-marburg.de>
References: <10EB8C08-29D4-467D-98A5-2DDA402CE22D@pharmazie.uni-marburg.de>
Message-ID: <6ED88E1F-103D-4BE6-BD35-32998F52864C@cgl.ucsf.edu>

Hi Daniel,
	Chimera learns that non-standard residues are modified forms of regular amino/nucleic acids from the MODRES records in PDB files.  If you added MODRES records for your residues to your input file, the sequence would show S/T instead of X.  The format for a MODRES record is documented here:

	http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#MODRES <http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#MODRES>

You could crib MODRES records for your residues from 1vrv (SEP) and 6ar2 (TPO).  You would have to edit the chain ID and sequence number fields of those records.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



> On Feb 5, 2020, at 7:34 AM, Daniel Hilger <daniel.hilger at pharmazie.uni-marburg.de> wrote:
> 
> Hi,
> 
> I modeled two phosphorylated residues in my structure. The primary sequence window in Chimera, however, is only showing a ?X? at those positions. Is there a possibility to change that to the original amino acid (S or T) or to show them as SEP or TPO in the sequence window?
> Thanks,
> Daniel
> 
> 
> Daniel Hilger, Dr.
> Group leader 
> Philipps-University Marburg
> Marbacher Weg 6
> 35032 Marburg
> Germany
> daniel.hilger at pharmazie.uni-marburg.de <mailto:daniel.hilger at pharmazie.uni-marburg.de>
> Phone: +49 6421 28 25930
> 
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From andysen at tamu.edu  Wed Feb  5 14:26:46 2020
From: andysen at tamu.edu (Sen, Anindito)
Date: Wed, 5 Feb 2020 22:26:46 +0000
Subject: [Chimera-users] moving parts of a density map in a Movie
Message-ID: <318D18AF-E16C-40A6-884C-63EEC73D9408@tamu.edu>

Dear All,



I have a  composite density map with 7 individual reconstructions combined together. For making a movie to show the different components and their organization- What will be the commands to make the individual density maps to move  out of their position (in the composite map) and fly back in, (one or multiple density maps  at a time).


Regards

Anindito Sen. Ph.D




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From meng at cgl.ucsf.edu  Wed Feb  5 15:51:20 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 5 Feb 2020 15:51:20 -0800
Subject: [Chimera-users] moving parts of a density map in a Movie
In-Reply-To: <318D18AF-E16C-40A6-884C-63EEC73D9408@tamu.edu>
References: <318D18AF-E16C-40A6-884C-63EEC73D9408@tamu.edu>
Message-ID: <3D4A4513-6C6D-472A-90FF-8C9767AC6272@cgl.ucsf.edu>

Hi Anindito,
If you just want to translate a specific map in one direction and then back to where it was, you can simply use the ?move? command with its model number, for example translating model #1 200 distance units (usually Angstroms if that?s what your maps are in) along vertical axis over 100 frames:

move y  200 100 models #1
move y -200 100 models #1

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>

See the manual page for details. You can translate along any vector, and of course you would change the distance value and number of frames as you like, and move more than one model at a time.

However, if you have more complicated ideas of exactly where you want each map to go, you would have to place them by hand and use savepos to save/name each set of positions, which can then be restored with ?reset? or ?fly".  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fly.html>

Each ?savepos? position includes all the models, so you can?t only move one model when it has all of them in different places.  You?d have to save a new position for each model position change.

There is also ?play radial? for radial explosion outward, but it is for multiscale surfaces, not map surfaces.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/play.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 Feb 5, 2020, at 2:26 PM, Sen, Anindito <andysen at tamu.edu> wrote:
> 
> Dear All,
> I have a  composite density map with 7 individual reconstructions combined together. For making a movie to show the different components and their organization- What will be the commands to make the individual density maps to move  out of their position (in the composite map) and fly back in, (one or multiple density maps  at a time).
> Regards
> Anindito Sen. Ph.D



From gretahodo96 at hotmail.com  Fri Feb  7 14:45:25 2020
From: gretahodo96 at hotmail.com (Greta Hodo)
Date: Fri, 7 Feb 2020 22:45:25 +0000
Subject: [Chimera-users] Docking
Message-ID: <PR2PR03MB5404B20FB557F978EB4DD05FA91C0@PR2PR03MB5404.eurprd03.prod.outlook.com>


Hi,
I have a problem with the result of autodock Vina. When I load a molecule in ?mol2? format and I use AutoDock Vina for docking, the docked molecule is altered. How can be possible? How can I solve my problem?

I attach the photo of the real molecule [cid:C2748141-718F-40C4-8964-A212C52FDB1A]

And this I how the molecule changes after the docking
[cid:C1EDE285-2873-437D-A034-5BB2D031BD67]
The 5-term ring becomes aromatic, while it should have only a double bond. ( this happens both if I save autodock vina result in ?mol2? format and ?pdb? format

Hope you can help me!
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From meng at cgl.ucsf.edu  Fri Feb  7 16:16:50 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 7 Feb 2020 16:16:50 -0800
Subject: [Chimera-users] Docking
In-Reply-To: <PR2PR03MB5404B20FB557F978EB4DD05FA91C0@PR2PR03MB5404.eurprd03.prod.outlook.com>
References: <PR2PR03MB5404B20FB557F978EB4DD05FA91C0@PR2PR03MB5404.eurprd03.prod.outlook.com>
Message-ID: <AAE41717-4EF7-45D0-9C0B-846FF64AF600@cgl.ucsf.edu>

Hi Greta,
I guess the only difference is whether the two carbons in the 5-member ring are CH or CH2, because Chimera does not use (or change) bond orders.  Are you sure that both structures can exist as real chemicals?  Maybe Chimera guesses it is an aromatic ring (more on this below) but that would also be true as soon as you opened the ligand structure, not as a result of the docking. So my question is then, how can you tell the molecule is different before and after?  It would have been much more useful to attach the before and after structures (coordinate files) than images of 2D chemical diagrams.

The following assumes that both structures you drew can exist as real chemicals.

Did it have hydrogens before you started the docking calculation? If not, it may be that the autodock ligand preparation script added hydrogens and had trouble identifying the bond orders (maybe the bond length is similar with single or aromatic bond) and added 1 H instead of 2 to each of those atoms.  In that case you could try adding hydrogens to the ligand with Chimera instead (e.g. command ?addh? or AddH tool) 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>
before docking.  If Chimera has the same problem as the autodock ligand preparation script, then delete the ligand hydrogens and make sure the atom types are assigned to sp3 carbon before trying to add them back again.  For example, select those two carbon atoms (Ctrl-click, Shift-Ctrl-click) and then use setattr command, something like:

setattr a idatmType C3 sel

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

Then add hydrogens, check that they are as expected, then do the docking.  Or you could use any other program/method to add hydrogens before opening the ligand structure in Chimera.

It may not make much difference since if I remember correctly, Vina doesn?t even use the hydrogens except to identify the types of the other atoms.  You would have to check the literature references to be sure about that, however.

Finally:
Note that the Autodock Vina tool uses a web server that only allows very little sampling, which is not adequate for most research purposes, as mentioned in the boxed warning on the manual page.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

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

> On Feb 7, 2020, at 2:45 PM, Greta Hodo <gretahodo96 at hotmail.com> wrote:
> 
> Hi,
> I have a problem with the result of autodock Vina. When I load a molecule in ?mol2? format and I use AutoDock Vina for docking, the docked molecule is altered. How can be possible? How can I solve my problem? 
> 
> I attach the photo of the real molecule <image0.jpeg>
> 
> And this I how the molecule changes after the docking 
> <image1.jpeg>
> The 5-term ring becomes aromatic, while it should have only a double bond. ( this happens both if I save autodock vina result in ?mol2? format and ?pdb? format
> 
> Hope you can help me!



From gretahodo96 at hotmail.com  Fri Feb  7 17:11:47 2020
From: gretahodo96 at hotmail.com (Greta Hodo)
Date: Sat, 8 Feb 2020 01:11:47 +0000
Subject: [Chimera-users] R:  Docking
In-Reply-To: <AAE41717-4EF7-45D0-9C0B-846FF64AF600@cgl.ucsf.edu>
References: <PR2PR03MB5404B20FB557F978EB4DD05FA91C0@PR2PR03MB5404.eurprd03.prod.outlook.com>,
 <AAE41717-4EF7-45D0-9C0B-846FF64AF600@cgl.ucsf.edu>
Message-ID: <PR2PR03MB5404AAE3AAC393F291A8FE95A91F0@PR2PR03MB5404.eurprd03.prod.outlook.com>

Hi Elaine,
thank you for the quick answer.
Before I start the docking calculation my molecule has all the hydrogens as expected (as you can see in the ''img1'' file attached you). After the docking calculation with Autodock Vina the molecule changes (as you can see in the ''img2'' file). How can I solve the problem?

Best,
Greta

________________________________
Da: Elaine Meng <meng at cgl.ucsf.edu>
Inviato: sabato 8 febbraio 2020 01:16
A: Greta Hodo <gretahodo96 at hotmail.com>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Oggetto: Re: [Chimera-users] Docking

Hi Greta,
I guess the only difference is whether the two carbons in the 5-member ring are CH or CH2, because Chimera does not use (or change) bond orders.  Are you sure that both structures can exist as real chemicals?  Maybe Chimera guesses it is an aromatic ring (more on this below) but that would also be true as soon as you opened the ligand structure, not as a result of the docking. So my question is then, how can you tell the molecule is different before and after?  It would have been much more useful to attach the before and after structures (coordinate files) than images of 2D chemical diagrams.

The following assumes that both structures you drew can exist as real chemicals.

Did it have hydrogens before you started the docking calculation? If not, it may be that the autodock ligand preparation script added hydrogens and had trouble identifying the bond orders (maybe the bond length is similar with single or aromatic bond) and added 1 H instead of 2 to each of those atoms.  In that case you could try adding hydrogens to the ligand with Chimera instead (e.g. command ?addh? or AddH tool)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>
before docking.  If Chimera has the same problem as the autodock ligand preparation script, then delete the ligand hydrogens and make sure the atom types are assigned to sp3 carbon before trying to add them back again.  For example, select those two carbon atoms (Ctrl-click, Shift-Ctrl-click) and then use setattr command, something like:

setattr a idatmType C3 sel

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

Then add hydrogens, check that they are as expected, then do the docking.  Or you could use any other program/method to add hydrogens before opening the ligand structure in Chimera.

It may not make much difference since if I remember correctly, Vina doesn?t even use the hydrogens except to identify the types of the other atoms.  You would have to check the literature references to be sure about that, however.

Finally:
Note that the Autodock Vina tool uses a web server that only allows very little sampling, which is not adequate for most research purposes, as mentioned in the boxed warning on the manual page.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

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

> On Feb 7, 2020, at 2:45 PM, Greta Hodo <gretahodo96 at hotmail.com> wrote:
>
> Hi,
> I have a problem with the result of autodock Vina. When I load a molecule in ?mol2? format and I use AutoDock Vina for docking, the docked molecule is altered. How can be possible? How can I solve my problem?
>
> I attach the photo of the real molecule <image0.jpeg>
>
> And this I how the molecule changes after the docking
> <image1.jpeg>
> The 5-term ring becomes aromatic, while it should have only a double bond. ( this happens both if I save autodock vina result in ?mol2? format and ?pdb? format
>
> Hope you can help me!

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From 444039430 at qq.com  Mon Feb 10 08:07:35 2020
From: 444039430 at qq.com (=?gb18030?B?wdbBqtTG?=)
Date: Tue, 11 Feb 2020 00:07:35 +0800
Subject: [Chimera-users] S1-8
Message-ID: <tencent_3507CC673AAADEFFA2CABE2A6705C8111009@qq.com>

Dear&nbsp;management?


I am a PHD student from Tianjin University in china. I saw a movie which is done in chimera (see the attachment), i saw they draw a circle around the text (NTD-A). i am very confuse that i do not know how to draw a shape in chimera. i ask for you that tell me how to draw a shape in command line. Thanks very much.


Best wishes,


Lin l
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From meng at cgl.ucsf.edu  Mon Feb 10 10:17:44 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 10 Feb 2020 10:17:44 -0800
Subject: [Chimera-users] R:  Docking
In-Reply-To: <PR2PR03MB5404AAE3AAC393F291A8FE95A91F0@PR2PR03MB5404.eurprd03.prod.outlook.com>
References: <PR2PR03MB5404B20FB557F978EB4DD05FA91C0@PR2PR03MB5404.eurprd03.prod.outlook.com>
 <AAE41717-4EF7-45D0-9C0B-846FF64AF600@cgl.ucsf.edu>
 <PR2PR03MB5404AAE3AAC393F291A8FE95A91F0@PR2PR03MB5404.eurprd03.prod.outlook.com>
Message-ID: <2A83A52C-94AC-4B8E-AF59-115E8CB41059@cgl.ucsf.edu>

Hi Greta,
In the ?Ligand options? try turning off  ?Merge charges and remove non-polar hydrogens,? i.e. set it to ?false?:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

That?s my only idea at this point.  However, it still doesn?t make sense because if you had it set to ?true? there should not be any hydrogens on the carbons in the output.

Elaine

> On Feb 7, 2020, at 5:11 PM, Greta Hodo <gretahodo96 at hotmail.com> wrote:
> 
> Hi Elaine,
> thank you for the quick answer.
> Before I start the docking calculation my molecule has all the hydrogens as expected (as you can see in the ''img1'' file attached you). After the docking calculation with Autodock Vina the molecule changes (as you can see in the ''img2'' file). How can I solve the problem?
> 
> Best,
> Greta
> 
> Da: Elaine Meng <meng at cgl.ucsf.edu>
> Inviato: sabato 8 febbraio 2020 01:16
> A: Greta Hodo <gretahodo96 at hotmail.com>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Oggetto: Re: [Chimera-users] Docking
>  
> Hi Greta,
> I guess the only difference is whether the two carbons in the 5-member ring are CH or CH2, because Chimera does not use (or change) bond orders.  Are you sure that both structures can exist as real chemicals?  Maybe Chimera guesses it is an aromatic ring (more on this below) but that would also be true as soon as you opened the ligand structure, not as a result of the docking. So my question is then, how can you tell the molecule is different before and after?  It would have been much more useful to attach the before and after structures (coordinate files) than images of 2D chemical diagrams.
> 
> The following assumes that both structures you drew can exist as real chemicals.
> 
> Did it have hydrogens before you started the docking calculation? If not, it may be that the autodock ligand preparation script added hydrogens and had trouble identifying the bond orders (maybe the bond length is similar with single or aromatic bond) and added 1 H instead of 2 to each of those atoms.  In that case you could try adding hydrogens to the ligand with Chimera instead (e.g. command ?addh? or AddH tool) 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>
> before docking.  If Chimera has the same problem as the autodock ligand preparation script, then delete the ligand hydrogens and make sure the atom types are assigned to sp3 carbon before trying to add them back again.  For example, select those two carbon atoms (Ctrl-click, Shift-Ctrl-click) and then use setattr command, something like:
> 
> setattr a idatmType C3 sel
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>
> 
> Then add hydrogens, check that they are as expected, then do the docking.  Or you could use any other program/method to add hydrogens before opening the ligand structure in Chimera.
> 
> It may not make much difference since if I remember correctly, Vina doesn?t even use the hydrogens except to identify the types of the other atoms.  You would have to check the literature references to be sure about that, however.
> 
> Finally:
> Note that the Autodock Vina tool uses a web server that only allows very little sampling, which is not adequate for most research purposes, as mentioned in the boxed warning on the manual page.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Feb 7, 2020, at 2:45 PM, Greta Hodo <gretahodo96 at hotmail.com> wrote:
> > 
> > Hi,
> > I have a problem with the result of autodock Vina. When I load a molecule in ?mol2? format and I use AutoDock Vina for docking, the docked molecule is altered. How can be possible? How can I solve my problem? 
> > 
> > I attach the photo of the real molecule <image0.jpeg>
> > 
> > And this I how the molecule changes after the docking 
> > <image1.jpeg>
> > The 5-term ring becomes aromatic, while it should have only a double bond. ( this happens both if I save autodock vina result in ?mol2? format and ?pdb? format
> > 
> > Hope you can help me!
> 
> <img1.png><img2.png>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From meng at cgl.ucsf.edu  Mon Feb 10 10:36:54 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 10 Feb 2020 10:36:54 -0800
Subject: [Chimera-users] S1-8
In-Reply-To: <tencent_3507CC673AAADEFFA2CABE2A6705C8111009@qq.com>
References: <tencent_3507CC673AAADEFFA2CABE2A6705C8111009@qq.com>
Message-ID: <FE138094-D571-4E28-8F68-83540CEC29CB@cgl.ucsf.edu>

Hi Lin l,
It appears that the movie was first made in Chimera, but then some other software was used to add the colored blobs and probably the white labels afterward.  There is no Chimera option to make arbitrary shapes like that.

However, you can add text and symbols with the 2d Labels tool or 2dlabels command, 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html>

...so you could add any shape that is available as a symbol.  For example, the circle or rounded-corner square can be copied from this page and pasted into the 2d Labels tool,
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/symbols.html>
... or specified as Unicode in the 2dlabels command, see the command manual page linked above.

You can change the colors and sizes of the 2d labels.  The movie command-file examples include some uses of the 2dlabels command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples>

(Or, you could choose to use some other software besides Chimera to annotate the movie after you make it.)

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

> On Feb 10, 2020, at 8:07 AM, ??? <444039430 at qq.com> wrote:
> 
> Dear management?
> I am a PHD student from Tianjin University in china. I saw a movie which is done in chimera (see the attachment), i saw they draw a circle around the text (NTD-A). i am very confuse that i do not know how to draw a shape in chimera. i ask for you that tell me how to draw a shape in command line. Thanks very much.
> Best wishes,
> 
> Lin l
> <S1-8.mp4>


From goddard at sonic.net  Mon Feb 10 15:14:52 2020
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 10 Feb 2020 15:14:52 -0800
Subject: [Chimera-users] [chimerax-users] Reproduce exact view
In-Reply-To: <13F7418A-F528-4961-892A-F0A8342B2113@cgl.ucsf.edu>
References: <CALmP0E+C_OQF0csWAkcuLm7-uGJ_jQU_Z6xY35T9iyorGuMEuw@mail.gmail.com>
 <CAM5goXSgvpdVQ7BTy-S3y4aWp=AmnPOU4YsT+PnrtawXtf8TBQ@mail.gmail.com>
 <64E72235-33BC-4895-9B8A-05B88ECA626C@cgl.ucsf.edu>
 <CAM5goXQzO5gMbNEp4-MM8Grnse2kMbxdKFq06O_7fu_JmpUpgQ@mail.gmail.com>
 <13F7418A-F528-4961-892A-F0A8342B2113@cgl.ucsf.edu>
Message-ID: <0365B314-9899-499A-8475-A8E6B868A18D@sonic.net>

Hi Elaine, Alexis,

  You can change a model number by command.  So if you replace model #3 with model #8 that you align to #3, then delete #3, then "rename #8 id #3" will change the model id of #8 to be #3.  For the step of aligning #8 to #3, if they are aligned already then #8 would open aligned to #3 unless you had moved #3 in which case you could use "view position #8 sameAs #3".  Of course if the new model has not been aligned to the old you may need to use the matchmaker command to align them.

	Tom


> On Feb 10, 2020, at 1:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Alexis,
> We removed the forward-compatibility warning during session saving a while ago, so as long as the version you?re using is not too old, we expect the session files to be forward compatible.  Still, I understand a reluctance to rely on them completely when it can take many hours or even days to set up everything the way you want.
> 
> Sometimes I just save the session now.  However, sometimes I use a ?belt and suspenders? approach by saving not just the session but also a command file that has just about everything I?d used for the setup except for interactive manual positioning.  I often include such a script  when I add a ?feature highlight? to the ChimeraX website.
> 
> I too have often wished for an easy way to replace one model in an existing session with another. Getting the matrices (view matrix), swapping out the model, and then reapplying the matrix may be the most exact way if the models are in the same coordinate system as each other.  Otherwise you could open the new model, match or fit it to the one you wish to replace, then close the one you want to get rid of.  That leaves you with different model numbers, however, so if it is important to get them the same you?d have to open the new model again, match it to itself, and remove the extra intermediate copy you?d opened first.  (Ugh.)
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Feb 10, 2020, at 1:22 PM, Alexis Rohou <a.rohou at gmail.com> wrote:
>> 
>> Thanks Elaine,
>> 
>> I should have added some explanation for my workflow:
>> 1. I read a while back that ChimeraX sessions may or may not be forward compatible, and I wanted to ensure long-term reproducibility of my figures
>> 2. a requirement I have is that I should be able to quickly remake the exact same figure after I change the input files. For example, perhaps I prototype an elaborate figure using a PDB that's a work in progress and later re-make it with an updated PDB. The advantage of a .cxc script is that I just have to change the filename near the beginning of the script and everything else stays the same. I can regenerate all my figures pretty quickly that way. That's the big payoff for investing the time to write a script upfront.
>> 
>> The view functionality does sound very nice though, especially since I don't currently have a way to achieve transitions with my scripts (other than perhaps creating views within the scripts themselves?). Elaine, is there a way to use sessions so that I could replace a model or map with a new version of a file after I've already created a session?
>> 
>> Cheers,
>> Alexis
>> 
>> On Mon, Feb 10, 2020 at 9:26 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hello,
>> Maybe I?m missing something, but the ?view? command allows saving and restoring named views.  These are included in saved session files.  I agree window size is also a factor, so you would make sure to set the same window size too.
>> 
>> E.g. once you have the view you like then use a command like:
>> 
>> view name myview
>> 
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name>
>> 
>> Then you can save the session file and/or move things around.  Later in the same session or after restoring the previously saved session from file,
>> 
>> view myview
>> 
>> ?will restore that view.  Restoring the session restores window size if you have that Window Preference set:
>> <http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#window>
>> 
>> or you could have noted the window size when you saved the view:
>> 
>> windowsize
>> 
>> ?and then use the reported values later to restore that size, e.g.
>> 
>> windowsize 600 400
>> 
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/windowsize.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 Feb 10, 2020, at 8:53 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
>>> 
>>> Hi Christophe,
>>> 
>>> I prepare my figures using ChimeraX command (.cxc) scripts and I believe I have a workflow that lets me reproduce exact views. I know it's not 100% robust, but it's reliable enough for me. It basically relies on a sequence of close; windowsize; view matrix; zoom; clip; save.
>>> 
>>> Here is a pseudo script. To work out the values you need for the matrices, just move your point of view and your models until you are happy, then do "view matrix".  I have not worked out a good way to get the distances for the clip planes. So I just play with them on the command line until I get the look I want, then save the values in my cxc file.
>>> 
>>> Hope this helps & that more experienced users can chime in with improvements.
>>> 
>>> Cheers,
>>> Alexis
>>> 
>>> 
>>> # close anything currently open
>>> close
>>> # go to relevant directory
>>> cd /my/absolute/path
>>> # 
>>> windowsize 1200 1200
>>> camera ortho
>>> clip near off far off front off back off
>>> # Open files
>>> open my_model.pdb name "my model"
>>> open my_map.mrc name "my map"
>>> # etc.
>>> 
>>> #insert here coloring, styles, for the model/map/background etc
>>> 
>>> # Go to your favorite view point, save a shot
>>> view matrix camera 1,0,0,182.59,0,1,0,229.79,0,0,1,352.89
>>> zoom 0.33
>>> clip near off far off front off back off; clip near -100.0 far +100.0 front off back off
>>> ~select
>>> save my_figure.png supersample 3 transparentBackground false
>>> 
>>> # If you need to move your models
>>> view matrix models #1,0.91269,-0.0093359,-0.40855,59.153,-0.40865,-0.018906,-0.91249,368.7,0.00079806,0.99977,-0.02107,-44.893,#2,-0.83654,-0.058918,-0.54474,344.52,-0.54355,-0.035951,0.83861,293.33,-0.068993,0.99762,-0.0019503,-42.032
>>> 
>>> # then take another shot
>>> view matrix camera 0.98289,-0.005269,-0.18408,131.07,-0.17421,-0.3506,-0.92018,70.662,-0.059691,0.93651,-0.34553,163.8
>>> clip near off far off front off back off; clip near -20.0 far +12.0 front off back off
>>> save Figures/TRPA1_3551_binding_site_details1.png supersample 3 transparentBackground false
>>> 
>>> 
>>> 
>>> 
>>> On Sun, Feb 9, 2020 at 10:01 AM Christophe Leterrier <christophe.leterrier at gmail.com> wrote:
>>> Hi,
>>> 
>>> I haven't been able to find how to
>>> - log
>>> - set
>>> - store
>>> - recall
>>> 
>>> a precise view (ie get the same exact image if I do a snapshot). 
>>> 
>>> First use case would within the same session (fixed computer, window size, no restart of the application in between). Second use case (more tricky?) would be independently of computer / window size / current session.
>>> 
>>> Thanks for your help!
>>> 
>>> Christophe
>> 
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu
>> Manage subscription:
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
> 



From Trevor.Rapson at csiro.au  Mon Feb 10 19:05:23 2020
From: Trevor.Rapson at csiro.au (Rapson, Trevor (A&F, Black Mountain))
Date: Tue, 11 Feb 2020 03:05:23 +0000
Subject: [Chimera-users] problem saving images
Message-ID: <SYAPR01MB2414DD3276A2D2CCB2133D8993180@SYAPR01MB2414.ausprd01.prod.outlook.com>

Dear Chimera team,
I have recently come across a problem saving images in Chimera where it saves the image but it opens as a completely black image (and very small file size).
I've tried changing a few different settings and that doesn't help. The error also seems to be there with when I save a video.
Your help is much appreciated.
Regards,
Trevor

Dr Trevor Rapson
Research Scientist
Agriculture and Food
CSIRO

Phone: +61 2 6246 4104
Trevor.Rapson at csiro.au<mailto:Trevor.Rapson at csiro.au>| www.csiro.au<http://www.csiro.au/>
Address: P.O. Box 1700, Canberra, ACT, Australia


PLEASE NOTE
The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference.

