From isha1520 at imtech.res.in  Wed Jan  1 23:08:20 2014
From: isha1520 at imtech.res.in (Isha)
Date: Thu, 02 Jan 2014 12:38:20 +0530
Subject: [Chimera-users] Error in generating sqm for FAD
Message-ID: <62a2958cbbacd17e544ff5fa5d04bae9@imtech.res.in>

 

Dear Sir/Mam 

 I used antechamber in chimera to add charges to ligand "FAD" using
am-bcc, amber ffo3r.1 and +5 charge (as depicted by chimera). The
procedure was Tools > structure editing > add H and then add charge. The
error shown is : 

Charge model: AMBER ff03.r1
Assigning partial charges to residue FAD (net charge +1) with am1-bcc
method
Running ANTECHAMBER command: C:/Program Files/Chimera
1.8.1/bin/amber12/binantechamber -ek qm_theory='AM1', -i
c:usersamehtaappdatalocaltemptmpjjpoaqante.in.mol2 -fi mol2 -o
c:usersamehtaappdatalocaltemptmpjjpoaqante.out.mol2 -fo mol2 -c bcc -nc
1 -j 5 -s 2
(FAD) 

(FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/bondtype"
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac 

(FAD) 

(FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/atomtype"
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff 

(FAD) Total number of electrons: 412; net charge: 1 

(FAD) 

(FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O
-i sqm.in -o sqm.out 

(FAD) Error: cannot run ""C:/Program Files/Chimera
1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c
properly, exit 

Failure running ANTECHAMBER for residue FAD

Please help as it is very urgent. Hope for your reply. I have also
attached the ligand. Please find the attachment. 

With Regards,
Isha
C/O Dr. Raman Parkesh
Protein Science & Engg.
Institute of Microbial Technology
Sector 39A, Chandigarh 160036
Ext: 0172-6665489
 
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From meng at cgl.ucsf.edu  Thu Jan  2 10:21:54 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 2 Jan 2014 10:21:54 -0800
Subject: [Chimera-users] rate of a reaction
In-Reply-To: <CAO+nnti1fDSY+i59Fa4ioQzwVF+k77OPUDLC=jHJ5m_zt-4P_g@mail.gmail.com>
References: <CAO+nnti1fDSY+i59Fa4ioQzwVF+k77OPUDLC=jHJ5m_zt-4P_g@mail.gmail.com>
Message-ID: <A04B11CC-DDB2-4A49-BE14-1ACE6AC7F97B@cgl.ucsf.edu>

Dear Haider Abbas,
Sorry, Chimera does not do that type of calculation. You have to use some other program.
Regards,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 31, 2013, at 9:21 PM, Haider Abbas <haiderabbasphy at gmail.com> wrote:

> Dear all user,
> 
> Could you please let me know how to calculate reaction rate of a barrierless chemical reaction in gas phase by chimera.
> 
> with regards
> Haider Abbas




From pett at cgl.ucsf.edu  Thu Jan  2 14:01:00 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 2 Jan 2014 14:01:00 -0800
Subject: [Chimera-users] Error in generating sqm for FAD
In-Reply-To: <62a2958cbbacd17e544ff5fa5d04bae9@imtech.res.in>
References: <62a2958cbbacd17e544ff5fa5d04bae9@imtech.res.in>
Message-ID: <21D23EA5-81B0-4C28-A42E-AF16CA8B0077@cgl.ucsf.edu>

Hi Isha,
	I have no problem charging the FAD, though it takes quite a long time to finish and I'm sure the protonation in my trial differs from yours, since the net charge for me is -2 whereas for you it is +1 (not +5; I don't know why you think it was +5 but the "-nc 1" part of the antechamber command you sent indicates a net charge of +1).
	The first problem is that the structure you sent is protonated wrong in two ways.  First, in your structure only non-carbon atoms are protonated.  Charge determination requires all protons be present.  Second, in your structure the oxygens of the flavin quinone ring are protonated and they should not be.
	Correcting these problems can be done in a few steps.  First, open the Chimera command line (Favorites->Command Line) and type "del H".  This will delete all the hydrogens.  Now we need to tell Chimera that the quinone oxygens are ketones, not alcohols.  To do this select the two oxygens and then type "setattr a idatmType O2 sel" (i.e. the atom type of the selected atoms is sp2 oxygen).  Then we need to tell chimera that the nitrogen between the those two should be protonated.  Do this by selecting that nitrogen and typing "setattr a idatmType Npl sel".
	Now add hydrogens by typing "addh".  You'll notice that the other nitrogen in the ring also gets protonated.  This is because Chimera favors a protonation state where the central flavin ring is positively charged and aromatic (i.e. a positively charged semiquinone).  To force the "classic" flavin protonation, select the extra proton and type "del sel".
	Now you will be able to run add charge.  Let me know if you have any further problems.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 1, 2014, at 11:08 PM, Isha <isha1520 at imtech.res.in> wrote:

> Dear Sir/Mam
> 
>  I used antechamber in chimera to add charges to ligand "FAD" using am-bcc, amber ffo3r.1 and +5 charge (as depicted by chimera). The procedure was Tools > structure editing > add H and then add charge. The error shown is :
> 
> 
> Charge model: AMBER ff03.r1
> Assigning partial charges to residue FAD (net charge +1) with am1-bcc method
> Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\amehta\appdata\local\temp\tmpjjpoaq\ante.in.mol2 -fi mol2 -o c:\users\amehta\appdata\local\temp\tmpjjpoaq\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2
> (FAD)
> 
> (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> 
> (FAD)
> 
> (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> 
> (FAD) Total number of electrons: 412; net charge: 1
> 
> (FAD)
> 
> (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out
> 
> (FAD) Error: cannot run ""C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
> 
> Failure running ANTECHAMBER for residue FAD
> 
> 
> Please help as it is very urgent. Hope for your reply. I have also attached the ligand. Please find the attachment.
> 
>  
> With Regards,
> Isha
> C/O Dr. Raman Parkesh
> Protein Science & Engg.
> Institute of Microbial Technology
> Sector 39A, Chandigarh 160036
> Ext: 0172-6665489
> <DE_fad.pdb>_______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




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From jug25 at psu.edu  Fri Jan  3 11:08:41 2014
From: jug25 at psu.edu (Jian Guan)
Date: Fri, 3 Jan 2014 14:08:41 -0500
Subject: [Chimera-users] How to measure the radius of density map
Message-ID: <000001cf08b7$37a596b0$a6f0c410$@psu.edu>

Hi all,
I have density map of virus (mrc format) and want to measure the radius of
it. I tried measure command, High-order structure-->Icosahedron surface.
Both of them need me to measure it manually by eye. Are there any tools to
measure the radius by chimera, so we can get more accurate result? Or does
anybody know how to measure it accurately? Thank you so much.
Sincerely yours,
Happy New Year.
Jian

-----Original Message-----
From: chimera-users-bounces at cgl.ucsf.edu
[mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of
chimera-users-request at cgl.ucsf.edu
Sent: 2014?1?2? 15:00
To: chimera-users at cgl.ucsf.edu
Subject: Chimera-users Digest, Vol 129, Issue 1

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Today's Topics:

   1. rate of a reaction (Haider Abbas)
   2. Error in generating sqm for FAD (Isha)
   3. Re: rate of a reaction (Elaine Meng)


----------------------------------------------------------------------

Message: 1
Date: Wed