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From 444039430 at qq.com  Mon Feb 10 19:31:45 2020
From: 444039430 at qq.com (=?gb18030?B?wdbBqtTG?=)
Date: Tue, 11 Feb 2020 11:31:45 +0800
Subject: [Chimera-users] =?gb18030?b?u9i4tKO6ICBTMS04?=
In-Reply-To: <FE138094-D571-4E28-8F68-83540CEC29CB@cgl.ucsf.edu>
References: <tencent_3507CC673AAADEFFA2CABE2A6705C8111009@qq.com>
 <FE138094-D571-4E28-8F68-83540CEC29CB@cgl.ucsf.edu>
Message-ID: <tencent_B48824E6061D7FEF08518B5F83B3DBE43A08@qq.com>

Dear Elaine Meng,


I got it and thanks very much.


Best wishes


Lin L.


------------------&nbsp;????&nbsp;------------------
???:&nbsp;"Elaine Meng"<meng at cgl.ucsf.edu&gt;;
????:&nbsp;2020?2?11?(???) ??2:36
???:&nbsp;"???"<444039430 at qq.com&gt;;
??:&nbsp;"chimera-users"<chimera-users at cgl.ucsf.edu&gt;;
??:&nbsp;Re: [Chimera-users] S1-8



Hi Lin l,
It appears that the movie was first made in Chimera, but then some other software was used to add the colored blobs and probably the white labels afterward.&nbsp; There is no Chimera option to make arbitrary shapes like that.

However, you can add text and symbols with the 2d Labels tool or 2dlabels command, 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html&gt;
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html&gt;

...so you could add any shape that is available as a symbol.&nbsp; For example, the circle or rounded-corner square can be copied from this page and pasted into the 2d Labels tool,
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/symbols.html&gt;
... or specified as Unicode in the 2dlabels command, see the command manual page linked above.

You can change the colors and sizes of the 2d labels.&nbsp; The movie command-file examples include some uses of the 2dlabels command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples&gt;

(Or, you could choose to use some other software besides Chimera to annotate the movie after you make it.)

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

&gt; On Feb 10, 2020, at 8:07 AM, ??? <444039430 at qq.com&gt; wrote:
&gt; 
&gt; Dear management?
&gt; I am a PHD student from Tianjin University in china. I saw a movie which is done in chimera (see the attachment), i saw they draw a circle around the text (NTD-A). i am very confuse that i do not know how to draw a shape in chimera. i ask for you that tell me how to draw a shape in command line. Thanks very much.
&gt; Best wishes,
&gt; 
&gt; Lin l
&gt; <S1-8.mp4&gt;
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From gretahodo96 at hotmail.com  Mon Feb 10 20:24:29 2020
From: gretahodo96 at hotmail.com (Greta Hodo)
Date: Tue, 11 Feb 2020 04:24:29 +0000
Subject: [Chimera-users] R:  Docking
In-Reply-To: <2A83A52C-94AC-4B8E-AF59-115E8CB41059@cgl.ucsf.edu>
References: <PR2PR03MB5404B20FB557F978EB4DD05FA91C0@PR2PR03MB5404.eurprd03.prod.outlook.com>
 <AAE41717-4EF7-45D0-9C0B-846FF64AF600@cgl.ucsf.edu>
 <PR2PR03MB5404AAE3AAC393F291A8FE95A91F0@PR2PR03MB5404.eurprd03.prod.outlook.com>,
 <2A83A52C-94AC-4B8E-AF59-115E8CB41059@cgl.ucsf.edu>
Message-ID: <PR2PR03MB540460C84C7667316389161AA9180@PR2PR03MB5404.eurprd03.prod.outlook.com>

Hi Elaine,
I did as you suggested me and I solved the problem, so thank you very much! Thank you for your time and for your quick answers

Best,
Greta 

> Il giorno 10 feb 2020, alle ore 19:17, Elaine Meng <meng at cgl.ucsf.edu> ha scritto:
> 
> ?Hi Greta,
> In the ?Ligand options? try turning off  ?Merge charges and remove non-polar hydrogens,? i.e. set it to ?false?:
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> 
> That?s my only idea at this point.  However, it still doesn?t make sense because if you had it set to ?true? there should not be any hydrogens on the carbons in the output.
> 
> Elaine
> 
>> On Feb 7, 2020, at 5:11 PM, Greta Hodo <gretahodo96 at hotmail.com> wrote:
>> 
>> Hi Elaine,
>> thank you for the quick answer.
>> Before I start the docking calculation my molecule has all the hydrogens as expected (as you can see in the ''img1'' file attached you). After the docking calculation with Autodock Vina the molecule changes (as you can see in the ''img2'' file). How can I solve the problem?
>> 
>> Best,
>> Greta
>> 
>> Da: Elaine Meng <meng at cgl.ucsf.edu>
>> Inviato: sabato 8 febbraio 2020 01:16
>> A: Greta Hodo <gretahodo96 at hotmail.com>
>> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
>> Oggetto: Re: [Chimera-users] Docking
>> 
>> Hi Greta,
>> I guess the only difference is whether the two carbons in the 5-member ring are CH or CH2, because Chimera does not use (or change) bond orders.  Are you sure that both structures can exist as real chemicals?  Maybe Chimera guesses it is an aromatic ring (more on this below) but that would also be true as soon as you opened the ligand structure, not as a result of the docking. So my question is then, how can you tell the molecule is different before and after?  It would have been much more useful to attach the before and after structures (coordinate files) than images of 2D chemical diagrams.
>> 
>> The following assumes that both structures you drew can exist as real chemicals.
>> 
>> Did it have hydrogens before you started the docking calculation? If not, it may be that the autodock ligand preparation script added hydrogens and had trouble identifying the bond orders (maybe the bond length is similar with single or aromatic bond) and added 1 H instead of 2 to each of those atoms.  In that case you could try adding hydrogens to the ligand with Chimera instead (e.g. command ?addh? or AddH tool) 
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>
>> before docking.  If Chimera has the same problem as the autodock ligand preparation script, then delete the ligand hydrogens and make sure the atom types are assigned to sp3 carbon before trying to add them back again.  For example, select those two carbon atoms (Ctrl-click, Shift-Ctrl-click) and then use setattr command, something like:
>> 
>> setattr a idatmType C3 sel
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>
>> 
>> Then add hydrogens, check that they are as expected, then do the docking.  Or you could use any other program/method to add hydrogens before opening the ligand structure in Chimera.
>> 
>> It may not make much difference since if I remember correctly, Vina doesn?t even use the hydrogens except to identify the types of the other atoms.  You would have to check the literature references to be sure about that, however.
>> 
>> Finally:
>> Note that the Autodock Vina tool uses a web server that only allows very little sampling, which is not adequate for most research purposes, as mentioned in the boxed warning on the manual page.
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
>> 
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>>> On Feb 7, 2020, at 2:45 PM, Greta Hodo <gretahodo96 at hotmail.com> wrote:
>>> 
>>> Hi,
>>> I have a problem with the result of autodock Vina. When I load a molecule in ?mol2? format and I use AutoDock Vina for docking, the docked molecule is altered. How can be possible? How can I solve my problem? 
>>> 
>>> I attach the photo of the real molecule <image0.jpeg>
>>> 
>>> And this I how the molecule changes after the docking 
>>> <image1.jpeg>
>>> The 5-term ring becomes aromatic, while it should have only a double bond. ( this happens both if I save autodock vina result in ?mol2? format and ?pdb? format
>>> 
>>> Hope you can help me!
>> 
>> <img1.png><img2.png>_______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 


From goddard at sonic.net  Tue Feb 11 10:59:39 2020
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 11 Feb 2020 10:59:39 -0800
Subject: [Chimera-users] problem saving images
In-Reply-To: <SYAPR01MB2414DD3276A2D2CCB2133D8993180@SYAPR01MB2414.ausprd01.prod.outlook.com>
References: <SYAPR01MB2414DD3276A2D2CCB2133D8993180@SYAPR01MB2414.ausprd01.prod.outlook.com>
Message-ID: <359B269C-A312-4AFF-8F70-28A7005DD79E@sonic.net>

Black saved images from Chimera almost always means your system graphics driver is buggy and updating the graphics driver is the solution.  Sometimes saving images with no supersampling (1x1) works for such drivers.  But movie recording uses no supersampling by default so if your movies are black then that probably will not help.

	Tom


> On Feb 10, 2020, at 7:05 PM, Rapson, Trevor (A&F, Black Mountain) <Trevor.Rapson at csiro.au> wrote:
> 
> Dear Chimera team,
> I have recently come across a problem saving images in Chimera where it saves the image but it opens as a completely black image (and very small file size).
> I?ve tried changing a few different settings and that doesn?t help. The error also seems to be there with when I save a video.
> Your help is much appreciated.
> Regards,
> Trevor
>  
> Dr Trevor Rapson
> Research Scientist 
> Agriculture and Food 
> CSIRO
>  
> Phone: +61 2 6246 4104
> Trevor.Rapson at csiro.au <mailto:Trevor.Rapson at csiro.au>| www.csiro.au <http://www.csiro.au/> 
> Address: P.O. Box 1700, Canberra, ACT, Australia
>  
>  
> PLEASE NOTE
> The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference.
>  
> Please consider the environment before printing this email.
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From emailanindito at yahoo.co.in  Tue Feb 11 19:29:06 2020
From: emailanindito at yahoo.co.in (Anindito Sen)
Date: Wed, 12 Feb 2020 03:29:06 +0000 (UTC)
Subject: [Chimera-users] changing density map from surface to mesh view
References: <417221180.1409866.1581478146923.ref@mail.yahoo.com>
Message-ID: <417221180.1409866.1581478146923@mail.yahoo.com>

Dear All,
While making a movie, what will be the command to change view of the density map from surface to mesh.
Regards

Anindito Sen. Ph.D

Microscopy and Imaging Center??
Texas A&M University?
301 Old Main Dr
College Station, TX 77843-2257
?
Office: ILSB Room 1133
Tel. 979-458-9881
fax: 979-847-8933

http://microscopy.tamu.edu

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From Semchonok at gmail.com  Wed Feb 12 05:57:37 2020
From: Semchonok at gmail.com (Dmitry Semchonok)
Date: Wed, 12 Feb 2020 14:57:37 +0100
Subject: [Chimera-users] Map is not visible in COOT
Message-ID: <BBAE2878-DAB9-49DD-A670-A2E503543CE5@gmail.com>

Dear colleagues,

I have cryo-em map saved in chimera.

But when we want to open it in with COOT the map is not visible.

Could you please give me any suggestions?

Thank you 

Sincerely,
Dmitry

From meng at cgl.ucsf.edu  Wed Feb 12 09:22:16 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 12 Feb 2020 09:22:16 -0800
Subject: [Chimera-users] changing density map from surface to mesh view
In-Reply-To: <417221180.1409866.1581478146923@mail.yahoo.com>
References: <417221180.1409866.1581478146923.ref@mail.yahoo.com>
 <417221180.1409866.1581478146923@mail.yahoo.com>
Message-ID: <3712813D-2309-4074-9F12-85DC19A09B6A@cgl.ucsf.edu>

Hi Anindito,
?volume? command ?style? option, e.g.

volume #4 style mesh
- or -
volume all style mesh

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.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 Feb 11, 2020, at 7:29 PM, Anindito Sen <emailanindito at yahoo.co.in> wrote:
> 
> Dear All,
> 
> While making a movie, what will be the command to change view of the density map from surface to mesh.
> 
> Regards
> 
> Anindito Sen. Ph.D



From goddard at sonic.net  Wed Feb 12 16:16:29 2020
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 12 Feb 2020 16:16:29 -0800
Subject: [Chimera-users] Map is not visible in COOT
In-Reply-To: <BBAE2878-DAB9-49DD-A670-A2E503543CE5@gmail.com>
References: <BBAE2878-DAB9-49DD-A670-A2E503543CE5@gmail.com>
Message-ID: <3F4A9487-C67C-4353-934A-843D8FBDABFC@sonic.net>

Hi Dmitry,

When you open the saved map in Chimera does it display correctly?  What map format are you using?  MRC?  What is the range of map values shown in Chimera volume viewer?  What are the origin index, voxel size and cell angles listed in the Chimera Volume Viewer coordinates panel (volume viewer menu Features / Coordinates)?  Have you ever saved a map in Chimera that does display in Coot?

I don't know what limitations Coot might have in the maps it can handle.  It seems more likely that Coot users or developers would be able to explain it.

	Tom



> On Feb 12, 2020, at 5:57 AM, Dmitry Semchonok <semchonok at gmail.com> wrote:
> 
> Dear colleagues,
> 
> I have cryo-em map saved in chimera.
> 
> But when we want to open it in with COOT the map is not visible.
> 
> Could you please give me any suggestions?
> 
> Thank you 
> 
> Sincerely,
> Dmitry
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From martingonzalezbuitron at gmail.com  Thu Feb 13 16:00:08 2020
From: martingonzalezbuitron at gmail.com (=?UTF-8?B?TWFydMOtbiBHb256w6FsZXogQnVpdHLDs24=?=)
Date: Fri, 14 Feb 2020 01:00:08 +0100
Subject: [Chimera-users] Default storage folder, ChimeraX
Message-ID: <CAOcbgHh-1yE5TdX=uFJU6kU4PEDu48viAb6fGUpkxuyMbkTrtw@mail.gmail.com>

Dears all,

Hope you are well.

I have started to use ChimeraX in Ubuntu and I realised that one folder was
created with my fetches and other things (i.e. ~/Download/ChimeraX/).

How can I change this to other of my own preference?

All the best,
Mart?n
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From J.Healey.1 at warwick.ac.uk  Fri Feb 14 02:09:22 2020
From: J.Healey.1 at warwick.ac.uk (Healey, Joseph)
Date: Fri, 14 Feb 2020 10:09:22 +0000
Subject: [Chimera-users] SplitCommand python
Message-ID: <D1E6FC7D-365D-4F06-B612-232B6DF9452D@live.warwick.ac.uk>

Hi Chimera Team,

I?m trying to reduce some overheads in one of my scripts part of which is coming from my use of `runCommand`. At the moment, I?m only using it for `split`, but I?d like to first test whether a model is already split to avoid unnecessary invocation.

I?m aware the python equivalent of the command is buried inside chimera.SplitMolecule and the command split_command, however it doesn?t seem to be importable, as when I try:

>>> from chimera import SplitMolecule
Traceback (most recent call last):
  File "<pyshell#25>", line 2, in <module>
ImportError: cannot import name SplitMolecule

I?m getting the above ImportError. I can import other members of the chimera class (e.g. chimera.openModels or chimera.Molecule and chimera itself without issue). I?ve seen in the source code that SplitMolecule gets imported elsewhere, and it has the __init__ file, so I assume I?m just doing something stupid with paths or similar. That said, SplitMolecule is clearly within the main chimera modules directory, so I would have expected it to only be one ?layer? below `chimera` itself. Can you elighten me?

I?m currently on chimera production version 1.14 (build 42094) 2019-11-13 06:05:13 UTC if that helps.

If you could point me in the right direction to understand how the code will check for multiple chains and decide to split by chain, that would also be a massive help.

Many thanks,

Joe


Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB
Research Fellow
Warwick Medical School
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620  | Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
Email: J.Healey.1 at warwick.ac.uk<mailto:J.Healey.1 at warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

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From meng at cgl.ucsf.edu  Fri Feb 14 08:37:01 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 14 Feb 2020 08:37:01 -0800
Subject: [Chimera-users] Default storage folder, ChimeraX
In-Reply-To: <CAOcbgHh-1yE5TdX=uFJU6kU4PEDu48viAb6fGUpkxuyMbkTrtw@mail.gmail.com>
References: <CAOcbgHh-1yE5TdX=uFJU6kU4PEDu48viAb6fGUpkxuyMbkTrtw@mail.gmail.com>
Message-ID: <1125681E-F16E-4936-A0AE-88C16DDB556D@cgl.ucsf.edu>

Hi Mart?n,
Currently there is no way in the user interface to change the ChimeraX downloads location, described here:

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch>

You could make a symbolic link to that location, but the files would still really be in the same place. 

Probably the location can be changed by editing somewhere in the Python code, but somebody else would have to advise on that.

You may be interested that there is a separate mailing list for ChimeraX, chimerax-users at cgl.ucsf.edu (CC?d on this message).
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 13, 2020, at 4:00 PM, Mart?n Gonz?lez Buitr?n <martingonzalezbuitron at gmail.com> wrote:
> 
> Dears all,
> Hope you are well.
> 
> I have started to use ChimeraX in Ubuntu and I realised that one folder was created with my fetches and other things (i.e. ~/Download/ChimeraX/).
> 
> How can I change this to other of my own preference?
> All the best,
> Mart?n



From pett at cgl.ucsf.edu  Fri Feb 14 08:50:18 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 14 Feb 2020 08:50:18 -0800
Subject: [Chimera-users] [chimerax-users]  Default storage folder,
	ChimeraX
In-Reply-To: <1125681E-F16E-4936-A0AE-88C16DDB556D@cgl.ucsf.edu>
References: <CAOcbgHh-1yE5TdX=uFJU6kU4PEDu48viAb6fGUpkxuyMbkTrtw@mail.gmail.com>
 <1125681E-F16E-4936-A0AE-88C16DDB556D@cgl.ucsf.edu>
Message-ID: <A9615C27-CF7D-4A8C-B21D-218F9DEA64D9@cgl.ucsf.edu>

If the reason you want to change the location is to put the storage on another disk, then you can use the ?symbolic link trick? in the other direction.  For instance, to have the file stored in /volumes/data/chimerax (and assuming /volumes/data/chimerax does not exist):

	mv ~/Downloads/ChimeraX /volumes/data/chimerax ; ln -s /volumes/data/chimerax ~/Downloads/ChimeraX

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Feb 14, 2020, at 8:37 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Mart?n,
> Currently there is no way in the user interface to change the ChimeraX downloads location, described here:
> 
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch>>
> 
> You could make a symbolic link to that location, but the files would still really be in the same place. 
> 
> Probably the location can be changed by editing somewhere in the Python code, but somebody else would have to advise on that.
> 
> You may be interested that there is a separate mailing list for ChimeraX, chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu> (CC?d on this message).
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Feb 13, 2020, at 4:00 PM, Mart?n Gonz?lez Buitr?n <martingonzalezbuitron at gmail.com> wrote:
>> 
>> Dears all,
>> Hope you are well.
>> 
>> I have started to use ChimeraX in Ubuntu and I realised that one folder was created with my fetches and other things (i.e. ~/Download/ChimeraX/).
>> 
>> How can I change this to other of my own preference?
>> All the best,
>> Mart?n
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
> Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users>
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From goddard at sonic.net  Fri Feb 14 09:30:14 2020
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 14 Feb 2020 09:30:14 -0800
Subject: [Chimera-users] SplitCommand python
In-Reply-To: <D1E6FC7D-365D-4F06-B612-232B6DF9452D@live.warwick.ac.uk>
References: <D1E6FC7D-365D-4F06-B612-232B6DF9452D@live.warwick.ac.uk>
Message-ID: <C465AAC0-FE0C-43C7-8628-458C5FA69CA0@sonic.net>

Hi Joe,

  You need to use

    import SplitMolecule

It is not a submodule of the chimera module.  I am not sure why we made all the Chimera tools be top level modules instead of under the chimera module.

  Are you splitting to make each chain a separate model?  If so then checking if a molecule needs splitting is the same as checking if it has one chain.

   Tom

> On Feb 14, 2020, at 8:14 AM, Healey, Joseph <J.Healey.1 at warwick.ac.uk> wrote:
> 
> ?
> Hi Chimera Team,
>  
> I?m trying to reduce some overheads in one of my scripts part of which is coming from my use of `runCommand`. At the moment, I?m only using it for `split`, but I?d like to first test whether a model is already split to avoid unnecessary invocation.
>  
> I?m aware the python equivalent of the command is buried inside chimera.SplitMolecule and the command split_command, however it doesn?t seem to be importable, as when I try:
>  
> >>> from chimera import SplitMolecule
> Traceback (most recent call last):
>   File "<pyshell#25>", line 2, in <module>
> ImportError: cannot import name SplitMolecule
>  
> I?m getting the above ImportError. I can import other members of the chimera class (e.g. chimera.openModels or chimera.Molecule and chimera itself without issue). I?ve seen in the source code that SplitMolecule gets imported elsewhere, and it has the __init__ file, so I assume I?m just doing something stupid with paths or similar. That said, SplitMolecule is clearly within the main chimera modules directory, so I would have expected it to only be one ?layer? below `chimera` itself. Can you elighten me?
>  
> I?m currently on chimera production version 1.14 (build 42094) 2019-11-13 06:05:13 UTC if that helps.
>  
> If you could point me in the right direction to understand how the code will check for multiple chains and decide to split by chain, that would also be a massive help.
>  
> Many thanks,
>  
> Joe
>  
>                                                                                    
> Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB
> Research Fellow
> Warwick Medical School
> University of Warwick
> Coventry
> CV47AL
> Mob: +44 (0) 7536 042620  | Twitter: @JRJHealey  |  Website
> Email: J.Healey.1 at warwick.ac.uk | ORCID: orcid.org/0000-0002-9569-6738
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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From goddard at sonic.net  Fri Feb 14 10:33:48 2020
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 14 Feb 2020 10:33:48 -0800
Subject: [Chimera-users] SplitCommand python
In-Reply-To: <D1E6FC7D-365D-4F06-B612-232B6DF9452D@live.warwick.ac.uk>
References: <D1E6FC7D-365D-4F06-B612-232B6DF9452D@live.warwick.ac.uk>
Message-ID: <FA10907F-4BF6-4354-975F-6298E76CBA80@sonic.net>

Here is a bit a Python code to count the number of chains in a molecule m.

>>> import chimera
>>> m = chimera.openModels.list()[0]
>>> m
<_molecule.Molecule object at 0x7fb988fed620>
>>> len(set(r.id.chainId for r in m.residues))
4

We have been working on ChimeraX the replacement for Chimera for a few years and it is quite a bit nicer.  In ChimeraX the code would be

m = session.models.list()[0]
m.num_chains

  Tom

> On Feb 14, 2020, at 2:09 AM, Healey, Joseph <J.Healey.1 at warwick.ac.uk> wrote:
> 
> Hi Chimera Team,
>  
> I?m trying to reduce some overheads in one of my scripts part of which is coming from my use of `runCommand`. At the moment, I?m only using it for `split`, but I?d like to first test whether a model is already split to avoid unnecessary invocation.
>  
> I?m aware the python equivalent of the command is buried inside chimera.SplitMolecule and the command split_command, however it doesn?t seem to be importable, as when I try:
>  
> >>> from chimera import SplitMolecule
> Traceback (most recent call last):
>   File "<pyshell#25>", line 2, in <module>
> ImportError: cannot import name SplitMolecule
>  
> I?m getting the above ImportError. I can import other members of the chimera class (e.g. chimera.openModels or chimera.Molecule and chimera itself without issue). I?ve seen in the source code that SplitMolecule gets imported elsewhere, and it has the __init__ file, so I assume I?m just doing something stupid with paths or similar. That said, SplitMolecule is clearly within the main chimera modules directory, so I would have expected it to only be one ?layer? below `chimera` itself. Can you elighten me?
>  
> I?m currently on chimera production version 1.14 (build 42094) 2019-11-13 06:05:13 UTC if that helps.
>  
> If you could point me in the right direction to understand how the code will check for multiple chains and decide to split by chain, that would also be a massive help.
>  
> Many thanks,
>  
> Joe
>  
>                                                                                    
> Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB
> Research Fellow
> Warwick Medical School
> University of Warwick
> Coventry
> CV47AL
> Mob: +44 (0) 7536 042620  | Twitter: @JRJHealey <https://twitter.com/JRJHealey>  |  Website <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
> Email: J.Healey.1 at warwick.ac.uk <mailto:J.Healey.1 at warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738 <http://orcid.org/0000-0002-9569-6738>
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From goddard at sonic.net  Fri Feb 14 10:42:10 2020
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 14 Feb 2020 10:42:10 -0800
Subject: [Chimera-users] Coloring N-terminal and C-terminal
In-Reply-To: <CAJ_F9u8TE069BCm0tWbskpwnbe9dcPuoZNQZrZL3+N6o4+S6-Q@mail.gmail.com>
References: <597EB1F3-960A-49AE-ABEF-DBE67A4B80C3@wustl.edu>
 <1574171782l.14286984l.0l@psu.edu>
 <4F8F62EA-1802-4D10-A8CB-C83F800F6F10@cgl.ucsf.edu>
 <E4FDDAEB-B4E0-48CB-BA9E-F77BDEDF2BB2@sonic.net>
 <CAJ_F9u8TE069BCm0tWbskpwnbe9dcPuoZNQZrZL3+N6o4+S6-Q@mail.gmail.com>
Message-ID: <551D43B8-EDB5-4F2E-8305-0C1ACEE65970@sonic.net>

You can rainbow color proteins from N (blue) to C (red) terminus to see where the ends are using menu Tools / Depiction / Rainbow, or the command rainbow.

	Tom


> On Feb 14, 2020, at 1:32 AM, Nail Besli  wrote:
> 
> how can I detect the N-terminal or C-teminal after docking of two proteins in Chimera 
> Thanks 
> 



From beslinail at gmail.com  Fri Feb 14 05:55:07 2020
From: beslinail at gmail.com (Nail Besli)
Date: Fri, 14 Feb 2020 16:55:07 +0300
Subject: [Chimera-users] Coloring N-terminal and C-terminal
In-Reply-To: <551D43B8-EDB5-4F2E-8305-0C1ACEE65970@sonic.net>
References: <597EB1F3-960A-49AE-ABEF-DBE67A4B80C3@wustl.edu>
 <1574171782l.14286984l.0l@psu.edu>
 <4F8F62EA-1802-4D10-A8CB-C83F800F6F10@cgl.ucsf.edu>
 <E4FDDAEB-B4E0-48CB-BA9E-F77BDEDF2BB2@sonic.net>
 <CAJ_F9u8TE069BCm0tWbskpwnbe9dcPuoZNQZrZL3+N6o4+S6-Q@mail.gmail.com>
 <551D43B8-EDB5-4F2E-8305-0C1ACEE65970@sonic.net>
Message-ID: <CAJ_F9u-2-4PN3czhsEk=s8eFGg17Hsg4quJHHnF8PVC2A4GF9w@mail.gmail.com>

Awesome, thanks!

On Fri, Feb 14, 2020 at 9:42 PM Tom Goddard <goddard at sonic.net> wrote:

> You can rainbow color proteins from N (blue) to C (red) terminus to see
> where the ends are using menu Tools / Depiction / Rainbow, or the command
> rainbow.
>
>         Tom
>
>
> > On Feb 14, 2020, at 1:32 AM, Nail Besli  wrote:
> >
> > how can I detect the N-terminal or C-teminal after docking of two
> proteins in Chimera
> > Thanks
> >
>
>
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From martingonzalezbuitron at gmail.com  Fri Feb 14 08:39:01 2020
From: martingonzalezbuitron at gmail.com (=?UTF-8?B?TWFydMOtbiBHb256w6FsZXogQnVpdHLDs24=?=)
Date: Fri, 14 Feb 2020 17:39:01 +0100
Subject: [Chimera-users] Default storage folder, ChimeraX
In-Reply-To: <1125681E-F16E-4936-A0AE-88C16DDB556D@cgl.ucsf.edu>
References: <CAOcbgHh-1yE5TdX=uFJU6kU4PEDu48viAb6fGUpkxuyMbkTrtw@mail.gmail.com>
 <1125681E-F16E-4936-A0AE-88C16DDB556D@cgl.ucsf.edu>
Message-ID: <CAOcbgHjatZ-uk9KtEyjDds8rCCpW_qEirvWAq=4n5F8hZs86wQ@mail.gmail.com>

Thanks a lot!

I will try to see the python code!

All the best,
Mart?n

El vie., 14 feb. 2020 a las 17:37, Elaine Meng (<meng at cgl.ucsf.edu>)
escribi?:

> Hi Mart?n,
> Currently there is no way in the user interface to change the ChimeraX
> downloads location, described here:
>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch>
>
> You could make a symbolic link to that location, but the files would still
> really be in the same place.
>
> Probably the location can be changed by editing somewhere in the Python
> code, but somebody else would have to advise on that.
>
> You may be interested that there is a separate mailing list for ChimeraX,
> chimerax-users at cgl.ucsf.edu (CC?d on this message).
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Feb 13, 2020, at 4:00 PM, Mart?n Gonz?lez Buitr?n <
> martingonzalezbuitron at gmail.com> wrote:
> >
> > Dears all,
> > Hope you are well.
> >
> > I have started to use ChimeraX in Ubuntu and I realised that one folder
> was created with my fetches and other things (i.e. ~/Download/ChimeraX/).
> >
> > How can I change this to other of my own preference?
> > All the best,
> > Mart?n
>
>
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From jtfuller at chem.ucla.edu  Fri Feb 14 12:44:18 2020
From: jtfuller at chem.ucla.edu (Jack Fuller)
Date: Fri, 14 Feb 2020 12:44:18 -0800
Subject: [Chimera-users] Hydrogen labeling scheme
Message-ID: <7E8A2A00-283D-44FB-A7F6-BAFBE643BB33@chem.ucla.edu>

Hello,

I am part of a computational chemistry research group that frequently uses chimera to add hydrogens to pdbs.  My coworkers and I have noticed that chimera uses several different labeling schemes for hydrogens.  We have been unable to determine how chimera chooses which scheme to use.  Is there a way to specify which scheme to use or to know which scheme chimera will choose?

Thank you,
Jack Fuller




From abhisek.mndl at gmail.com  Fri Feb 14 23:37:53 2020
From: abhisek.mndl at gmail.com (abhisek Mondal)
Date: Fri, 14 Feb 2020 23:37:53 -0800
Subject: [Chimera-users] missing color option in model panel
Message-ID: <CA+DemH9hKHwsookDoJkcU7raRaH9PJ==pLOYgL+fz7RX5jRjYQ@mail.gmail.com>

Hi,

Newest version of chimera does not have the color option in the model
panel. Is this a bug of some sort?
Please see the attached image.

Regards
Abhisek

-- 
*Abhisek Mondal, Ph.D.*











*Cardiovascular Research InstituteUniversity of California San Francisco555
Mission Bay Blvd. South. Rm 482Dan Minor's LabSan Francisco, CA 94158USPS
address:UCSFAbhisek Mondal, Ph.D.Cardiovascular Research Institute, Box
3122555 Mission Bay Blvd., Floor 4San Francisco, CA 94143*
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From meng at cgl.ucsf.edu  Sat Feb 15 11:05:17 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 15 Feb 2020 11:05:17 -0800
Subject: [Chimera-users] missing color option in model panel
In-Reply-To: <CA+DemH9hKHwsookDoJkcU7raRaH9PJ==pLOYgL+fz7RX5jRjYQ@mail.gmail.com>
References: <CA+DemH9hKHwsookDoJkcU7raRaH9PJ==pLOYgL+fz7RX5jRjYQ@mail.gmail.com>
Message-ID: <75E6534D-48BA-45B5-A179-0946DE90AD90@cgl.ucsf.edu>

Hi Abhisek,
Volume models don?t have this color well in Model Panel.  The atomic models do.  It has always been this way, as far as I know.  See for example attached image with both kinds of models.

You can see/use color wells for the volume displays in the Volume Viewer tool.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Feb 14, 2020, at 11:37 PM, abhisek Mondal <abhisek.mndl at gmail.com> wrote:
> 
> Hi,
> Newest version of chimera does not have the color option in the model panel. Is this a bug of some sort?
> Please see the attached image.
> Regards
> Abhisek

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From yehuda.halfon at weizmann.ac.il  Mon Feb 17 07:03:17 2020
From: yehuda.halfon at weizmann.ac.il (Yehuda Halfon)
Date: Mon, 17 Feb 2020 15:03:17 +0000
Subject: [Chimera-users] Mx 230 gpu, chimera and chimerax
Message-ID: <AM0P191MB07554484EEA080A5902397DAD8160@AM0P191MB0755.EURP191.PROD.OUTLOOK.COM>

Hi all,
A friend of mine in my lab wants to buy a new laptop with mx230. Will it work fine with chimera and chimerax?

The cpu is i5-10210u and 8 GB of ram.


Thanks a lot,
Yehuda Halfon

PS

I know this isn't the chimerax mailing list but I hope to get a double answer in one mail
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From e.barzegari at kums.ac.ir  Mon Feb 17 00:55:01 2020
From: e.barzegari at kums.ac.ir (Ebrahim Barzegari)
Date: Mon, 17 Feb 2020 12:25:01 +0330
Subject: [Chimera-users] BLAST Database error
Message-ID: <1792d954cee24d12b8909c9acfa07eab@kums.ac.ir>

 
 I'm doing Blast protein for a single sequence. After selecting the 
database (pdb) and setting other params, I receive this error in Reply log: 

 BLAST Database error: Error: Not a valid version 4 database.
 How can I sort out it? 
 Thanks for help 
  
  

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From J.Healey.1 at warwick.ac.uk  Mon Feb 17 05:06:13 2020
From: J.Healey.1 at warwick.ac.uk (Healey, Joseph)
Date: Mon, 17 Feb 2020 13:06:13 +0000
Subject: [Chimera-users] SplitCommand python
In-Reply-To: <FA10907F-4BF6-4354-975F-6298E76CBA80@sonic.net>
References: <D1E6FC7D-365D-4F06-B612-232B6DF9452D@live.warwick.ac.uk>
 <FA10907F-4BF6-4354-975F-6298E76CBA80@sonic.net>
Message-ID: <C9BB09BA-9507-467C-B7F2-F2F98511C217@live.warwick.ac.uk>

Hi Tom,

Perfect ? thanks for clearing up the confusion!

I?m looking forward to moving over to scripting for ChimeraX (not least because I work on large structures), but it hasn?t quite got the featureset I need just yet?

Many thanks for the help,

Joe



Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB
Research Fellow
Warwick Medical School
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620  | Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
Email: J.Healey.1 at warwick.ac.uk<mailto:J.Healey.1 at warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738


From: Tom Goddard <goddard at sonic.net>
Date: Friday, 14 February 2020 at 18:34
To: "Healey, Joseph" <J.Healey.1 at warwick.ac.uk>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] SplitCommand python

Here is a bit a Python code to count the number of chains in a molecule m.

>>> import chimera
>>> m = chimera.openModels.list()[0]
>>> m
<_molecule.Molecule object at 0x7fb988fed620>
>>> len(set(r.id.chainId for r in m.residues))
4

We have been working on ChimeraX the replacement for Chimera for a few years and it is quite a bit nicer.  In ChimeraX the code would be

m = session.models.list()[0]
m.num_chains

  Tom

On Feb 14, 2020, at 2:09 AM, Healey, Joseph <J.Healey.1 at warwick.ac.uk<mailto:J.Healey.1 at warwick.ac.uk>> wrote:

Hi Chimera Team,

I?m trying to reduce some overheads in one of my scripts part of which is coming from my use of `runCommand`. At the moment, I?m only using it for `split`, but I?d like to first test whether a model is already split to avoid unnecessary invocation.

I?m aware the python equivalent of the command is buried inside chimera.SplitMolecule and the command split_command, however it doesn?t seem to be importable, as when I try:

>>> from chimera import SplitMolecule
Traceback (most recent call last):
  File "<pyshell#25>", line 2, in <module>
ImportError: cannot import name SplitMolecule

I?m getting the above ImportError. I can import other members of the chimera class (e.g. chimera.openModels or chimera.Molecule and chimera itself without issue). I?ve seen in the source code that SplitMolecule gets imported elsewhere, and it has the __init__ file, so I assume I?m just doing something stupid with paths or similar. That said, SplitMolecule is clearly within the main chimera modules directory, so I would have expected it to only be one ?layer? below `chimera` itself. Can you elighten me?

I?m currently on chimera production version 1.14 (build 42094) 2019-11-13 06:05:13 UTC if that helps.

If you could point me in the right direction to understand how the code will check for multiple chains and decide to split by chain, that would also be a massive help.

Many thanks,

Joe


Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB
Research Fellow
Warwick Medical School
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620  | Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
Email: J.Healey.1 at warwick.ac.uk<mailto:J.Healey.1 at warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738<http://orcid.org/0000-0002-9569-6738>

_______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From meng at cgl.ucsf.edu  Tue Feb 18 09:49:02 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 18 Feb 2020 09:49:02 -0800
Subject: [Chimera-users] BLAST Database error
In-Reply-To: <1792d954cee24d12b8909c9acfa07eab@kums.ac.ir>
References: <1792d954cee24d12b8909c9acfa07eab@kums.ac.ir>
Message-ID: <02E96241-7FCB-4DC2-BAC8-CCDD108E3EA7@cgl.ucsf.edu>

Hello,
I don?t see this problem, when testing with Chimera 1.13, 1.14 or current daily build.  

If you have an older version of Chimera, try getting the 1.14 release.
<http://www.rbvi.ucsf.edu/chimera/download.html>

If version 1.14 gives you the error it may be your specific input.  Use Chimera menu: Help? Report a Bug, and in the form describe everything needed to show the problem including the specific sequence you were searching with, and include your email if you want feedback.  This form is more useful than just sending email because it automatically includes information about your computer system and version of Chimera. 

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

> On Feb 17, 2020, at 12:55 AM, Ebrahim Barzegari <e.barzegari at kums.ac.ir> wrote:
> 
> I'm doing Blast protein for a single sequence. After selecting the database (pdb) and setting other params, I receive this error in Reply log: 
> BLAST Database error: Error: Not a valid version 4 database.
> How can I sort out it? 
> Thanks for help 
>  


From conrad at cgl.ucsf.edu  Tue Feb 18 10:00:00 2020
From: conrad at cgl.ucsf.edu (Conrad Huang)
Date: Tue, 18 Feb 2020 10:00:00 -0800
Subject: [Chimera-users] BLAST Database error
In-Reply-To: <02E96241-7FCB-4DC2-BAC8-CCDD108E3EA7@cgl.ucsf.edu>
References: <1792d954cee24d12b8909c9acfa07eab@kums.ac.ir>
 <02E96241-7FCB-4DC2-BAC8-CCDD108E3EA7@cgl.ucsf.edu>
Message-ID: <9ae5caea-bdac-b5c1-79b1-cb06c0be45da@cgl.ucsf.edu>

This problem was "fixed" last week on the cluster node that was running 
the BLAST service.  Unfortunately, the service migrated to an unfixed 
node, which is why you saw the error.  The problem should be fixed on 
all our cluster nodes now.  Sorry for the problem.

Conrad

On 2/18/2020 9:49 AM, Elaine Meng wrote:
> Hello,
> I don?t see this problem, when testing with Chimera 1.13, 1.14 or current daily build.
> 
> If you have an older version of Chimera, try getting the 1.14 release.
> <http://www.rbvi.ucsf.edu/chimera/download.html>
> 
> If version 1.14 gives you the error it may be your specific input.  Use Chimera menu: Help? Report a Bug, and in the form describe everything needed to show the problem including the specific sequence you were searching with, and include your email if you want feedback.  This form is more useful than just sending email because it automatically includes information about your computer system and version of Chimera.
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Feb 17, 2020, at 12:55 AM, Ebrahim Barzegari <e.barzegari at kums.ac.ir> wrote:
>>
>> I'm doing Blast protein for a single sequence. After selecting the database (pdb) and setting other params, I receive this error in Reply log:
>> BLAST Database error: Error: Not a valid version 4 database.
>> How can I sort out it?
>> Thanks for help
>>   
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

From goddard at sonic.net  Tue Feb 18 14:49:58 2020
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 18 Feb 2020 14:49:58 -0800
Subject: [Chimera-users] Mx 230 gpu, chimera and chimerax
In-Reply-To: <AM0P191MB07554484EEA080A5902397DAD8160@AM0P191MB0755.EURP191.PROD.OUTLOOK.COM>
References: <AM0P191MB07554484EEA080A5902397DAD8160@AM0P191MB0755.EURP191.PROD.OUTLOOK.COM>
Message-ID: <2B3D9F22-5DC0-4B0F-8270-1555FA6E7052@sonic.net>

Hi Yehuda,

  The mx230 graphics is slow, similar to Intel graphics but that is usable with Chimera.  NotebookCheck says this about the mx230

	https://www.notebookcheck.net/NVIDIA-GeForce-MX230-Graphics-Card.382351.0.html <https://www.notebookcheck.net/NVIDIA-GeForce-MX230-Graphics-Card.382351.0.html>

Performance

Thanks to the newer Pascal architecture, the MX230 is significantly faster than the old GeForce MX130 (Maxwell based). <https://www.notebookcheck.net/NVIDIA-GeForce-MX130-GPU-Benchmarks-and-Specs.258054.0.html> Demanding games of 2019 run only in lowest resolution and detail settings and may stutter (e.g. Anno 1800 or Rage 2 ran with under 30fps in our benchmarks). Less demanding games like Overwatch, Fifa 19 or Rocket League, however, can be played in higher detail and resolution settings without stuttering (see benchmarks below).

Chimera looking at large data (500,000 atoms, or Gbyte density maps) is like a demanding video game, so this laptop would not be ideal for looking at large data sets, but would be fine for moderate size data.  The CPU is a typical low power laptop CPU, again adequate for moderate size data.

	Tom



> On Feb 17, 2020, at 7:03 AM, Yehuda Halfon <yehuda.halfon at weizmann.ac.il> wrote:
> 
> Hi all, 
> A friend of mine in my lab wants to buy a new laptop with mx230. Will it work fine with chimera and chimerax? 
> 
> The cpu is i5-10210u and 8 GB of ram. 
> 
> 
> Thanks a lot, 
> Yehuda Halfon 
> 
> PS
> 
> I know this isn't the chimerax mailing list but I hope to get a double answer in one mail
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From adi.uoh at gmail.com  Wed Feb 19 01:01:11 2020
From: adi.uoh at gmail.com (Aditya Padhi)
Date: Wed, 19 Feb 2020 18:01:11 +0900
Subject: [Chimera-users] Problem during Residue interaction network
	generation
Message-ID: <CABfSPKB88ENF1a3t6ASDk9LNj02u2oF_aMU-UKGQLoUfqTHU3w@mail.gmail.com>

Dear Chimera users,

I am using the StructueViz plugin of Cytoscape to launch Chimera and then
loading the MD trajectory from Gromacs, where I need to generate the
residue interaction network. After this step, when I click "apply" for
displaying the interaction network in Cytoscape, it often shows "Importing
Residue Network from Chimera", sometimes "getting data for attribute
secondarystructure" and sometimes "getting data for attribute ishelix".
Even after I wait for half a day, the message continues to show and I am
not able to work on Cytoscape.
I have even tried to reduce the number of frames of the MD trajectory to
see if that helps, but that doesn't work even.

Can anyone help me to how to resolve this problem?
With best regards
Aditya
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From pett at cgl.ucsf.edu  Wed Feb 19 13:12:45 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 19 Feb 2020 13:12:45 -0800
Subject: [Chimera-users] Hydrogen labeling scheme
In-Reply-To: <7E8A2A00-283D-44FB-A7F6-BAFBE643BB33@chem.ucla.edu>
References: <7E8A2A00-283D-44FB-A7F6-BAFBE643BB33@chem.ucla.edu>
Message-ID: <A0892927-4F2F-4A89-87A8-07F20715818B@cgl.ucsf.edu>

Hi Jack,
	Chimera tries to use hydrogen names that follow PDB-standard naming if possible.  That means the hydrogen name is the same as the heavy atom it?s attached to, with the chemical-element part of the heavy atom name replaced with ?H? and with digits appended if multiple hydrogens are being added to the atom (or primes [?] if the heavy atom name ends with a prime).  It handles well-known exceptions to the rule (e.g. hydrogens added to N6 in ATP are HN61 and HN62).  The digits added don?t necessarily start at 1 ? if adding two hydrogens to an atom with two other heavy atoms bonded to it, the numbering starts at 2.  This is all for PDB version 3.  There are some additional rules for PDB version 2 which you probably have no need to know since PDB version 2 is ancient at this point.
	For some structures (e.g. some small molecules), the above scheme doesn?t work either because prerequisites are lacking (e.g. atom names don?t start with the atomic symbol) or the resulting hydrogen names aren?t unique.  Depending on the issue, a fallback approach is used:

1) Names don't start with atomic symbol or heavy atom names not unique within the residue:  prepend the heavy atom atomic symbol with ?H? and add digits as needed to make the name unique within the residue.

2) Otherwise: for atoms where the post-atomic-symbol part of the name is unique within the residue, replace the atomic symbol with ?H?, otherwise prepend ?H?.  In both cases add digits if multiple hydrogens being added to atom.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



> On Feb 14, 2020, at 12:44 PM, Jack Fuller <jtfuller at chem.ucla.edu> wrote:
> 
> Hello,
> 
> I am part of a computational chemistry research group that frequently uses chimera to add hydrogens to pdbs.  My coworkers and I have noticed that chimera uses several different labeling schemes for hydrogens.  We have been unable to determine how chimera chooses which scheme to use.  Is there a way to specify which scheme to use or to know which scheme chimera will choose?
> 
> Thank you,
> Jack Fuller
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From pett at cgl.ucsf.edu  Wed Feb 19 14:17:57 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 19 Feb 2020 14:17:57 -0800
Subject: [Chimera-users] Problem during Residue interaction network
 generation
In-Reply-To: <CABfSPKB88ENF1a3t6ASDk9LNj02u2oF_aMU-UKGQLoUfqTHU3w@mail.gmail.com>
References: <CABfSPKB88ENF1a3t6ASDk9LNj02u2oF_aMU-UKGQLoUfqTHU3w@mail.gmail.com>
Message-ID: <52244A27-FF93-4978-B80F-A8A4D2F692D4@cgl.ucsf.edu>

Hi Aditya,
	I don?t know why your system is so slow.  All the tests I tried just now worked reasonably quickly, even with large trajectories.  I?d like you to try something.  Do exactly what you were doing before, but instead of using your trajectory, use the attached multi-MODEL PDB file for the trajectory (when you start the MD Movie tool, choose ?PDB? as the trajectory format and ?single file? within that format).  Does computing a residue interaction network using that trajectory also get hung up?

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



> On Feb 19, 2020, at 1:01 AM, Aditya Padhi <adi.uoh at gmail.com> wrote:
> 
> Dear Chimera users,
> 
> I am using the StructueViz plugin of Cytoscape to launch Chimera and then loading the MD trajectory from Gromacs, where I need to generate the residue interaction network. After this step, when I click "apply" for displaying the interaction network in Cytoscape, it often shows "Importing Residue Network from Chimera", sometimes "getting data for attribute secondarystructure" and sometimes "getting data for attribute ishelix". Even after I wait for half a day, the message continues to show and I am not able to work on Cytoscape.
> I have even tried to reduce the number of frames of the MD trajectory to see if that helps, but that doesn't work even.
> 
> Can anyone help me to how to resolve this problem?
> With best regards
> Aditya
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From peter.engelhardt at helsinki.fi  Thu Feb 20 04:47:41 2020
From: peter.engelhardt at helsinki.fi (Engelhardt, Peter)
Date: Thu, 20 Feb 2020 12:47:41 +0000
Subject: [Chimera-users] How to change font size for scale bar
Message-ID: <560BFD3E-75E2-49B1-9AB8-B4E09B8775F4@helsinki.fi>

Hi 
We can?t find any options for font size in scale bar wondering if possible.
Any suggestions 

Cheers
Peter

Sent from my iPhone


From adi.uoh at gmail.com  Wed Feb 19 17:06:41 2020
From: adi.uoh at gmail.com (Aditya Padhi)
Date: Thu, 20 Feb 2020 10:06:41 +0900
Subject: [Chimera-users] Problem during Residue interaction network
	generation
In-Reply-To: <52244A27-FF93-4978-B80F-A8A4D2F692D4@cgl.ucsf.edu>
References: <CABfSPKB88ENF1a3t6ASDk9LNj02u2oF_aMU-UKGQLoUfqTHU3w@mail.gmail.com>
 <52244A27-FF93-4978-B80F-A8A4D2F692D4@cgl.ucsf.edu>
Message-ID: <CABfSPKCOMBxRO7wn_aCY-j=nzWm5erJhFjXkByUvycca6AGEfg@mail.gmail.com>

Dear Eric,

Thank you very much for your quick response.
I have used the 1mtx.pdb file sent by you and did exactly as you suggested
to generate the RIN.
Yes, this file worked without any delay or issues, and I could generate the
RIN successfully.
Can you please suggest whether something is wrong in my input MD
trajectory?
FYI, I have tried almost 10 different mutant systems, each represents 100ns
trajectory generated from Gromacs.

I look forward to hear from you.
With best regards
Aditya

On Thu, Feb 20, 2020 at 7:18 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Aditya,
> I don?t know why your system is so slow.  All the tests I tried just now
> worked reasonably quickly, even with large trajectories.  I?d like you to
> try something.  Do exactly what you were doing before, but instead of using
> your trajectory, use the attached multi-MODEL PDB file for the trajectory
> (when you start the MD Movie tool, choose ?PDB? as the trajectory format
> and ?single file? within that format).  Does computing a residue
> interaction network using that trajectory also get hung up?
>
> ?Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Feb 19, 2020, at 1:01 AM, Aditya Padhi <adi.uoh at gmail.com> wrote:
>
> Dear Chimera users,
>
> I am using the StructueViz plugin of Cytoscape to launch Chimera and then
> loading the MD trajectory from Gromacs, where I need to generate the
> residue interaction network. After this step, when I click "apply" for
> displaying the interaction network in Cytoscape, it often shows "Importing
> Residue Network from Chimera", sometimes "getting data for attribute
> secondarystructure" and sometimes "getting data for attribute ishelix".
> Even after I wait for half a day, the message continues to show and I am
> not able to work on Cytoscape.
> I have even tried to reduce the number of frames of the MD trajectory to
> see if that helps, but that doesn't work even.
>
> Can anyone help me to how to resolve this problem?
> With best regards
> Aditya
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>

-- 
******************************************
Aditya Kumar Padhi, Ph.D. (IIT Delhi)
JSPS Postdoctoral Researcher
RIKEN - Yokohama, Japan
Contact no: +81-70-3999-2091
******************************************
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From meng at cgl.ucsf.edu  Thu Feb 20 10:11:51 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 20 Feb 2020 10:11:51 -0800
Subject: [Chimera-users] How to change font size for scale bar
In-Reply-To: <560BFD3E-75E2-49B1-9AB8-B4E09B8775F4@helsinki.fi>
References: <560BFD3E-75E2-49B1-9AB8-B4E09B8775F4@helsinki.fi>
Message-ID: <B03EDB41-048A-4891-A837-D7A3154DC596@cgl.ucsf.edu>

Hi Peter,
The scale bar is implemented as atoms/bonds and the text is essentially an atom label.  Atom label size (all labels at once) can be set in the Preferences (open from Favorites menu), category: Labels.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Labels>

This is mentioned in the Scale Bar ?limitations? section at the bottom of the page but is easy to miss?
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/scalebar.html>

For more control over label size independent of any atom labels, you could make the label blank in in the Scale Bar tool and instead add it as a 2D Label (menu: Tools? Utilities? 2D Label). 2D labels may also include symbols such as the Angstrom symbol.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.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 Feb 20, 2020, at 4:47 AM, Engelhardt, Peter <peter.engelhardt at helsinki.fi> wrote:
> 
> Hi 
> We can?t find any options for font size in scale bar wondering if possible.
> Any suggestions 
> Cheers
> Peter



From dgutierrez at gradcenter.cuny.edu  Thu Feb 20 10:18:29 2020
From: dgutierrez at gradcenter.cuny.edu (Dominique  Gutierrez)
Date: Thu, 20 Feb 2020 18:18:29 +0000
Subject: [Chimera-users] "subtract selected segment from map" from a
	specific map
Message-ID: <MN2PR18MB3183A3B640675945AB57D08185130@MN2PR18MB3183.namprd18.prod.outlook.com>

Hello,

Can I use the "subtract selected segment  from map" in Segger tool to subtract the selected from a specific map and not just the map used for segmentation. In my case the segmented map is from a vop subtracted intermediate used to facilitate segmentation but I would like to quickly subtract several segments from the original map. Or is the only way to do that with vop subtract?



Best,
Dominique
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From goddard at sonic.net  Thu Feb 20 10:29:44 2020
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 20 Feb 2020 10:29:44 -0800
Subject: [Chimera-users] "subtract selected segment from map" from a
 specific map
In-Reply-To: <MN2PR18MB3183A3B640675945AB57D08185130@MN2PR18MB3183.namprd18.prod.outlook.com>
References: <MN2PR18MB3183A3B640675945AB57D08185130@MN2PR18MB3183.namprd18.prod.outlook.com>
Message-ID: <AE05DE9B-DA9B-4A13-863B-ECE31A5DDA32@sonic.net>

Hi Dominique,

  Segger menu Regions / Subtract Selected From Map operates on the map listed in the "Segment Map" menu at the top of the Segger dialog.  So when I segment one map, then change the Segment Map menu to another map and use that menu entry it subtracts from that new map that was not the one the segmentation was calculated from.  The new map does need to be the same size in grid points and have the same alignment.

	Tom


> On Feb 20, 2020, at 10:18 AM, Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu> wrote:
> 
> Hello,
> 
> Can I use the "subtract selected segment  from map" in Segger tool to subtract the selected from a specific map and not just the map used for segmentation. In my case the segmented map is from a vop subtracted intermediate used to facilitate segmentation but I would like to quickly subtract several segments from the original map. Or is the only way to do that with vop subtract?  
> 
> 
> 
> Best,
> Dominique
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From mgochin at lbl.gov  Thu Feb 20 11:46:49 2020
From: mgochin at lbl.gov (Miriam Gochin)
Date: Thu, 20 Feb 2020 11:46:49 -0800
Subject: [Chimera-users] Aligning a 2Fo-Fc map with the molecule in Chimera
Message-ID: <CAF+VGjHkFo96PtOdFuUm7UPBMre0JS5v90LYU3V4PiVzpZVGTA@mail.gmail.com>

The 2F0-Fc map was created with Phenix.  I tried the "vop cover #1 atom #0"
command but got the following error:

NameError: global name 'step' is not defined

  File
"/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py",
line 9, in map_covering_box
    g = volume.grid_data(subregion = 'all', step = step, mask_zone = False)

Hoping to figure out how to make it work.

Many thanks,
---------------------------------
Miriam Gochin
Touro University California / LBL
miriam.gochin at tu.edu
mgochin at lbl.gov
707-638-5463
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From goddard at sonic.net  Thu Feb 20 11:55:57 2020
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 20 Feb 2020 11:55:57 -0800
Subject: [Chimera-users] Aligning a 2Fo-Fc map with the molecule in
 Chimera
In-Reply-To: <CAF+VGjHkFo96PtOdFuUm7UPBMre0JS5v90LYU3V4PiVzpZVGTA@mail.gmail.com>
References: <CAF+VGjHkFo96PtOdFuUm7UPBMre0JS5v90LYU3V4PiVzpZVGTA@mail.gmail.com>
Message-ID: <73F86674-52DF-4ECE-80A2-03BF1DD1E051@sonic.net>

Hi Miriam,

  We appreciate your long use of Chimera!  That bug was fixed 7 years ago.  Time to install a new Chimera.

	Tom


> On Feb 20, 2020, at 11:46 AM, Miriam Gochin <mgochin at lbl.gov> wrote:
> 
> The 2F0-Fc map was created with Phenix.  I tried the "vop cover #1 atom #0" command but got the following error:
> 
> NameError: global name 'step' is not defined
> 
>   File "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py", line 9, in map_covering_box
>     g = volume.grid_data(subregion = 'all', step = step, mask_zone = False)
> 
> Hoping to figure out how to make it work.
> 
> Many thanks,
> ---------------------------------
> Miriam Gochin
> Touro University California / LBL
> miriam.gochin at tu.edu <mailto:miriam.gochin at tu.edu>
> mgochin at lbl.gov <mailto:mgochin at lbl.gov>
> 707-638-5463  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From mgochin at lbl.gov  Thu Feb 20 13:26:07 2020
From: mgochin at lbl.gov (Miriam Gochin)
Date: Thu, 20 Feb 2020 13:26:07 -0800
Subject: [Chimera-users] Aligning a 2Fo-Fc map with the molecule in
	Chimera
In-Reply-To: <73F86674-52DF-4ECE-80A2-03BF1DD1E051@sonic.net>
References: <CAF+VGjHkFo96PtOdFuUm7UPBMre0JS5v90LYU3V4PiVzpZVGTA@mail.gmail.com>
 <73F86674-52DF-4ECE-80A2-03BF1DD1E051@sonic.net>
Message-ID: <CAF+VGjG-ivTz0jrGpxXvAi6p5_UUZjx4RVsKNSyV38yAX_X-HA@mail.gmail.com>

Thanks for date shaming me!!   It works - you guys are great.  Is there any
way to select certain parts of the map, if for example you just want to see
the electron density of one molecule instead of all the symmetry copies?

Miriam

PS.  7 years isn't even close.

On Thu, Feb 20, 2020 at 11:56 AM Tom Goddard <goddard at sonic.net> wrote:

> Hi Miriam,
>
>   We appreciate your long use of Chimera!  That bug was fixed 7 years
> ago.  Time to install a new Chimera.
>
> Tom
>
>
> On Feb 20, 2020, at 11:46 AM, Miriam Gochin <mgochin at lbl.gov> wrote:
>
> The 2F0-Fc map was created with Phenix.  I tried the "vop cover #1 atom
> #0" command but got the following error:
>
> NameError: global name 'step' is not defined
>
>   File
> "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py",
> line 9, in map_covering_box
>     g = volume.grid_data(subregion = 'all', step = step, mask_zone = False)
>
> Hoping to figure out how to make it work.
>
> Many thanks,
> ---------------------------------
> Miriam Gochin
> Touro University California / LBL
> miriam.gochin at tu.edu
> mgochin at lbl.gov
> 707-638-5463
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
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From goddard at sonic.net  Thu Feb 20 13:37:07 2020
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 20 Feb 2020 13:37:07 -0800
Subject: [Chimera-users] Aligning a 2Fo-Fc map with the molecule in
 Chimera
In-Reply-To: <CAF+VGjG-ivTz0jrGpxXvAi6p5_UUZjx4RVsKNSyV38yAX_X-HA@mail.gmail.com>
References: <CAF+VGjHkFo96PtOdFuUm7UPBMre0JS5v90LYU3V4PiVzpZVGTA@mail.gmail.com>
 <73F86674-52DF-4ECE-80A2-03BF1DD1E051@sonic.net>
 <CAF+VGjG-ivTz0jrGpxXvAi6p5_UUZjx4RVsKNSyV38yAX_X-HA@mail.gmail.com>
Message-ID: <D4DDEFA0-2718-432B-9B87-051293CF24FF@sonic.net>

Hi Miriam,

  Sorry!  To show the map just near the atoms use Volume Viewer menu Features / Zone, select your atoms (e.g. command "select #0") and press the Zone button.  This just hides the density beyond some distance (e.g. 3 Angstroms) from the selected atoms.

	Tom



> On Feb 20, 2020, at 1:26 PM, Miriam Gochin <mgochin at lbl.gov> wrote:
> 
> Thanks for date shaming me!!   It works - you guys are great.  Is there any way to select certain parts of the map, if for example you just want to see the electron density of one molecule instead of all the symmetry copies?
> 
> Miriam
> 
> PS.  7 years isn't even close.
> 
> On Thu, Feb 20, 2020 at 11:56 AM Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
> Hi Miriam,
> 
>   We appreciate your long use of Chimera!  That bug was fixed 7 years ago.  Time to install a new Chimera.
> 
> 	Tom
> 
> 
>> On Feb 20, 2020, at 11:46 AM, Miriam Gochin <mgochin at lbl.gov <mailto:mgochin at lbl.gov>> wrote:
>> 
>> The 2F0-Fc map was created with Phenix.  I tried the "vop cover #1 atom #0" command but got the following error:
>> 
>> NameError: global name 'step' is not defined
>> 
>>   File "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py", line 9, in map_covering_box
>>     g = volume.grid_data(subregion = 'all', step = step, mask_zone = False)
>> 
>> Hoping to figure out how to make it work.
>> 
>> Many thanks,
>> ---------------------------------
>> Miriam Gochin
>> Touro University California / LBL
>> miriam.gochin at tu.edu <mailto:miriam.gochin at tu.edu>
>> mgochin at lbl.gov <mailto:mgochin at lbl.gov>
>> 707-638-5463  
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
> 

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From mgochin at lbl.gov  Thu Feb 20 13:40:31 2020
From: mgochin at lbl.gov (Miriam Gochin)
Date: Thu, 20 Feb 2020 13:40:31 -0800
Subject: [Chimera-users] Aligning a 2Fo-Fc map with the molecule in
	Chimera
In-Reply-To: <D4DDEFA0-2718-432B-9B87-051293CF24FF@sonic.net>
References: <CAF+VGjHkFo96PtOdFuUm7UPBMre0JS5v90LYU3V4PiVzpZVGTA@mail.gmail.com>
 <73F86674-52DF-4ECE-80A2-03BF1DD1E051@sonic.net>
 <CAF+VGjG-ivTz0jrGpxXvAi6p5_UUZjx4RVsKNSyV38yAX_X-HA@mail.gmail.com>
 <D4DDEFA0-2718-432B-9B87-051293CF24FF@sonic.net>
Message-ID: <CAF+VGjF-07yA-aQDnb-4=SBHB6uGXMKTN8HC6V5o1ArnhE3bDA@mail.gmail.com>

Thank you so much for your help.  Works great.

On Thu, Feb 20, 2020 at 1:37 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Miriam,
>
>   Sorry!  To show the map just near the atoms use Volume Viewer menu
> Features / Zone, select your atoms (e.g. command "select #0") and press the
> Zone button.  This just hides the density beyond some distance (e.g. 3
> Angstroms) from the selected atoms.
>
> Tom
>
>
>
> On Feb 20, 2020, at 1:26 PM, Miriam Gochin <mgochin at lbl.gov> wrote:
>
> Thanks for date shaming me!!   It works - you guys are great.  Is there
> any way to select certain parts of the map, if for example you just want to
> see the electron density of one molecule instead of all the symmetry copies?
>
> Miriam
>
> PS.  7 years isn't even close.
>
> On Thu, Feb 20, 2020 at 11:56 AM Tom Goddard <goddard at sonic.net> wrote:
>
>> Hi Miriam,
>>
>>   We appreciate your long use of Chimera!  That bug was fixed 7 years
>> ago.  Time to install a new Chimera.
>>
>> Tom
>>
>>
>> On Feb 20, 2020, at 11:46 AM, Miriam Gochin <mgochin at lbl.gov> wrote:
>>
>> The 2F0-Fc map was created with Phenix.  I tried the "vop cover #1 atom
>> #0" command but got the following error:
>>
>> NameError: global name 'step' is not defined
>>
>>   File
>> "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py",
>> line 9, in map_covering_box
>>     g = volume.grid_data(subregion = 'all', step = step, mask_zone =
>> False)
>>
>> Hoping to figure out how to make it work.
>>
>> Many thanks,
>> ---------------------------------
>> Miriam Gochin
>> Touro University California / LBL
>> miriam.gochin at tu.edu
>> mgochin at lbl.gov
>> 707-638-5463
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription:
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>>
>
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From pett at cgl.ucsf.edu  Thu Feb 20 14:09:17 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 20 Feb 2020 14:09:17 -0800
Subject: [Chimera-users] Problem during Residue interaction network
 generation
In-Reply-To: <CABfSPKCOMBxRO7wn_aCY-j=nzWm5erJhFjXkByUvycca6AGEfg@mail.gmail.com>
References: <CABfSPKB88ENF1a3t6ASDk9LNj02u2oF_aMU-UKGQLoUfqTHU3w@mail.gmail.com>
 <52244A27-FF93-4978-B80F-A8A4D2F692D4@cgl.ucsf.edu>
 <CABfSPKCOMBxRO7wn_aCY-j=nzWm5erJhFjXkByUvycca6AGEfg@mail.gmail.com>
Message-ID: <7615B39C-42F4-44B6-B0A9-1FDA2D0F09AE@cgl.ucsf.edu>

Hi Aditya,
	Try using trjconv with the -skip option to write out a much smaller trajectory file (20 frames or less, see: gmx trjconv ? GROMACS 2018.3 documentation <http://manual.gromacs.org/documentation/2018.3/onlinehelp/gmx-trjconv.html>).  Is that slow or fast?  If it?s slow, the file should be small enough that you can mail it to me directly (not the list!) along with your topology file, and then maybe I can reproduce the issue.  Also, what version of Cytoscape are you using?

?Eric

> On Feb 19, 2020, at 5:06 PM, Aditya Padhi <adi.uoh at gmail.com> wrote:
> 
> Dear Eric,
> 
> Thank you very much for your quick response.
> I have used the 1mtx.pdb file sent by you and did exactly as you suggested to generate the RIN. 
> Yes, this file worked without any delay or issues, and I could generate the RIN successfully.
> Can you please suggest whether something is wrong in my input MD trajectory? 
> FYI, I have tried almost 10 different mutant systems, each represents 100ns trajectory generated from Gromacs.
> 
> I look forward to hear from you.
> With best regards
> Aditya
> 
> On Thu, Feb 20, 2020 at 7:18 AM Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
> Hi Aditya,
> 	I don?t know why your system is so slow.  All the tests I tried just now worked reasonably quickly, even with large trajectories.  I?d like you to try something.  Do exactly what you were doing before, but instead of using your trajectory, use the attached multi-MODEL PDB file for the trajectory (when you start the MD Movie tool, choose ?PDB? as the trajectory format and ?single file? within that format).  Does computing a residue interaction network using that trajectory also get hung up?
> 
> ?Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
>> On Feb 19, 2020, at 1:01 AM, Aditya Padhi <adi.uoh at gmail.com <mailto:adi.uoh at gmail.com>> wrote:
>> 
>> Dear Chimera users,
>> 
>> I am using the StructueViz plugin of Cytoscape to launch Chimera and then loading the MD trajectory from Gromacs, where I need to generate the residue interaction network. After this step, when I click "apply" for displaying the interaction network in Cytoscape, it often shows "Importing Residue Network from Chimera", sometimes "getting data for attribute secondarystructure" and sometimes "getting data for attribute ishelix". Even after I wait for half a day, the message continues to show and I am not able to work on Cytoscape.
>> I have even tried to reduce the number of frames of the MD trajectory to see if that helps, but that doesn't work even.
>> 
>> Can anyone help me to how to resolve this problem?
>> With best regards
>> Aditya
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
> 
> 
> 
> -- 
> ******************************************
> Aditya Kumar Padhi, Ph.D. (IIT Delhi)
> JSPS Postdoctoral Researcher
> RIKEN - Yokohama, Japan
> Contact no: +81-70-3999-2091
> ******************************************

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From mr_yuzhou at yahoo.com  Fri Feb 21 17:13:02 2020
From: mr_yuzhou at yahoo.com (Yu Zhou)
Date: Sat, 22 Feb 2020 01:13:02 +0000 (UTC)
Subject: [Chimera-users] Color surface by electrostatic potential vs color
 by value at atom position
References: <1170255500.3942.1582333983107.ref@mail.yahoo.com>
Message-ID: <1170255500.3942.1582333983107@mail.yahoo.com>


Hi there,

I want to color protein surface by electrostatic potential datacalculated using APBS 1.5. I tried two methods in Chimera and got quite differentresults. The resulted images can be found in attachment. 

In the first attached figure (fig1_ep surface) the surface wascolored by the ?Electrostatic Surface Coloring? tool, in the second attachedfigure (fig2_value atom) the surface was colored by the ?Values at AtomPositions? tool. Same color palette (red: -35, white: 0, blue: +35) and potential file was used in bothcases. 

Thanks for your help.

Yu Zhou

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From meng at cgl.ucsf.edu  Fri Feb 21 17:28:16 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 21 Feb 2020 17:28:16 -0800
Subject: [Chimera-users] Color surface by electrostatic potential vs
 color by value at atom position
In-Reply-To: <1170255500.3942.1582333983107@mail.yahoo.com>
References: <1170255500.3942.1582333983107.ref@mail.yahoo.com>
 <1170255500.3942.1582333983107@mail.yahoo.com>
Message-ID: <D2870F59-34BA-48D8-B2D4-794912A4BA4A@cgl.ucsf.edu>

Hi Yu Zhou,
The electrostatic potential coloring default is to use values calculated 1.4 Angstroms outward from the molecular surface (at approximately the solvent-accessible surface).  You can see or change this ?offset? value if you click the Options button on the Surface Color tool.  However, even if you set offset to 0, it will be evaluating the value at the molecular surface.

The default offset of 1.4 is recommended for coloring by electrostatic potential, however, which is why we made it the default.  The solvent-accessible surface is approximately how close the center of a ligand atom could get to the protein and represents what an interacting molecule would ?see."

Values at atom positions gets the values at the atomic centers of the protein, which are inside the surface.  You definitely should not use those values because the potential exactly at the same position as a charge (which is placed at the atomic center) is a spike, essentially a singularity, that does not represent what a molecule interacting with the protein would ?see.?  In other words, a ligand atom would never be placed at exactly the same position as an atom in the protein. It does not make any sense to use this approach for coloring by electrostatic potential.

There is a diagram here showing the relationship between the atoms of the protein, molecular surface, and solvent-accessible surface.  The molecular surface is the one displayed by Chimera.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

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

> On Feb 21, 2020, at 5:13 PM, Yu Zhou <mr_yuzhou at yahoo.com> wrote:
> 
> Hi there,
> I want to color protein surface by electrostatic potential data calculated using APBS 1.5. I tried two methods in Chimera and got quite different results. The resulted images can be found in attachment. 
> In the first attached figure (fig1_ep surface) the surface was colored by the ?Electrostatic Surface Coloring? tool, in the second attached figure (fig2_value atom) the surface was colored by the ?Values at Atom Positions? tool. Same color palette (red: -35, white: 0, blue: +35) and potential file was used in both cases.
> Thanks for your help.
> Yu Zhou



From mr_yuzhou at yahoo.com  Fri Feb 21 17:50:45 2020
From: mr_yuzhou at yahoo.com (Yu Zhou)
Date: Sat, 22 Feb 2020 01:50:45 +0000 (UTC)
Subject: [Chimera-users] Color surface by electrostatic potential vs
 color by value at atom position
In-Reply-To: <D2870F59-34BA-48D8-B2D4-794912A4BA4A@cgl.ucsf.edu>
References: <1170255500.3942.1582333983107.ref@mail.yahoo.com>
 <1170255500.3942.1582333983107@mail.yahoo.com>
 <D2870F59-34BA-48D8-B2D4-794912A4BA4A@cgl.ucsf.edu>
Message-ID: <1639991520.1549.1582336245210@mail.yahoo.com>

 Elaine
 Many thanks for you prompt reply, which is very helpful to me.

Yu

    On Friday, February 21, 2020, 07:28:18 PM CST, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 
 Hi Yu Zhou,
The electrostatic potential coloring default is to use values calculated 1.4 Angstroms outward from the molecular surface (at approximately the solvent-accessible surface).? You can see or change this ?offset? value if you click the Options button on the Surface Color tool.? However, even if you set offset to 0, it will be evaluating the value at the molecular surface.

The default offset of 1.4 is recommended for coloring by electrostatic potential, however, which is why we made it the default.? The solvent-accessible surface is approximately how close the center of a ligand atom could get to the protein and represents what an interacting molecule would ?see."

Values at atom positions gets the values at the atomic centers of the protein, which are inside the surface.? You definitely should not use those values because the potential exactly at the same position as a charge (which is placed at the atomic center) is a spike, essentially a singularity, that does not represent what a molecule interacting with the protein would ?see.?? In other words, a ligand atom would never be placed at exactly the same position as an atom in the protein. It does not make any sense to use this approach for coloring by electrostatic potential.

There is a diagram here showing the relationship between the atoms of the protein, molecular surface, and solvent-accessible surface.? The molecular surface is the one displayed by Chimera.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

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

> On Feb 21, 2020, at 5:13 PM, Yu Zhou <mr_yuzhou at yahoo.com> wrote:
> 
> Hi there,
> I want to color protein surface by electrostatic potential data calculated using APBS 1.5. I tried two methods in Chimera and got quite different results. The resulted images can be found in attachment. 
> In the first attached figure (fig1_ep surface) the surface was colored by the ?Electrostatic Surface Coloring? tool, in the second attached figure (fig2_value atom) the surface was colored by the ?Values at Atom Positions? tool. Same color palette (red: -35, white: 0, blue: +35) and potential file was used in both cases.
> Thanks for your help.
> Yu Zhou
  
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From tp42 at nyu.edu  Sun Feb 23 04:11:03 2020
From: tp42 at nyu.edu (Thirumurugan Prakasam)
Date: Sun, 23 Feb 2020 04:11:03 -0800
Subject: [Chimera-users] (no subject)
Message-ID: <CABBuN7oRzYXYh55WPa45r0oCJh8vTzx1dPA63x7nkVS19FtWkA@mail.gmail.com>

Hi,
I am trying to make metal coordination bond as a dotted line and also I
need to make electron clouds around the atoms as in the picture below
(Please provide me short guidelines on how to make nice cartoon). Please
help me sort this two issues.
Looking forward to hearing from you,
Many thanks,
Thiru
[image: image.png]

-- 
Thirumurugan Prakasam,
Research Scientist,
New York University Abu Dhabi,
Experimental Research Building
Building C1, Saadiyat Island
Abu Dhabi, UAE
Phone no: +971-561976358
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From meng at cgl.ucsf.edu  Mon Feb 24 09:17:46 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 24 Feb 2020 09:17:46 -0800
Subject: [Chimera-users] adding dashed lines, showing transparent spheres
In-Reply-To: <CABBuN7oRzYXYh55WPa45r0oCJh8vTzx1dPA63x7nkVS19FtWkA@mail.gmail.com>
References: <CABBuN7oRzYXYh55WPa45r0oCJh8vTzx1dPA63x7nkVS19FtWkA@mail.gmail.com>
Message-ID: <61FEB16A-E54C-48A1-9766-B1A1829BD493@cgl.ucsf.edu>

Hi Thiru,
(I added a subject line to the message so others may be able to find it later.)

(A) There are a couple ways to add a dashed or dotted line, but one easy way if you only need to add a few is to first just make distance measurements, and then hide the distance values.  For example, show Distances tool (menu: Tools? Structure Analysis? Distances).  Then for each line you want to add, Ctrl-click one atom to select it, Shift-Ctrl second atom to select it ?. now there are two atoms selected and you can add the line between them by clicking the ?Create? button on the Distances tool.

With the Distances tool you can set ?Labels? to ?None? and change the distance color, line width, and line style.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>

You should do this when only one copy of the structure is open, and shown as sticks.  Part (B) below   describes opening a second copy to show the spheres, and if you do that first, you will have to use Model Panel to hide the spheres model temporarily (uncheck the ?S? box) so that you can add the distance measurements to the sticks.

(B) To show transparent spheres and sticks at the same time, open the same structure twice.  Then show one copy as spheres and make it partially transparent.  For example, commands:

open pubchem:448537
open pubchem:448537
repr sphere #1
trans 50 #1
set bg_color white

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/represent.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>

The 50 means 50% transparent.  You could use some other value.  Also you could change the colors of the spheres (model #1 in this example) and sticks (model #0 in this example) as you like.

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

> On Feb 23, 2020, at 4:11 AM, Thirumurugan Prakasam <tp42 at nyu.edu> wrote:
> 
> Hi,
> I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues.
> Looking forward to hearing from you,
> Many thanks,
> Thiru
> <image.png>
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From dgutierrez at gradcenter.cuny.edu  Mon Feb 24 09:50:44 2020
From: dgutierrez at gradcenter.cuny.edu (Dominique  Gutierrez)
Date: Mon, 24 Feb 2020 17:50:44 +0000
Subject: [Chimera-users] chimera exiting every time after clicking browse
Message-ID: <MN2PR18MB318318AF28781901B43910F985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>

Hello,

I have MacOS Catalina 10.15.3. Chimera is exiting every time after clicking browse. Versions 1.13 and 1.14 are doing this.

Best,
Dominique
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From deligkaris at gmail.com  Mon Feb 24 11:57:41 2020
From: deligkaris at gmail.com (Christos Deligkaris)
Date: Mon, 24 Feb 2020 13:57:41 -0600
Subject: [Chimera-users] visualizing potential with volume data
Message-ID: <CAAHQ3wnCgCWQzqBv0=LCTgE4HBBzcu=eMTZwWAFAC0t-s7J13Q@mail.gmail.com>

dear all,

I have obtained a cube file from NWChem with the electrostatic
potential around a molecule. I visualized the molecular surface using
Actions->Surface->Show and then colored it using the volume data
(followed instructions
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in
tools->surface color (electrostatic surface coloring)) .

Since I do not have my data stored in a potential file, can I still do
the surface offset? The chimera tool webpage discusses why that is
preferred than showing the potential on the solvent excluded surface
and it seems to me that option to not be available with volume data.

Also, my surface does not look like the electrostatic potential
surface shown here:
https://www.cgl.ucsf.edu/chimera/data/tutorials/maps08/volume-basics.html
. The molecular surface we get with Action->Surface->Show seems to be
constructed with greater atomic radii than the one shown in that
image. I am not sure how important that is though. Is there a way to
ask Chimera to visualize the electrostatic potential volume data with
the same options Chimera would use if it was reading a Delphi, PBS
file?

Best wishes,

Christos Deligkaris, PhD
Assistant Professor of Physics

From tp42 at nyu.edu  Mon Feb 24 10:31:02 2020
From: tp42 at nyu.edu (Thirumurugan Prakasam)
Date: Mon, 24 Feb 2020 22:31:02 +0400
Subject: [Chimera-users] adding dashed lines, showing transparent spheres
In-Reply-To: <61FEB16A-E54C-48A1-9766-B1A1829BD493@cgl.ucsf.edu>
References: <CABBuN7oRzYXYh55WPa45r0oCJh8vTzx1dPA63x7nkVS19FtWkA@mail.gmail.com>
 <61FEB16A-E54C-48A1-9766-B1A1829BD493@cgl.ucsf.edu>
Message-ID: <CABBuN7oO2sn2e2hjeKydRAobandmrA9TJa9Kar2T7c0qTbMivQ@mail.gmail.com>

Thank you soo much for your update and support. I will try.
Thanks
Thiru

On Monday, February 24, 2020, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Thiru,
> (I added a subject line to the message so others may be able to find it
later.)
>
> (A) There are a couple ways to add a dashed or dotted line, but one easy
way if you only need to add a few is to first just make distance
measurements, and then hide the distance values.  For example, show
Distances tool (menu: Tools? Structure Analysis? Distances).  Then for each
line you want to add, Ctrl-click one atom to select it, Shift-Ctrl second
atom to select it ?. now there are two atoms selected and you can add the
line between them by clicking the ?Create? button on the Distances tool.
>
> With the Distances tool you can set ?Labels? to ?None? and change the
distance color, line width, and line style.
> <
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_ContributedSoftware_structuremeas_structuremeas.html-23distances&d=DwIFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=GE3ZfZWTV3qAQwbrb_Dh9Jc4z3-xDklkVZTf8IQl1c4&s=mTaIq5duDt2KEUvjZ22s7x2ef0JCMbb5qxd6N99pbLQ&e=
>
>
> You should do this when only one copy of the structure is open, and shown
as sticks.  Part (B) below   describes opening a second copy to show the
spheres, and if you do that first, you will have to use Model Panel to hide
the spheres model temporarily (uncheck the ?S? box) so that you can add the
distance measurements to the sticks.
>
> (B) To show transparent spheres and sticks at the same time, open the
same structure twice.  Then show one copy as spheres and make it partially
transparent.  For example, commands:
>
> open pubchem:448537
> open pubchem:448537
> repr sphere #1
> trans 50 #1
> set bg_color white
>
> <
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_represent.html&d=DwIFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=GE3ZfZWTV3qAQwbrb_Dh9Jc4z3-xDklkVZTf8IQl1c4&s=ATsOk1_wSRwAMqCIwFex8WeDxbwIx2hXCOEbm2efLPA&e=
>
> <
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_transparency.html&d=DwIFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=GE3ZfZWTV3qAQwbrb_Dh9Jc4z3-xDklkVZTf8IQl1c4&s=6aGA_PyYN5-BQKjot6hrZUgL7uS9BoYcdlsAvJt0Xw8&e=
>
>
> The 50 means 50% transparent.  You could use some other value.  Also you
could change the colors of the spheres (model #1 in this example) and
sticks (model #0 in this example) as you like.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Feb 23, 2020, at 4:11 AM, Thirumurugan Prakasam <tp42 at nyu.edu> wrote:
>>
>> Hi,
>> I am trying to make metal coordination bond as a dotted line and also I
need to make electron clouds around the atoms as in the picture below
(Please provide me short guidelines on how to make nice cartoon). Please
help me sort this two issues.
>> Looking forward to hearing from you,
>> Many thanks,
>> Thiru
>> <image.png>
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription:
https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Dusers&d=DwIFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=GE3ZfZWTV3qAQwbrb_Dh9Jc4z3-xDklkVZTf8IQl1c4&s=Cl-k2Jrev7zBmDXDRiLr-k2h_t_oqE2fd8OCKSrdglo&e=
>
>

-- 
Thirumurugan Prakasam,
Research Scientist,
New York University Abu Dhabi,
Experimental Research Building
Building C1, Saadiyat Island
Abu Dhabi, UAE
Phone no: +971-561976358
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From pett at cgl.ucsf.edu  Mon Feb 24 12:54:33 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 24 Feb 2020 12:54:33 -0800
Subject: [Chimera-users] chimera exiting every time after clicking browse
In-Reply-To: <MN2PR18MB318318AF28781901B43910F985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>
References: <MN2PR18MB318318AF28781901B43910F985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>
Message-ID: <8E369DD9-5F8D-4206-9A8E-AF9F6BCA6FF3@cgl.ucsf.edu>

Hi Dominique,
	Does this mean that you cannot start Chimera at all, or that you when you browse for a file to open from within Chimera that it exits?

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



> On Feb 24, 2020, at 9:50 AM, Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu> wrote:
> 
> Hello,
> 
> I have MacOS Catalina 10.15.3. Chimera is exiting every time after clicking browse. Versions 1.13 and 1.14 are doing this.
> 
> Best,
> Dominique
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From dgutierrez at gradcenter.cuny.edu  Mon Feb 24 13:05:54 2020
From: dgutierrez at gradcenter.cuny.edu (Dominique  Gutierrez)
Date: Mon, 24 Feb 2020 21:05:54 +0000
Subject: [Chimera-users] chimera exiting every time after clicking browse
In-Reply-To: <8E369DD9-5F8D-4206-9A8E-AF9F6BCA6FF3@cgl.ucsf.edu>
References: <MN2PR18MB318318AF28781901B43910F985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>,
 <8E369DD9-5F8D-4206-9A8E-AF9F6BCA6FF3@cgl.ucsf.edu>
Message-ID: <MN2PR18MB31833DCACA944C7E5E64F74985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>

Hello,


The second one. I can open chimera from the command line with the maps I want or from a file browser but if I click browse in a session, the session immediately exits.

Best,
Dominique
________________________________
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Monday, February 24, 2020 3:54 PM
To: Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] chimera exiting every time after clicking browse

Hi Dominique,
Does this mean that you cannot start Chimera at all, or that you when you browse for a file to open from within Chimera that it exits?

?Eric

Eric Pettersen
UCSF Computer Graphics Lab



On Feb 24, 2020, at 9:50 AM, Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu<mailto:dgutierrez at gradcenter.cuny.edu>> wrote:

Hello,

I have MacOS Catalina 10.15.3. Chimera is exiting every time after clicking browse. Versions 1.13 and 1.14 are doing this.

Best,
Dominique
_______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From meng at cgl.ucsf.edu  Mon Feb 24 13:22:39 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 24 Feb 2020 13:22:39 -0800
Subject: [Chimera-users] visualizing potential with volume data
In-Reply-To: <CAAHQ3wnCgCWQzqBv0=LCTgE4HBBzcu=eMTZwWAFAC0t-s7J13Q@mail.gmail.com>
References: <CAAHQ3wnCgCWQzqBv0=LCTgE4HBBzcu=eMTZwWAFAC0t-s7J13Q@mail.gmail.com>
Message-ID: <E17A0AB1-5B45-4770-B3FE-E3A7AEF4EC67@cgl.ucsf.edu>

Dear Christos,
If the option to color by ?electrostatic potential? is chosen in the Surface Color dialog, then no matter what kind of volume data file you opened, it has the electrostatic options including offset 1.4 A.  You can click Options on the dialog to check that they are all set to the values that you want.

The surface image you gave a link to looks the same to me as the other molecular surfaces in Chimera, in terms of shape.  The coloring is too saturated in my opinion (i.e. should have more ?white? instead of all blue and red) but that is just a choice of the coloring levels, not related to the shape of the surface.  Maybe it was made a long time ago without using an offset, but I don?t know ?  I didn?t make that image.

If you want to compare what you get using the same settings, and more appropriate coloring levels in my opinion, instead take a look at the image tutorial ?coloring by surface properties?:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.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 Feb 24, 2020, at 11:57 AM, Christos Deligkaris <deligkaris at gmail.com> wrote:
> 
> dear all,
> 
> I have obtained a cube file from NWChem with the electrostatic
> potential around a molecule. I visualized the molecular surface using
> Actions->Surface->Show and then colored it using the volume data
> (followed instructions
> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in
> tools->surface color (electrostatic surface coloring)) .
> 
> Since I do not have my data stored in a potential file, can I still do
> the surface offset? The chimera tool webpage discusses why that is
> preferred than showing the potential on the solvent excluded surface
> and it seems to me that option to not be available with volume data.
> 
> Also, my surface does not look like the electrostatic potential
> surface shown here:
> https://www.cgl.ucsf.edu/chimera/data/tutorials/maps08/volume-basics.html
> . The molecular surface we get with Action->Surface->Show seems to be
> constructed with greater atomic radii than the one shown in that
> image. I am not sure how important that is though. Is there a way to
> ask Chimera to visualize the electrostatic potential volume data with
> the same options Chimera would use if it was reading a Delphi, PBS
> file?
> 
> Best wishes,
> 
> Christos Deligkaris, PhD
> Assistant Professor of Physics



From pett at cgl.ucsf.edu  Mon Feb 24 13:32:28 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 24 Feb 2020 13:32:28 -0800
Subject: [Chimera-users] chimera exiting every time after clicking browse
In-Reply-To: <MN2PR18MB31833DCACA944C7E5E64F74985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>
References: <MN2PR18MB318318AF28781901B43910F985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>
 <8E369DD9-5F8D-4206-9A8E-AF9F6BCA6FF3@cgl.ucsf.edu>
 <MN2PR18MB31833DCACA944C7E5E64F74985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>
Message-ID: <00679D17-4455-4330-9C08-70C515F9F9EB@cgl.ucsf.edu>

Hi Dominique,
	In the Mac Finder, use the Go?Go To Folder? menu item and in the resulting dialog type ~/.chimera .  This will get you to the folder where Chimera saves preferences.  In that folder rename the ?preferences? file to some other name.  Then start Chimera and see if that makes any difference.

?Eric

> On Feb 24, 2020, at 1:05 PM, Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu> wrote:
> 
> Hello,
> 
> 
> The second one. I can open chimera from the command line with the maps I want or from a file browser but if I click browse in a session, the session immediately exits.
> 
> Best,
> Dominique
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Sent: Monday, February 24, 2020 3:54 PM
> To: Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] chimera exiting every time after clicking browse
>  
> Hi Dominique,
> Does this mean that you cannot start Chimera at all, or that you when you browse for a file to open from within Chimera that it exits?
> 
> ?Eric
> 
> 
> Eric Pettersen
> UCSF Computer Graphics Lab
> 
> 
> 
>> On Feb 24, 2020, at 9:50 AM, Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu <mailto:dgutierrez at gradcenter.cuny.edu>> wrote:
>> 
>> Hello,
>> 
>> I have MacOS Catalina 10.15.3. Chimera is exiting every time after clicking browse. Versions 1.13 and 1.14 are doing this.
>> 
>> Best,
>> Dominique
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From dgutierrez at gradcenter.cuny.edu  Mon Feb 24 13:56:50 2020
From: dgutierrez at gradcenter.cuny.edu (Dominique  Gutierrez)
Date: Mon, 24 Feb 2020 21:56:50 +0000
Subject: [Chimera-users] chimera exiting every time after clicking browse
In-Reply-To: <00679D17-4455-4330-9C08-70C515F9F9EB@cgl.ucsf.edu>
References: <MN2PR18MB318318AF28781901B43910F985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>
 <8E369DD9-5F8D-4206-9A8E-AF9F6BCA6FF3@cgl.ucsf.edu>
 <MN2PR18MB31833DCACA944C7E5E64F74985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>,
 <00679D17-4455-4330-9C08-70C515F9F9EB@cgl.ucsf.edu>
Message-ID: <MN2PR18MB318327FCA65383912C62E23485EC0@MN2PR18MB3183.namprd18.prod.outlook.com>

Hello Eric,

That worked. Thank you!

Best,
Dominique
________________________________
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Monday, February 24, 2020 4:32 PM
To: Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] chimera exiting every time after clicking browse

Hi Dominique,
In the Mac Finder, use the Go?Go To Folder? menu item and in the resulting dialog type ~/.chimera .  This will get you to the folder where Chimera saves preferences.  In that folder rename the ?preferences? file to some other name.  Then start Chimera and see if that makes any difference.

?Eric

On Feb 24, 2020, at 1:05 PM, Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu<mailto:dgutierrez at gradcenter.cuny.edu>> wrote:

Hello,


The second one. I can open chimera from the command line with the maps I want or from a file browser but if I click browse in a session, the session immediately exits.

Best,
Dominique
________________________________
From: Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>>
Sent: Monday, February 24, 2020 3:54 PM
To: Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu<mailto:dgutierrez at gradcenter.cuny.edu>>
Cc: chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] chimera exiting every time after clicking browse

Hi Dominique,
Does this mean that you cannot start Chimera at all, or that you when you browse for a file to open from within Chimera that it exits?

?Eric

Eric Pettersen
UCSF Computer Graphics Lab



On Feb 24, 2020, at 9:50 AM, Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu<mailto:dgutierrez at gradcenter.cuny.edu>> wrote:

Hello,

I have MacOS Catalina 10.15.3. Chimera is exiting every time after clicking browse. Versions 1.13 and 1.14 are doing this.

Best,
Dominique
_______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From pett at cgl.ucsf.edu  Mon Feb 24 13:57:41 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 24 Feb 2020 13:57:41 -0800
Subject: [Chimera-users] chimera exiting every time after clicking browse
In-Reply-To: <MN2PR18MB318327FCA65383912C62E23485EC0@MN2PR18MB3183.namprd18.prod.outlook.com>
References: <MN2PR18MB318318AF28781901B43910F985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>
 <8E369DD9-5F8D-4206-9A8E-AF9F6BCA6FF3@cgl.ucsf.edu>
 <MN2PR18MB31833DCACA944C7E5E64F74985EC0@MN2PR18MB3183.namprd18.prod.outlook.com>
 <00679D17-4455-4330-9C08-70C515F9F9EB@cgl.ucsf.edu>
 <MN2PR18MB318327FCA65383912C62E23485EC0@MN2PR18MB3183.namprd18.prod.outlook.com>
Message-ID: <28EE98A5-D0AD-4B4A-B449-19D8391990B7@cgl.ucsf.edu>

Glad it worked!

?Eric

> On Feb 24, 2020, at 1:56 PM, Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu> wrote:
> 
> Hello Eric,
> 
> That worked. Thank you!
> 
> Best,
> Dominique
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Sent: Monday, February 24, 2020 4:32 PM
> To: Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] chimera exiting every time after clicking browse
>  
> Hi Dominique,
> In the Mac Finder, use the Go?Go To Folder? menu item and in the resulting dialog type ~/.chimera .  This will get you to the folder where Chimera saves preferences.  In that folder rename the ?preferences? file to some other name.  Then start Chimera and see if that makes any difference.
> 
> ?Eric
> 
>> On Feb 24, 2020, at 1:05 PM, Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu <mailto:dgutierrez at gradcenter.cuny.edu>> wrote:
>> 
>> Hello,
>> 
>> 
>> The second one. I can open chimera from the command line with the maps I want or from a file browser but if I click browse in a session, the session immediately exits.
>> 
>> Best,
>> Dominique
>> From: Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>>
>> Sent: Monday, February 24, 2020 3:54 PM
>> To: Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu <mailto:dgutierrez at gradcenter.cuny.edu>>
>> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
>> Subject: Re: [Chimera-users] chimera exiting every time after clicking browse
>>  
>> Hi Dominique,
>> Does this mean that you cannot start Chimera at all, or that you when you browse for a file to open from within Chimera that it exits?
>> 
>> ?Eric
>> 
>> 
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>> 
>> 
>> 
>>> On Feb 24, 2020, at 9:50 AM, Dominique Gutierrez <dgutierrez at gradcenter.cuny.edu <mailto:dgutierrez at gradcenter.cuny.edu>> wrote:
>>> 
>>> Hello,
>>> 
>>> I have MacOS Catalina 10.15.3. Chimera is exiting every time after clicking browse. Versions 1.13 and 1.14 are doing this.
>>> 
>>> Best,
>>> Dominique
>>> _______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From tasneem1188 at gmail.com  Mon Feb 24 13:45:03 2020
From: tasneem1188 at gmail.com (Tasneem Vaid)
Date: Mon, 24 Feb 2020 15:45:03 -0600
Subject: [Chimera-users] visualizing formal charges
Message-ID: <CALA4EtJkG+6LvSH64Q-nu2WoDj2C16S95FYKU5jkhFpRSzzHUA@mail.gmail.com>

Hi everyone,

I want to see the formal charges on the ligand as well as the receptor. Is
there a way to get that in Chimera?

There is an option of setting charges under ?label?, but that gives partial
charges and not formal.

Thanks,
Tasneem
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From meng at cgl.ucsf.edu  Mon Feb 24 15:20:49 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 24 Feb 2020 15:20:49 -0800
Subject: [Chimera-users] visualizing formal charges
In-Reply-To: <CALA4EtJkG+6LvSH64Q-nu2WoDj2C16S95FYKU5jkhFpRSzzHUA@mail.gmail.com>
References: <CALA4EtJkG+6LvSH64Q-nu2WoDj2C16S95FYKU5jkhFpRSzzHUA@mail.gmail.com>
Message-ID: <7ECA40D1-7921-4637-A5A4-D1DABE6C21BE@cgl.ucsf.edu>

Hi Tasneem,
Sorry, I can?t think of a way to directly label by formal charge, other than by creating these labels manually yourself.  If you add hydrogens, you may be able to infer the formal charge just by looking at the hydrogens, or if you label by atom type, you may be able to infer the formal charge based on the knowledge of which types represent formal charge.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

Commands to label by atom type: 

labelopt info idatmType
la O | N

(that middle thing is a vertical bar, not a capital letter I or lowercase letter l)

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/labelopt.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#atprops>

If you know the formal charge and you just want to create labels illustrating this for a figure, you can manually add them as 2D Labels, or by changing the text in the regular (?3D? labels) using the ?setattr? command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

E.g. 

open 1gcn
disp
setattr a label "-? :asp,glu at od1
setattr a label ?+? :lys at nz

For 2D Labels (that don?t move when you move the structure) see:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.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 Feb 24, 2020, at 1:45 PM, Tasneem Vaid <tasneem1188 at gmail.com> wrote:
> 
> Hi everyone,
> I want to see the formal charges on the ligand as well as the receptor. Is there a way to get that in Chimera? 
> There is an option of setting charges under ?label?, but that gives partial charges and not formal.
> Thanks,
> Tasneem 



From pett at cgl.ucsf.edu  Mon Feb 24 15:27:12 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 24 Feb 2020 15:27:12 -0800
Subject: [Chimera-users] visualizing formal charges
In-Reply-To: <7ECA40D1-7921-4637-A5A4-D1DABE6C21BE@cgl.ucsf.edu>
References: <CALA4EtJkG+6LvSH64Q-nu2WoDj2C16S95FYKU5jkhFpRSzzHUA@mail.gmail.com>
 <7ECA40D1-7921-4637-A5A4-D1DABE6C21BE@cgl.ucsf.edu>
Message-ID: <31428F80-87FA-44EE-88CB-B10F8DB021B7@cgl.ucsf.edu>

In the rare case where a PDB lists the formal charges in columns 79-80 of the ATOM record (as per: wwPDB Format version 3.3: Coordinate Section <http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM>; [and very few entries have that info]), then the atoms in Chimera will have a ?formalCharge? attribute that you can label by,

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Feb 24, 2020, at 3:20 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Tasneem,
> Sorry, I can?t think of a way to directly label by formal charge, other than by creating these labels manually yourself.  If you add hydrogens, you may be able to infer the formal charge just by looking at the hydrogens, or if you label by atom type, you may be able to infer the formal charge based on the knowledge of which types represent formal charge.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>
> 
> Commands to label by atom type: 
> 
> labelopt info idatmType
> la O | N
> 
> (that middle thing is a vertical bar, not a capital letter I or lowercase letter l)
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/labelopt.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#atprops>
> 
> If you know the formal charge and you just want to create labels illustrating this for a figure, you can manually add them as 2D Labels, or by changing the text in the regular (?3D? labels) using the ?setattr? command.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> 
> E.g. 
> 
> open 1gcn
> disp
> setattr a label "-? :asp,glu at od1
> setattr a label ?+? :lys at nz
> 
> For 2D Labels (that don?t move when you move the structure) see:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.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 Feb 24, 2020, at 1:45 PM, Tasneem Vaid <tasneem1188 at gmail.com> wrote:
>> 
>> Hi everyone,
>> I want to see the formal charges on the ligand as well as the receptor. Is there a way to get that in Chimera? 
>> There is an option of setting charges under ?label?, but that gives partial charges and not formal.
>> Thanks,
>> Tasneem 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From svle at tiscali.it  Mon Feb 24 23:25:17 2020
From: svle at tiscali.it (svle at tiscali.it)
Date: Tue, 25 Feb 2020 08:25:17 +0100
Subject: [Chimera-users] Font size in menu bar
Message-ID: <2329e8ba15a1fc20dee8306c06af9fbb@tiscali.it>

  
Hi, 
there exists a method to increase the font size  
for the menu
bar? 
Thanks in advance 
Saverio  


Con Tiscali Mobile Smart 30 4G hai minuti illimitati, 100 SMS e 30 Giga in 4G a soli 8,99? al mese. http://tisca.li/smart30

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From Cheryl.Cain at ucsf.edu  Tue Feb 25 09:33:44 2020
From: Cheryl.Cain at ucsf.edu (Cain, Cheryl A)
Date: Tue, 25 Feb 2020 17:33:44 +0000
Subject: [Chimera-users] FW: website broken?
In-Reply-To: <25d2a1b7-2cf2-c357-523a-789a6c5f24ae@hpc.nih.gov>
References: <25d2a1b7-2cf2-c357-523a-789a6c5f24ae@hpc.nih.gov>
Message-ID: <194D44CC-5541-4E25-B000-63A323F885AD@ucsf.edu>

Hello,

Passing on this message to the help desk.

Thanks,
Cheryl

Cheryl Cain
Operations Coordinator
Department of Pharmaceutical Chemistry
UCSF
***Please note that my work hours are Tu-Wed-Th, 9am-4pm***
 

?On 2/24/20, 7:56 AM, "Hoover, David (NIH/CIT) [E]" <hooverdm at hpc.nih.gov> wrote:

    Hi,
    
    The homepage for Chimera (https://www.cgl.ucsf.edu/chimera/) appears to be down or blocked.  Is everything ok?
    
    David
    -- 
    David Hoover, Ph.D.
    Computational Biologist
    High Performance Computing Services, Center for Information Technology, National Institutes of Health
    12 South Dr., Rm 2N207
    Bethesda, MD 20892, USA
    TEL: (+1) 301-435-2986
    Email: hooverdm at hpc.nih.gov
    



From meng at cgl.ucsf.edu  Tue Feb 25 12:51:15 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 25 Feb 2020 12:51:15 -0800
Subject: [Chimera-users] FW: website broken?
In-Reply-To: <194D44CC-5541-4E25-B000-63A323F885AD@ucsf.edu>
References: <25d2a1b7-2cf2-c357-523a-789a6c5f24ae@hpc.nih.gov>
 <194D44CC-5541-4E25-B000-63A323F885AD@ucsf.edu>
Message-ID: <67205FC3-8C7A-4442-9CE5-BA13807CAA9C@cgl.ucsf.edu>

We had a temporary issue with the website, should be OK now.
Elaine


> On Feb 25, 2020, at 9:33 AM, Cain, Cheryl A <Cheryl.Cain at ucsf.edu> wrote:
> 
> Hello,
> 
> Passing on this message to the help desk.
> 
> Thanks,
> Cheryl
> 
> Cheryl Cain
> Operations Coordinator
> Department of Pharmaceutical Chemistry
> UCSF
> ***Please note that my work hours are Tu-Wed-Th, 9am-4pm***
> 
> 
> ?On 2/24/20, 7:56 AM, "Hoover, David (NIH/CIT) [E]" <hooverdm at hpc.nih.gov> wrote:
> 
>    Hi,
> 
>    The homepage for Chimera (https://www.cgl.ucsf.edu/chimera/) appears to be down or blocked.  Is everything ok?
> 
>    David
>    -- 
>    David Hoover, Ph.D.
>    Computational Biologist
>    High Performance Computing Services, Center for Information Technology, National Institutes of Health
>    12 South Dr., Rm 2N207
>    Bethesda, MD 20892, USA
>    TEL: (+1) 301-435-2986
>    Email: hooverdm at hpc.nih.gov
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From pett at cgl.ucsf.edu  Tue Feb 25 14:29:09 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 25 Feb 2020 14:29:09 -0800
Subject: [Chimera-users] Font size in menu bar
In-Reply-To: <2329e8ba15a1fc20dee8306c06af9fbb@tiscali.it>
References: <2329e8ba15a1fc20dee8306c06af9fbb@tiscali.it>
Message-ID: <C670EB22-DD48-424B-85C7-EE4F8A5DBE1B@cgl.ucsf.edu>

There is no Chimera-specific way to increase the menu font size.  Typically whatever method is used for increasing menu font sizes in general for the OS you are running will work.  You may have to google for that, e.g. google ?mac menu font size?.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



> On Feb 24, 2020, at 11:25 PM, svle at tiscali.it wrote:
> 
> Hi,
> there exists a method to increase the font size
> for the menu bar?
> Thanks in advance
> Saverio
> 
> 
> 
> Con Tiscali Mobile Smart 30 4G hai minuti illimitati, 100 SMS e 30 Giga in 4G a soli 8,99? al mese. http://tisca.li/smart30 <http://tisca.li/smart30>
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From davidsaez at udec.cl  Tue Feb 25 20:07:26 2020
From: davidsaez at udec.cl (=?UTF-8?Q?David_S=C3=A1ez?=)
Date: Wed, 26 Feb 2020 01:07:26 -0300
Subject: [Chimera-users] Biological assembly from the asymmetric unit and
	using it for MD
Message-ID: <CAHC+6jjYEUxnCvaNz1yAba8vAXdd4o_pbmf=L1X83TLNZUQiDg@mail.gmail.com>

Hi,

very basic question here. I found ways to generate the tetramer biological
assembly  starting from the monomer asymmetric unit . (Downloading the BA
directly from RCSB and alternatively using the BU function in Chimera's
Model panel). The procedures are equivalent AFAIU.

Now, this generated structure should be a valid starting point for
molecular dynamics simulations? Does anybody have experience with that?.
There are other structures showing the tetramer, but the resolution is too
low.

Thanks!

David.
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From miguel.romero at icvv.es  Wed Feb 26 07:25:17 2020
From: miguel.romero at icvv.es (Miguel Romero)
Date: Wed, 26 Feb 2020 16:25:17 +0100
Subject: [Chimera-users] Contour plot of intersurf surface
Message-ID: <2557dade-b750-dac1-d9d9-a5948490b73e@icvv.es>

Hello,

I am looking for a way to generate a contour plot from the interface 
surface generated with the intersurf command. The idea is to have a 2D 
representation of the interface. I would really appreciate any suggestion.

Thanks in advance,
Miguel


From meng at cgl.ucsf.edu  Wed Feb 26 09:29:18 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 26 Feb 2020 09:29:18 -0800
Subject: [Chimera-users] Biological assembly from the asymmetric unit
 and using it for MD
In-Reply-To: <CAHC+6jjYEUxnCvaNz1yAba8vAXdd4o_pbmf=L1X83TLNZUQiDg@mail.gmail.com>
References: <CAHC+6jjYEUxnCvaNz1yAba8vAXdd4o_pbmf=L1X83TLNZUQiDg@mail.gmail.com>
Message-ID: <203306C5-D28F-42D3-8EB3-D76F6B479EEF@cgl.ucsf.edu>

Hi David,
The assemblies defined in the Protein Databank are the most valid information available, i.e., I can?t think of what else you would use. There may be limitations from the resolution of the structure, as well as what the authors believe to be the biological assembly, but that will always be the case.  Also if you are going to invest computational time on MD, presumably you will read carefully any publication that describes the structure (see the page for that entry at the RCSB PDB website for the reference).

If you are concerned about the inferred stoichiometry (e.g. dimer or a tetramer?) you can use programs like PISA or look in databases like 3DComplex and PiQSi:

<http://www.ccp4.ac.uk/pisa/>
<http://www.3dcomplex.org/>
<http://www.piqsi.org/>

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

> On Feb 25, 2020, at 8:07 PM, David S?ez <davidsaez at udec.cl> wrote:
> 
> Hi, 
> very basic question here. I found ways to generate the tetramer biological assembly  starting from the monomer asymmetric unit . (Downloading the BA directly from RCSB and alternatively using the BU function in Chimera's Model panel). The procedures are equivalent AFAIU. 
> Now, this generated structure should be a valid starting point for molecular dynamics simulations? Does anybody have experience with that?. There are other structures showing the tetramer, but the resolution is too low.
> Thanks!
> David.



From meng at cgl.ucsf.edu  Wed Feb 26 09:39:11 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 26 Feb 2020 09:39:11 -0800
Subject: [Chimera-users] Contour plot of intersurf surface
In-Reply-To: <2557dade-b750-dac1-d9d9-a5948490b73e@icvv.es>
References: <2557dade-b750-dac1-d9d9-a5948490b73e@icvv.es>
Message-ID: <651BF3B5-DC72-4767-B4B9-A45D6DC6F47D@cgl.ucsf.edu>

Hi Miguel,
I can?t think of a way to generate a 2D representation from the intersurf surface.  It is unclear to me exactly what you mean, however.  What are the contours showing?  If the 3D shape, why not just show as 3D?

You may want to take a look at another program, MolSurfer, which generates 2D representations of hydrophobicity and electrostatic potential at an interface.  I never used it myself, but that is what the paper about this program (link below) shows.

Molsurfer web server:
<https://molsurfer.h-its.org/>

Molsurfer paper:
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168994/>

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

> On Feb 26, 2020, at 7:25 AM, Miguel Romero <miguel.romero at icvv.es> wrote:
> 
> Hello,
> I am looking for a way to generate a contour plot from the interface surface generated with the intersurf command. The idea is to have a 2D representation of the interface. I would really appreciate any suggestion.
> Thanks in advance,
> Miguel



From davidsaez at udec.cl  Wed Feb 26 11:59:59 2020
From: davidsaez at udec.cl (=?UTF-8?Q?David_S=C3=A1ez?=)
Date: Wed, 26 Feb 2020 16:59:59 -0300
Subject: [Chimera-users] Biological assembly from the asymmetric unit
 and using it for MD
In-Reply-To: <203306C5-D28F-42D3-8EB3-D76F6B479EEF@cgl.ucsf.edu>
References: <CAHC+6jjYEUxnCvaNz1yAba8vAXdd4o_pbmf=L1X83TLNZUQiDg@mail.gmail.com>
 <203306C5-D28F-42D3-8EB3-D76F6B479EEF@cgl.ucsf.edu>
Message-ID: <CAHC+6jjsdU7Yc2P5yUxUyTHSkcMhU2iAdoqoQYB0kNhd2bq_Gw@mail.gmail.com>

Dear Elaine,

Many thanks for your reply. I already read the articles and I am sure the
stoichiometry is correct. My concern was more related to the possible
issues raised from an asymmetric unit smaller than the biological assembly
(I have never seen this case before). But I was doing some research and
expanding my very limited knowledge about crystallograhy, after removing
some clashing solvent molecules, the MD should run OK.

Thanks again for your help.

David.

On Wed, Feb 26, 2020 at 2:29 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi David,
> The assemblies defined in the Protein Databank are the most valid
> information available, i.e., I can?t think of what else you would use.
> There may be limitations from the resolution of the structure, as well as
> what the authors believe to be the biological assembly, but that will
> always be the case.  Also if you are going to invest computational time on
> MD, presumably you will read carefully any publication that describes the
> structure (see the page for that entry at the RCSB PDB website for the
> reference).
>
> If you are concerned about the inferred stoichiometry (e.g. dimer or a
> tetramer?) you can use programs like PISA or look in databases like
> 3DComplex and PiQSi:
>
> <http://www.ccp4.ac.uk/pisa/>
> <http://www.3dcomplex.org/>
> <http://www.piqsi.org/>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Feb 25, 2020, at 8:07 PM, David S?ez <davidsaez at udec.cl> wrote:
> >
> > Hi,
> > very basic question here. I found ways to generate the tetramer
> biological assembly  starting from the monomer asymmetric unit .
> (Downloading the BA directly from RCSB and alternatively using the BU
> function in Chimera's Model panel). The procedures are equivalent AFAIU.
> > Now, this generated structure should be a valid starting point for
> molecular dynamics simulations? Does anybody have experience with that?.
> There are other structures showing the tetramer, but the resolution is too
> low.
> > Thanks!
> > David.
>
>
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From shawn.rumrill at rutgers.edu  Wed Feb 26 09:30:35 2020
From: shawn.rumrill at rutgers.edu (Shawn Rumrill)
Date: Wed, 26 Feb 2020 17:30:35 +0000
Subject: [Chimera-users] Unable to Install ChimeraX 1.14 on MacOS 10.15.3
Message-ID: <3015BC73-2E57-45F0-A737-BB6E6605585D@cabm.rutgers.edu>

Hello,

I recently tried installing ChimeraX 1.14 on my MacBook Pro OS 10.15.3. I receive a message that the software cannot be installed because it cannot be verified and needs to be updated. So you have any solution to this problem? Screenshot of error message attached.

Best,

Shawn Rumrill
srr131 at cabm.rutgers.edu<mailto:srr131 at cabm.rutgers.edu>

[cid:F2EDAD80-53DE-442C-B590-72AD2EE15870 at ruw.rutgers.edu]
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From pett at cgl.ucsf.edu  Wed Feb 26 12:57:34 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 26 Feb 2020 12:57:34 -0800
Subject: [Chimera-users] Unable to Install ChimeraX 1.14 on MacOS 10.15.3
In-Reply-To: <3015BC73-2E57-45F0-A737-BB6E6605585D@cabm.rutgers.edu>
References: <3015BC73-2E57-45F0-A737-BB6E6605585D@cabm.rutgers.edu>
Message-ID: <6BB137F5-1A4A-492E-A4F2-0C6D2F926C5A@cgl.ucsf.edu>

Hi Shawn,
	We are aware of this issue and are working on it.  Please see this previous mailing-list post for a workaround: [Chimera-users] Chimera Download issue <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-February/016457.html>

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Feb 26, 2020, at 9:30 AM, Shawn Rumrill <shawn.rumrill at rutgers.edu> wrote:
> 
> Hello,
> 
> I recently tried installing ChimeraX 1.14 on my MacBook Pro OS 10.15.3. I receive a message that the software cannot be installed because it cannot be verified and needs to be updated. So you have any solution to this problem? Screenshot of error message attached.
> 
> Best,
> 
> Shawn Rumrill
> srr131 at cabm.rutgers.edu <mailto:srr131 at cabm.rutgers.edu>
> 
> <Screen Shot 2020-02-26 at 12.27.23 PM.png>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From coyote_v2002 at yahoo.com  Thu Feb 27 01:14:34 2020
From: coyote_v2002 at yahoo.com (Visvaldas K.)
Date: Thu, 27 Feb 2020 09:14:34 +0000 (UTC)
Subject: [Chimera-users] Ctrl-Shift-click iimpaired on MacOS Mojave
References: <1093746315.873598.1582794874805.ref@mail.yahoo.com>
Message-ID: <1093746315.873598.1582794874805@mail.yahoo.com>

Dear Chimera Users,
recently I noticed a bug (?): I am not able to multiple select atoms using Ctrl-Shift-click easily, as I was able before (I am not sure when the problem started).
If I use mouse, sometimes I am able to select two atoms after a while by going back and forth between the two atoms and keep clicking, and after some time I succeed to select, but but the required number of tries is? unpredictable. However, with the touchpad, forget it, it does not work at all.
Needless to say, I find this to be very annoying. 

I tried today's Chimera daily build, versions 14 and 13.1 with the same results.
I am running MacOS Mojave.

Sincerely yours,
Visvaldas
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From miguel.romero at icvv.es  Thu Feb 27 03:54:16 2020
From: miguel.romero at icvv.es (Miguel Romero)
Date: Thu, 27 Feb 2020 12:54:16 +0100
Subject: [Chimera-users] Contour plot of intersurf surface
In-Reply-To: <651BF3B5-DC72-4767-B4B9-A45D6DC6F47D@cgl.ucsf.edu>
References: <2557dade-b750-dac1-d9d9-a5948490b73e@icvv.es>
 <651BF3B5-DC72-4767-B4B9-A45D6DC6F47D@cgl.ucsf.edu>
Message-ID: <34e6e188-2ddb-9b64-6fe2-4f7eb0d029c3@icvv.es>

Hello Elaine,

Thank you for your response. It's been very useful.

Yes, I am looking for something similar to MolSurfer's output: 2D 
projections of interface surfaces. The only problem I see with MolSurfer 
is that I have not been able to find a way to download the images of the 
2D projections yet.

Do you think those type of 2D projections could be done with Chimera? I 
am thinking, for instance, in generating the 2D projections from the 
vertex coordinates of the surface generated with Chimera intersurf 
command. Does it seem a good idea?

Thank you very much,
Miguel

On 26/2/20 18:39, Elaine Meng wrote:
> Hi Miguel,
> I can?t think of a way to generate a 2D representation from the intersurf surface.  It is unclear to me exactly what you mean, however.  What are the contours showing?  If the 3D shape, why not just show as 3D?
>
> You may want to take a look at another program, MolSurfer, which generates 2D representations of hydrophobicity and electrostatic potential at an interface.  I never used it myself, but that is what the paper about this program (link below) shows.
>
> Molsurfer web server:
> <https://molsurfer.h-its.org/>
>
> Molsurfer paper:
> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168994/>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Feb 26, 2020, at 7:25 AM, Miguel Romero <miguel.romero at icvv.es> wrote:
>>
>> Hello,
>> I am looking for a way to generate a contour plot from the interface surface generated with the intersurf command. The idea is to have a 2D representation of the interface. I would really appreciate any suggestion.
>> Thanks in advance,
>> Miguel

From Fiora2019 at 163.com  Wed Feb 26 22:00:35 2020
From: Fiora2019 at 163.com (=?utf-8?Q?=E9=99=88=E6=96=87=E5=BF=83?=)
Date: Thu, 27 Feb 2020 14:00:35 +0800
Subject: [Chimera-users] debug
Message-ID: <5E575B12.3CCCC8.22899@mail-m971.mail.163.com>



When I open chimera, introduction webpages will continuously open and many interfaces pop out. Could you please help me solve the problem? Thanks a lot.
??? Windows 10 ?????

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From deligkaris at gmail.com  Thu Feb 27 08:21:02 2020
From: deligkaris at gmail.com (Christos Deligkaris)
Date: Thu, 27 Feb 2020 10:21:02 -0600
Subject: [Chimera-users] visualizing potential with volume data
In-Reply-To: <E17A0AB1-5B45-4770-B3FE-E3A7AEF4EC67@cgl.ucsf.edu>
References: <CAAHQ3wnCgCWQzqBv0=LCTgE4HBBzcu=eMTZwWAFAC0t-s7J13Q@mail.gmail.com>
 <E17A0AB1-5B45-4770-B3FE-E3A7AEF4EC67@cgl.ucsf.edu>
Message-ID: <CAAHQ3wmJ7_skz8FYEi2M2SpUoH6bBg35QOw_YzwjKQVJkrqPyw@mail.gmail.com>

Thank you Elaine, now I understand better. I was under the impression
that using cube files was only consistent with the options related to
"volume data". I checked that using an offset of 0 with the
electrostatic potential option gives the same result as the volume
data value.

Related to this:  Can I use a cube file to generate an equipotential map?

Do you recommend Chimera or ChimeraX? What are the strengths of
ChimeraX currently?

Best wishes,

Christos Deligkaris, PhD
Assistant Professor of Physics

On Mon, Feb 24, 2020 at 3:22 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Dear Christos,
> If the option to color by ?electrostatic potential? is chosen in the Surface Color dialog, then no matter what kind of volume data file you opened, it has the electrostatic options including offset 1.4 A.  You can click Options on the dialog to check that they are all set to the values that you want.
>
> The surface image you gave a link to looks the same to me as the other molecular surfaces in Chimera, in terms of shape.  The coloring is too saturated in my opinion (i.e. should have more ?white? instead of all blue and red) but that is just a choice of the coloring levels, not related to the shape of the surface.  Maybe it was made a long time ago without using an offset, but I don?t know ?  I didn?t make that image.
>
> If you want to compare what you get using the same settings, and more appropriate coloring levels in my opinion, instead take a look at the image tutorial ?coloring by surface properties?:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.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 Feb 24, 2020, at 11:57 AM, Christos Deligkaris <deligkaris at gmail.com> wrote:
> >
> > dear all,
> >
> > I have obtained a cube file from NWChem with the electrostatic
> > potential around a molecule. I visualized the molecular surface using
> > Actions->Surface->Show and then colored it using the volume data
> > (followed instructions
> > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in
> > tools->surface color (electrostatic surface coloring)) .
> >
> > Since I do not have my data stored in a potential file, can I still do
> > the surface offset? The chimera tool webpage discusses why that is
> > preferred than showing the potential on the solvent excluded surface
> > and it seems to me that option to not be available with volume data.
> >
> > Also, my surface does not look like the electrostatic potential
> > surface shown here:
> > https://www.cgl.ucsf.edu/chimera/data/tutorials/maps08/volume-basics.html
> > . The molecular surface we get with Action->Surface->Show seems to be
> > constructed with greater atomic radii than the one shown in that
> > image. I am not sure how important that is though. Is there a way to
> > ask Chimera to visualize the electrostatic potential volume data with
> > the same options Chimera would use if it was reading a Delphi, PBS
> > file?
> >
> > Best wishes,
> >
> > Christos Deligkaris, PhD
> > Assistant Professor of Physics
>


From peter.engelhardt at helsinki.fi  Thu Feb 27 09:44:09 2020
From: peter.engelhardt at helsinki.fi (Engelhardt, Peter)
Date: Thu, 27 Feb 2020 17:44:09 +0000
Subject: [Chimera-users] How to change font size for scale bar
In-Reply-To: <B03EDB41-048A-4891-A837-D7A3154DC596@cgl.ucsf.edu>
References: <560BFD3E-75E2-49B1-9AB8-B4E09B8775F4@helsinki.fi>,
 <B03EDB41-048A-4891-A837-D7A3154DC596@cgl.ucsf.edu>
Message-ID: <HE1PR0701MB2715A7257BB82FB60C12D4669AEB0@HE1PR0701MB2715.eurprd07.prod.outlook.com>

Dear Elaine Meng,

No problem anymore

Many thanks

Cheers
Peter



___________________________________

Peter Engelhardt, Dr.Sc., Docent
Adjunct Professor in Molecular Genetics
Unit of Molecular Electron Tomography

Nanomicroscopy Center (NMC),
Department of Applied Physics
Aalto University, School of Science and Technology,
Puumiehenkuja 2, FI02150 Espoo
Finland

Email: Peter.Engelhardt at Helsinki.Fi<https://webmail.helsinki.fi/horde/imp/dynamic.php?page=message&buid=2535&mailbox=SU5CT1guU2VudA&token=54ajrYkbcvzm9_7lJktocA2&uniq=1445589606808#>
Email: Peter.Engelhardt at Aalto.Fi<https://webmail.helsinki.fi/horde/imp/dynamic.php?page=message&buid=2535&mailbox=SU5CT1guU2VudA&token=54ajrYkbcvzm9_7lJktocA2&uniq=1445589606808#>

<http://www.lce.hut.fi/~engelhar/>
URL: https://users.aalto.fi/~engelhp1/
Mobil: +358-400193342

Home address:
Lindstedstv?gen 1 B 7
FIN-02700 Grankulla,
Finland

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, February 20, 2020 8:11 PM
To: Engelhardt, Peter <peter.engelhardt at helsinki.fi>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] How to change font size for scale bar

Hi Peter,
The scale bar is implemented as atoms/bonds and the text is essentially an atom label.  Atom label size (all labels at once) can be set in the Preferences (open from Favorites menu), category: Labels.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Labels>

This is mentioned in the Scale Bar ?limitations? section at the bottom of the page but is easy to miss?
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/scalebar.html>

For more control over label size independent of any atom labels, you could make the label blank in in the Scale Bar tool and instead add it as a 2D Label (menu: Tools? Utilities? 2D Label). 2D labels may also include symbols such as the Angstrom symbol.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.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 Feb 20, 2020, at 4:47 AM, Engelhardt, Peter <peter.engelhardt at helsinki.fi> wrote:
>
> Hi
> We can?t find any options for font size in scale bar wondering if possible.
> Any suggestions
> Cheers
> Peter

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From peter.engelhardt at helsinki.fi  Thu Feb 27 10:05:45 2020
From: peter.engelhardt at helsinki.fi (Engelhardt, Peter)
Date: Thu, 27 Feb 2020 18:05:45 +0000
Subject: [Chimera-users] Auto-Stereo 3D
Message-ID: <HE1PR0701MB2715E7D1A5B95BB2ED20B9FA9AEB0@HE1PR0701MB2715.eurprd07.prod.outlook.com>

Dear Chimera developers,

We are most interested of always using stereo in Chimera.
Lately there have been presented Auto-Stereo 3D displays: https://www.tri-evolution.com/en/auto-stereo-3d/
Auto-Stereo 3D - TRI Evolution ? 3D without glasses<https://www.tri-evolution.com/en/auto-stereo-3d/>
We unfold digital vision. We unfold your product and video data in ?GLASSES-FREE 3D?. We offer numerous services and solutions for perfect handling of the latest auto stereo 3D technology. We are an official Solutions Partner of 3D Global. Find out everything worth knowing about our AS3D offer in this section. AS3D Hardware AS3D Hardware More [?]
www.tri-evolution.com
Because of this convenience in 'no need to use any stereo glasses' we wonder if Chimera is supporting Auto-stereo 3D displays, now or in near future.

We thank you in advance

Cheers
Peter

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From meng at cgl.ucsf.edu  Thu Feb 27 10:07:16 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 27 Feb 2020 10:07:16 -0800
Subject: [Chimera-users] Contour plot of intersurf surface
In-Reply-To: <34e6e188-2ddb-9b64-6fe2-4f7eb0d029c3@icvv.es>
References: <2557dade-b750-dac1-d9d9-a5948490b73e@icvv.es>
 <651BF3B5-DC72-4767-B4B9-A45D6DC6F47D@cgl.ucsf.edu>
 <34e6e188-2ddb-9b64-6fe2-4f7eb0d029c3@icvv.es>
Message-ID: <F507EB0A-ED44-4854-88EA-3E1AFE93C450@cgl.ucsf.edu>

Hello Miguel,
Seems like you could just take a screenshot of the MolSurfer display, if that is high enough resolution.

There are many good ideas, of course, but we only have limited resources to work on them!  However, I personally have never wished for a 2D projection of an interface. Instead I would just color the surfaces of the two parts forming the interface and then rotate them apart in opposite directions like an open book, to show complementarity.  There is an example of this "open book" approach in the image tutorials? although that tutorial does not color by hydrophobicity or electrostatics, you could imagine doing that, e.g. combining it with parts of the ?surface properties? tutorial.

Opened Interface tutorial
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
Surface properties coloring tutorial
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

Our group?s development effort is now in the ChimeraX program.  You may want to look at the ?interfaces? tool in ChimeraX? see the ?Interface Residue Plot? section at the bottom.  However, it does not currently show coloring by electrostatic potential or other properties.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>

Also ChimeraX is being structured for more outside development of plugins, with a Toolshed website that allows others to upload the plugins they wrote (i.e. if you would be interested in developing a plugin yourself) as well as download plugins from others.
<https://cxtoolshed.rbvi.ucsf.edu/>

If you become interested in ChimeraX, there is a separate chimerax-users at cgl.ucsf.edu mailing list you can join or just send questions.
<http://www.rbvi.ucsf.edu/chimerax/index.html>
<http://www.rbvi.ucsf.edu/chimerax/docs/contact.html>

Best,
Elaine

> On Feb 27, 2020, at 3:54 AM, Miguel Romero <miguel.romero at icvv.es> wrote:
> 
> Hello Elaine,
> 
> Thank you for your response. It's been very useful.
> 
> Yes, I am looking for something similar to MolSurfer's output: 2D projections of interface surfaces. The only problem I see with MolSurfer is that I have not been able to find a way to download the images of the 2D projections yet.
> 
> Do you think those type of 2D projections could be done with Chimera? I am thinking, for instance, in generating the 2D projections from the vertex coordinates of the surface generated with Chimera intersurf command. Does it seem a good idea?
> 
> Thank you very much,
> Miguel
> 
> On 26/2/20 18:39, Elaine Meng wrote:
>> Hi Miguel,
>> I can?t think of a way to generate a 2D representation from the intersurf surface.  It is unclear to me exactly what you mean, however.  What are the contours showing?  If the 3D shape, why not just show as 3D?
>> 
>> You may want to take a look at another program, MolSurfer, which generates 2D representations of hydrophobicity and electrostatic potential at an interface.  I never used it myself, but that is what the paper about this program (link below) shows.
>> 
>> Molsurfer web server:
>> <https://molsurfer.h-its.org/>
>> 
>> Molsurfer paper:
>> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168994/>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Feb 26, 2020, at 7:25 AM, Miguel Romero <miguel.romero at icvv.es> wrote:
>>> 
>>> Hello,
>>> I am looking for a way to generate a contour plot from the interface surface generated with the intersurf command. The idea is to have a 2D representation of the interface. I would really appreciate any suggestion.
>>> Thanks in advance,
>>> Miguel



From meng at cgl.ucsf.edu  Thu Feb 27 10:31:53 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 27 Feb 2020 10:31:53 -0800
Subject: [Chimera-users] visualizing potential with volume data
In-Reply-To: <CAAHQ3wmJ7_skz8FYEi2M2SpUoH6bBg35QOw_YzwjKQVJkrqPyw@mail.gmail.com>
References: <CAAHQ3wnCgCWQzqBv0=LCTgE4HBBzcu=eMTZwWAFAC0t-s7J13Q@mail.gmail.com>
 <E17A0AB1-5B45-4770-B3FE-E3A7AEF4EC67@cgl.ucsf.edu>
 <CAAHQ3wmJ7_skz8FYEi2M2SpUoH6bBg35QOw_YzwjKQVJkrqPyw@mail.gmail.com>
Message-ID: <B0CE2FD0-B80D-48CE-A0D6-CDCE35108771@cgl.ucsf.edu>

Hi Christos,
For electrostatic potential (regardless of input file format) it is recommended to use an offset of 1.4 Angstroms for coloring a molecular surface, as discussed in this recent post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-February/016514.html>

Yes, any volume data (values on a 3D grid) including electrostatic potential, density, etc. read from any volume data format can be shown as isosurfaces.  Just don?t use the Surface Coloring tool.  Use the Volume Viewer tool, style ?surface? or ?mesh? ? if you open one of the formats automatically recognized as electrostatic potential, the contour surfaces are hidden  and the Surface Color dialog is shown.  Just dismiss the Surface Color dialog and start Volume Viewer (Tools? Volume Data? Volume Viewer) and show the contour surfaces by clicking the small ?eye? icon (oval) to the right of the step value. It may take several seconds to read the electrostatic potential and display it after you click the icon, depending on the size of the file.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

(I believe the isopotential (contour) surfaces are what is shown automatically when you open a cube file anyway.)  Then in Volume Viewer you can move the thresholds (vertical bars) horizontally along the data histogram to change the contour levels, click the square color well to change colors, etc. as explained here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf>

Whether I recommend Chimera or ChimeraX depends on what you are trying to do.  Generally I would recommend having both.  There is nothing to stop you from having both and using whichever one suits you for a given task: each does some things the other does not, at least yet.  I mostly use ChimeraX and find its commands are easier to remember, but also I need to use it more because I write documentation for new features.

Some of the main advantages of ChimeraX vs. Chimera are listed here:
<http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html>

For features still missing from ChimeraX, see ?missing features? in the download page:
<http://www.rbvi.ucsf.edu/chimerax/download.html>

We are actively developing ChimeraX, so it will have more capabilities nearly every day.  You can scan through the ?feature highlights? and more comprehensively, take a look at the tools and commands listed in the User Guide index:
<http://www.rbvi.ucsf.edu/chimerax/features.html>
<http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html>

There is also a Toolshed web repository for ChimeraX plugins:
<https://cxtoolshed.rbvi.ucsf.edu/>

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

> On Feb 27, 2020, at 8:21 AM, Christos Deligkaris <deligkaris at gmail.com> wrote:
> 
> Thank you Elaine, now I understand better. I was under the impression
> that using cube files was only consistent with the options related to
> "volume data". I checked that using an offset of 0 with the
> electrostatic potential option gives the same result as the volume
> data value.
> 
> Related to this:  Can I use a cube file to generate an equipotential map?
> 
> Do you recommend Chimera or ChimeraX? What are the strengths of
> ChimeraX currently?
> 
> Best wishes,
> 
> Christos Deligkaris, PhD
> Assistant Professor of Physics
> 
> On Mon, Feb 24, 2020 at 3:22 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Dear Christos,
>> If the option to color by ?electrostatic potential? is chosen in the Surface Color dialog, then no matter what kind of volume data file you opened, it has the electrostatic options including offset 1.4 A.  You can click Options on the dialog to check that they are all set to the values that you want.
>> 
>> The surface image you gave a link to looks the same to me as the other molecular surfaces in Chimera, in terms of shape.  The coloring is too saturated in my opinion (i.e. should have more ?white? instead of all blue and red) but that is just a choice of the coloring levels, not related to the shape of the surface.  Maybe it was made a long time ago without using an offset, but I don?t know ?  I didn?t make that image.
>> 
>> If you want to compare what you get using the same settings, and more appropriate coloring levels in my opinion, instead take a look at the image tutorial ?coloring by surface properties?:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.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 Feb 24, 2020, at 11:57 AM, Christos Deligkaris <deligkaris at gmail.com> wrote:
>>> 
>>> dear all,
>>> 
>>> I have obtained a cube file from NWChem with the electrostatic
>>> potential around a molecule. I visualized the molecular surface using
>>> Actions->Surface->Show and then colored it using the volume data
>>> (followed instructions
>>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in
>>> tools->surface color (electrostatic surface coloring)) .
>>> 
>>> Since I do not have my data stored in a potential file, can I still do
>>> the surface offset? The chimera tool webpage discusses why that is
>>> preferred than showing the potential on the solvent excluded surface
>>> and it seems to me that option to not be available with volume data.
>>> 
>>> Also, my surface does not look like the electrostatic potential
>>> surface shown here:
>>> https://www.cgl.ucsf.edu/chimera/data/tutorials/maps08/volume-basics.html
>>> . The molecular surface we get with Action->Surface->Show seems to be
>>> constructed with greater atomic radii than the one shown in that
>>> image. I am not sure how important that is though. Is there a way to
>>> ask Chimera to visualize the electrostatic potential volume data with
>>> the same options Chimera would use if it was reading a Delphi, PBS
>>> file?
>>> 
>>> Best wishes,
>>> 
>>> Christos Deligkaris, PhD
>>> Assistant Professor of Physics
>> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From pett at cgl.ucsf.edu  Thu Feb 27 12:00:41 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 27 Feb 2020 12:00:41 -0800
Subject: [Chimera-users] Ctrl-Shift-click iimpaired on MacOS Mojave
In-Reply-To: <1093746315.873598.1582794874805@mail.yahoo.com>
References: <1093746315.873598.1582794874805.ref@mail.yahoo.com>
 <1093746315.873598.1582794874805@mail.yahoo.com>
Message-ID: <78C60813-B63A-4AD7-BA5E-61693A04C7C4@cgl.ucsf.edu>

Hi Visvaldas,
	I?m having no trouble shift-clicking to select multiple atoms using my desktop mac running Mojave.  Are the atoms depicted as wireframe or something else?  Also, double clicking does not work (known Tk Mac bug), in case that?s what you were doing.  Perhaps you should use Help?Report A Bug to report this, which will provide much more detail about the Mac you are using, version of Chimera, etc.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



> On Feb 27, 2020, at 1:14 AM, Visvaldas K. <coyote_v2002 at yahoo.com> wrote:
> 
> Dear Chimera Users,
> 
> recently I noticed a bug (?): I am not able to multiple select atoms using Ctrl-Shift-click easily, as I was able before (I am not sure when the problem started).
> 
> If I use mouse, sometimes I am able to select two atoms after a while by going back and forth between the two atoms and keep clicking, and after some time I succeed to select, but but the required number of tries is  unpredictable. However, with the touchpad, forget it, it does not work at all.
> 
> Needless to say, I find this to be very annoying. 
> 
> I tried today's Chimera daily build, versions 14 and 13.1 with the same results.
> 
> I am running MacOS Mojave.
> 
> Sincerely yours,
> 
> Visvaldas
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From miguel.romero at icvv.es  Thu Feb 27 12:43:47 2020
From: miguel.romero at icvv.es (Miguel Romero)
Date: Thu, 27 Feb 2020 21:43:47 +0100
Subject: [Chimera-users] Contour plot of intersurf surface
In-Reply-To: <F507EB0A-ED44-4854-88EA-3E1AFE93C450@cgl.ucsf.edu>
References: <2557dade-b750-dac1-d9d9-a5948490b73e@icvv.es>
 <651BF3B5-DC72-4767-B4B9-A45D6DC6F47D@cgl.ucsf.edu>
 <34e6e188-2ddb-9b64-6fe2-4f7eb0d029c3@icvv.es>
 <F507EB0A-ED44-4854-88EA-3E1AFE93C450@cgl.ucsf.edu>
Message-ID: <1BF6DB9A-9E73-48A6-9486-59B86E5FDBE4@icvv.es>

Dear Elaine,

Thank you very much for your detailed and usuful answers. You provide great support.

Cheers,
Miguel

El 27 de febrero de 2020 19:07:16 CET, Elaine Meng <meng at cgl.ucsf.edu> escribi?:
>Hello Miguel,
>Seems like you could just take a screenshot of the MolSurfer display,
>if that is high enough resolution.
>
>There are many good ideas, of course, but we only have limited
>resources to work on them!  However, I personally have never wished for
>a 2D projection of an interface. Instead I would just color the
>surfaces of the two parts forming the interface and then rotate them
>apart in opposite directions like an open book, to show
>complementarity.  There is an example of this "open book" approach in
>the image tutorials? although that tutorial does not color by
>hydrophobicity or electrostatics, you could imagine doing that, e.g.
>combining it with parts of the ?surface properties? tutorial.
>
>Opened Interface tutorial
><http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
>Surface properties coloring tutorial
><http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
>
>Our group?s development effort is now in the ChimeraX program.  You may
>want to look at the ?interfaces? tool in ChimeraX? see the ?Interface
>Residue Plot? section at the bottom.  However, it does not currently
>show coloring by electrostatic potential or other properties.
><http://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>
>
>Also ChimeraX is being structured for more outside development of
>plugins, with a Toolshed website that allows others to upload the
>plugins they wrote (i.e. if you would be interested in developing a
>plugin yourself) as well as download plugins from others.
><https://cxtoolshed.rbvi.ucsf.edu/>
>
>If you become interested in ChimeraX, there is a separate
>chimerax-users at cgl.ucsf.edu mailing list you can join or just send
>questions.
><http://www.rbvi.ucsf.edu/chimerax/index.html>
><http://www.rbvi.ucsf.edu/chimerax/docs/contact.html>
>
>Best,
>Elaine
>
>> On Feb 27, 2020, at 3:54 AM, Miguel Romero <miguel.romero at icvv.es>
>wrote:
>> 
>> Hello Elaine,
>> 
>> Thank you for your response. It's been very useful.
>> 
>> Yes, I am looking for something similar to MolSurfer's output: 2D
>projections of interface surfaces. The only problem I see with
>MolSurfer is that I have not been able to find a way to download the
>images of the 2D projections yet.
>> 
>> Do you think those type of 2D projections could be done with Chimera?
>I am thinking, for instance, in generating the 2D projections from the
>vertex coordinates of the surface generated with Chimera intersurf
>command. Does it seem a good idea?
>> 
>> Thank you very much,
>> Miguel
>> 
>> On 26/2/20 18:39, Elaine Meng wrote:
>>> Hi Miguel,
>>> I can?t think of a way to generate a 2D representation from the
>intersurf surface.  It is unclear to me exactly what you mean, however.
>What are the contours showing?  If the 3D shape, why not just show as
>3D?
>>> 
>>> You may want to take a look at another program, MolSurfer, which
>generates 2D representations of hydrophobicity and electrostatic
>potential at an interface.  I never used it myself, but that is what
>the paper about this program (link below) shows.
>>> 
>>> Molsurfer web server:
>>> <https://molsurfer.h-its.org/>
>>> 
>>> Molsurfer paper:
>>> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168994/>
>>> 
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>>> On Feb 26, 2020, at 7:25 AM, Miguel Romero <miguel.romero at icvv.es>
>wrote:
>>>> 
>>>> Hello,
>>>> I am looking for a way to generate a contour plot from the
>interface surface generated with the intersurf command. The idea is to
>have a 2D representation of the interface. I would really appreciate
>any suggestion.
>>>> Thanks in advance,
>>>> Miguel
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From pett at cgl.ucsf.edu  Thu Feb 27 16:16:28 2020
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 27 Feb 2020 16:16:28 -0800
Subject: [Chimera-users] debug
In-Reply-To: <5E575B12.3CCCC8.22899@mail-m971.mail.163.com>
References: <5E575B12.3CCCC8.22899@mail-m971.mail.163.com>
Message-ID: <384523FA-BA43-4908-B40B-8A54234A6F0A@cgl.ucsf.edu>

Hi,
	Can you zip up the contents of the ?.chimera? folder under your home folder and send that to me?  That will help me figure this out.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



> On Feb 26, 2020, at 10:00 PM, ??? <Fiora2019 at 163.com> wrote:
> 
>  
>  
> When I open chimera, introduction webpages will continuously open and many interfaces pop out. Could you please help me solve the problem? Thanks a lot.
> ??? Windows 10 ??? <https://go.microsoft.com/fwlink/?LinkId=550986>??
>  
> <????_20200227085719.jpg><????_20200227085726.jpg>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From gregc at cgl.ucsf.edu  Thu Feb 27 17:01:56 2020
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 27 Feb 2020 17:01:56 -0800
Subject: [Chimera-users] Auto-Stereo 3D
In-Reply-To: <HE1PR0701MB2715E7D1A5B95BB2ED20B9FA9AEB0@HE1PR0701MB2715.eurprd07.prod.outlook.com>
References: <HE1PR0701MB2715E7D1A5B95BB2ED20B9FA9AEB0@HE1PR0701MB2715.eurprd07.prod.outlook.com>
Message-ID: <549b245e-bc7a-bb1a-acfd-2a3eb4d2682b@cgl.ucsf.edu>

We are always interested in new 3d viewing technologies. However, any 
support for new technologies would be done as part of ChimeraX, 
https://www.rbvi.ucsf.edu/chimerax/, the Chimera successor.? ? With our 
limited resources, it's unlikely that we would implement anything soon, 
but we would welcome and assist a contributed ChimeraX bundle.


I'd like to suggest that instead of waiting for AS3D to become a viable 
option, that you either get a stereo 3D projector for presenting 3D to 
groups, similar to a movie theatre, or a VR headset for single person 
3D.? Those appear to be the only available long term solutions right 
now.? If you can find a 3D TV anymore, that would work too.


And don't forget that Chimera and ChimeraX require a workstation 
graphics card for stereo 3D -- so a mid- to high-end AMD FirePro or 
NVIDIA Quadro.


 ??? HTH,


 ??? Greg


On 2/27/20 10:05 AM, Engelhardt, Peter wrote:
> Dear Chimera developers,
>
> We are most interested of always using stereo in Chimera.
> Lately there have been presented?Auto-Stereo 3D displays: 
> https://www.tri-evolution.com/en/auto-stereo-3d/
> Auto-Stereo 3D - TRI Evolution ? 3D without glasses 
> <https://www.tri-evolution.com/en/auto-stereo-3d/>
> We unfold digital vision. We unfold your product and video data in 
> ?GLASSES-FREE 3D?. We offer numerous services and solutions for 
> perfect handling of the latest auto stereo 3D technology. We are an 
> official Solutions Partner of 3D Global. Find out everything worth 
> knowing about our AS3D offer in this section. AS3D Hardware AS3D 
> Hardware More [?]
> www.tri-evolution.com
>
> Because of this convenience in 'no need to use any stereo glasses' we 
> wonder if Chimera is supporting Auto-stereo 3D displays, now or in 
> near future.
>
> We thank you in advance
>
> Cheers
> Peter
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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From goddard at sonic.net  Thu Feb 27 17:06:11 2020
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 27 Feb 2020 17:06:11 -0800
Subject: [Chimera-users] Auto-Stereo 3D
In-Reply-To: <549b245e-bc7a-bb1a-acfd-2a3eb4d2682b@cgl.ucsf.edu>
References: <HE1PR0701MB2715E7D1A5B95BB2ED20B9FA9AEB0@HE1PR0701MB2715.eurprd07.prod.outlook.com>
 <549b245e-bc7a-bb1a-acfd-2a3eb4d2682b@cgl.ucsf.edu>
Message-ID: <A05D68BC-5C36-478A-93CB-0BA2F8DA3707@sonic.net>

One of the 3D displays that do not use glasses is called Looking Glass.

	https://lookingglassfactory.com <https://lookingglassfactory.com/>

Chimera does not work with it, but a friend (Tom Skillman) has one and said it is interesting.

	Tom


> On Feb 27, 2020, at 5:01 PM, Greg Couch <gregc at cgl.ucsf.edu> wrote:
> 
> We are always interested in new 3d viewing technologies.  However, any support for new technologies would be done as part of ChimeraX, https://www.rbvi.ucsf.edu/chimerax/ <https://www.rbvi.ucsf.edu/chimerax/>, the Chimera successor.    With our limited resources, it's unlikely that we would implement anything soon, but we would welcome and assist a contributed ChimeraX bundle.
> 
> I'd like to suggest that instead of waiting for AS3D to become a viable option, that you either get a stereo 3D projector for presenting 3D to groups, similar to a movie theatre, or a VR headset for single person 3D.  Those appear to be the only available long term solutions right now.  If you can find a 3D TV anymore, that would work too.
> 
> And don't forget that Chimera and ChimeraX require a workstation graphics card for stereo 3D -- so a mid- to high-end AMD FirePro or NVIDIA Quadro.
> 
>     HTH,
> 
>     Greg
> 
> On 2/27/20 10:05 AM, Engelhardt, Peter wrote:
>> Dear Chimera developers,
>> 
>> We are most interested of always using stereo in Chimera. 
>> Lately there have been presented Auto-Stereo 3D displays: https://www.tri-evolution.com/en/auto-stereo-3d/ <https://www.tri-evolution.com/en/auto-stereo-3d/>
>> Auto-Stereo 3D - TRI Evolution ? 3D without glasses <https://www.tri-evolution.com/en/auto-stereo-3d/>
>> We unfold digital vision. We unfold your product and video data in ?GLASSES-FREE 3D?. We offer numerous services and solutions for perfect handling of the latest auto stereo 3D technology. We are an official Solutions Partner of 3D Global. Find out everything worth knowing about our AS3D offer in this section. AS3D Hardware AS3D Hardware More [?]
>> www.tri-evolution.com <http://www.tri-evolution.com/>
>> Because of this convenience in 'no need to use any stereo glasses' we wonder if Chimera is supporting Auto-stereo 3D displays, now or in near future.
>> 
>> We thank you in advance 
>> 
>> Cheers
>> Peter
>> 
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From Semchonok at gmail.com  Fri Feb 28 01:58:05 2020
From: Semchonok at gmail.com (Dmitry Semchonok)
Date: Fri, 28 Feb 2020 10:58:05 +0100
Subject: [Chimera-users] Comparison of cryo-em maps
Message-ID: <34148250-B127-4369-A20D-EFF5C10E18CF@gmail.com>

Dear colleagues,

I have similar cryo-em maps that have also some differences.
I want to compare them.

Is there a tool in chimera that can compare the cryo-em maps?

Thank you!

Sincerely,
Dmitry
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From gabsbi at rit.edu  Fri Feb 28 05:20:06 2020
From: gabsbi at rit.edu (Gregory Babbitt)
Date: Fri, 28 Feb 2020 13:20:06 +0000
Subject: [Chimera-users] Auto-Stereo 3D
In-Reply-To: <A05D68BC-5C36-478A-93CB-0BA2F8DA3707@sonic.net>
References: <HE1PR0701MB2715E7D1A5B95BB2ED20B9FA9AEB0@HE1PR0701MB2715.eurprd07.prod.outlook.com>
 <549b245e-bc7a-bb1a-acfd-2a3eb4d2682b@cgl.ucsf.edu>,
 <A05D68BC-5C36-478A-93CB-0BA2F8DA3707@sonic.net>
Message-ID: <1582896012338.95944@rit.edu>

I just now put a Facebook challenge out to our university student Bioinformatics Club to work on creating a ChimeraX  plug in support for holographic screens for the ChimeraX toolshed.  I'll let you know if they organize a group around it.  I could also put my Computer Languages group class project on the task next year too.


Dr. Gregory A Babbitt
Associate Professor
T.H. Gosnell School of Life Sciences
Rochester Institute of Technology
Rochester  NY     USA
software website: http://people.rit.edu/gabsbi
YouTube channel  https://www.youtube.com/channel/UCJTBqGq01pBCMDQikn566Kw

________________________________
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Tom Goddard <goddard at sonic.net>
Sent: Thursday, February 27, 2020 8:06 PM
To: chimera-users at cgl.ucsf.edu
Cc: Engelhardt, Peter
Subject: Re: [Chimera-users] Auto-Stereo 3D

One of the 3D displays that do not use glasses is called Looking Glass.

https://lookingglassfactory.com

Chimera does not work with it, but a friend (Tom Skillman) has one and said it is interesting.

Tom


On Feb 27, 2020, at 5:01 PM, Greg Couch <gregc at cgl.ucsf.edu<mailto:gregc at cgl.ucsf.edu>> wrote:

We are always interested in new 3d viewing technologies.  However, any support for new technologies would be done as part of ChimeraX, https://www.rbvi.ucsf.edu/chimerax/, the Chimera successor.    With our limited resources, it's unlikely that we would implement anything soon, but we would welcome and assist a contributed ChimeraX bundle.

I'd like to suggest that instead of waiting for AS3D to become a viable option, that you either get a stereo 3D projector for presenting 3D to groups, similar to a movie theatre, or a VR headset for single person 3D.  Those appear to be the only available long term solutions right now.  If you can find a 3D TV anymore, that would work too.

And don't forget that Chimera and ChimeraX require a workstation graphics card for stereo 3D -- so a mid- to high-end AMD FirePro or NVIDIA Quadro.

    HTH,

    Greg

On 2/27/20 10:05 AM, Engelhardt, Peter wrote:
Dear Chimera developers,

We are most interested of always using stereo in Chimera.
Lately there have been presented Auto-Stereo 3D displays: https://www.tri-evolution.com/en/auto-stereo-3d/
Auto-Stereo 3D - TRI Evolution - 3D without glasses<https://www.tri-evolution.com/en/auto-stereo-3d/>
We unfold digital vision. We unfold your product and video data in "GLASSES-FREE 3D". We offer numerous services and solutions for perfect handling of the latest auto stereo 3D technology. We are an official Solutions Partner of 3D Global. Find out everything worth knowing about our AS3D offer in this section. AS3D Hardware AS3D Hardware More [...]
www.tri-evolution.com<http://www.tri-evolution.com/>

Because of this convenience in 'no need to use any stereo glasses' we wonder if Chimera is supporting Auto-stereo 3D displays, now or in near future.

We thank you in advance

Cheers
Peter




_______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


_______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From meng at cgl.ucsf.edu  Fri Feb 28 09:00:33 2020
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 28 Feb 2020 09:00:33 -0800
Subject: [Chimera-users] Comparison of cryo-em maps
In-Reply-To: <34148250-B127-4369-A20D-EFF5C10E18CF@gmail.com>
References: <34148250-B127-4369-A20D-EFF5C10E18CF@gmail.com>
Message-ID: <174680DF-B587-463A-BC02-E26D8ABAF8B1@cgl.ucsf.edu>

Hi Dmitry,
Depends what you mean by ?compare.?

Some thoughts are: 

(A) subtract one map from the other to see the differences: command ?vop subtract?
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>

(B) show the same isosurface level for both, Measure Volume and Area (under Tools? Volume Data) or the corresponding commands ?measure volume? ?measure area?

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurevol.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#volume>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#area>

(C) morph between their isosurfaces with Morph Map tool or command ?vop morph"
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morphmap/morphmap.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#morph>

This tutorial has an example of morphing between two EM maps (about halfway down the page):
<http://www.rbvi.ucsf.edu/chimera/data/tutorials/eman07/chimera-eman-2007.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 Feb 28, 2020, at 1:58 AM, Dmitry Semchonok <Semchonok at gmail.com> wrote:
> 
> Dear colleagues,
> I have similar cryo-em maps that have also some differences.
> I want to compare them.
> Is there a tool in chimera that can compare the cryo-em maps?
> Thank you!
> Sincerely,
> Dmitry



From goddard at sonic.net  Fri Feb 28 11:52:46 2020
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 28 Feb 2020 11:52:46 -0800
Subject: [Chimera-users] Auto-Stereo 3D
In-Reply-To: <1582896012338.95944@rit.edu>
References: <HE1PR0701MB2715E7D1A5B95BB2ED20B9FA9AEB0@HE1PR0701MB2715.eurprd07.prod.outlook.com>
 <549b245e-bc7a-bb1a-acfd-2a3eb4d2682b@cgl.ucsf.edu>
 <A05D68BC-5C36-478A-93CB-0BA2F8DA3707@sonic.net>
 <1582896012338.95944@rit.edu>
Message-ID: <81C109D2-910B-4219-8BD3-017ADD87D5E0@sonic.net>

Hi Gregory,

  That would be cool to have ChimeraX interactive holographic display.  This could be easy or hard depending on what is required to talk to these displays.  I believe the generally require having several rendered views, like 8 views for the Auto Stereo 3D products or 45 for the looking glass display.

	https://www.tri-evolution.com/en/auto-stereo-3d/as3d-hardware/ <https://www.tri-evolution.com/en/auto-stereo-3d/as3d-hardware/>

	https://lookingglassfactory.com <https://lookingglassfactory.com/>

The trouble is the primary SDK for these displays is Unity.  ChimeraX is based on Python / C++ / OpenGL, not Unity.  I did not see any Python SDKs for these devices which would be the ideal situation for a ChimeraX plugin.  I saw a C API for Looking Glass in private beta -- would require some extensive programming skills to use that in ChimeraX.  Perhaps these holographic displays just take a single tiled image with the multiple views and you don't need any SDK, ChimeraX could certainly create the tiled views.

  If the device SDKs make it possible, the place to look in ChimeraX for how to make weird multi-view cameras is

	https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/core/graphics/camera.py <https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/core/graphics/camera.py>

	https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/core/graphics/camera360.py <https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/core/graphics/camera360.py>

For instance the SplitStereoCamera class makes side-by-side tiled left and right eye views.  And here are the ChimeraX user docs on the available camera modes that might help

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

Definitely let us know if you get someone trying to code a holographic ChimeraX camera -- we'd be happy to advise on the details.

  Tom


> On Feb 28, 2020, at 5:20 AM, Gregory Babbitt <gabsbi at rit.edu> wrote:
> 
> I just now put a Facebook challenge out to our university student Bioinformatics Club to work on creating a ChimeraX  plug in support for holographic screens for the ChimeraX toolshed.  I'll let you know if they organize a group around it.  I could also put my Computer Languages group class project on the task next year too.
> 
> Dr. Gregory A Babbitt
> Associate Professor
> T.H. Gosnell School of Life Sciences
> Rochester Institute of Technology
> Rochester  NY     USA
> software website: http://people.rit.edu/gabsbi? <http://people.rit.edu/gabsbi> 
> YouTube channel  https://www.youtube.com/channel/UCJTBqGq01pBCMDQikn566Kw <https://www.youtube.com/channel/UCJTBqGq01pBCMDQikn566Kw>
> 
> From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Tom Goddard <goddard at sonic.net>
> Sent: Thursday, February 27, 2020 8:06 PM
> To: chimera-users at cgl.ucsf.edu
> Cc: Engelhardt, Peter
> Subject: Re: [Chimera-users] Auto-Stereo 3D
>  
> One of the 3D displays that do not use glasses is called Looking Glass.
> 
> https://lookingglassfactory.com <https://lookingglassfactory.com/>
> 
> Chimera does not work with it, but a friend (Tom Skillman) has one and said it is interesting.
> 
> Tom
> 
> 
>> On Feb 27, 2020, at 5:01 PM, Greg Couch <gregc at cgl.ucsf.edu <mailto:gregc at cgl.ucsf.edu>> wrote:
>> 
>> We are always interested in new 3d viewing technologies.  However, any support for new technologies would be done as part of ChimeraX, https://www.rbvi.ucsf.edu/chimerax/ <https://www.rbvi.ucsf.edu/chimerax/>, the Chimera successor.    With our limited resources, it's unlikely that we would implement anything soon, but we would welcome and assist a contributed ChimeraX bundle.
>> 
>> I'd like to suggest that instead of waiting for AS3D to become a viable option, that you either get a stereo 3D projector for presenting 3D to groups, similar to a movie theatre, or a VR headset for single person 3D.  Those appear to be the only available long term solutions right now.  If you can find a 3D TV anymore, that would work too.
>> 
>> And don't forget that Chimera and ChimeraX require a workstation graphics card for stereo 3D -- so a mid- to high-end AMD FirePro or NVIDIA Quadro.
>> 
>>     HTH,
>> 
>>     Greg
>> 
>> On 2/27/20 10:05 AM, Engelhardt, Peter wrote:
>>> Dear Chimera developers,
>>> 
>>> We are most interested of always using stereo in Chimera. 
>>> Lately there have been presented Auto-Stereo 3D displays: https://www.tri-evolution.com/en/auto-stereo-3d/ <https://www.tri-evolution.com/en/auto-stereo-3d/>
>>> Auto-Stereo 3D - TRI Evolution ? 3D without glasses <https://www.tri-evolution.com/en/auto-stereo-3d/>
>>> We unfold digital vision. We unfold your product and video data in ?GLASSES-FREE 3D?. We offer numerous services and solutions for perfect handling of the latest auto stereo 3D technology. We are an official Solutions Partner of 3D Global. Find out everything worth knowing about our AS3D offer in this section. AS3D Hardware AS3D Hardware More [?]
>>> www.tri-evolution.com <http://www.tri-evolution.com/>
>>> Because of this convenience in 'no need to use any stereo glasses' we wonder if Chimera is supporting Auto-stereo 3D displays, now or in near future.
>>> 
>>> We thank you in advance 
>>> 
>>> Cheers
>>> Peter
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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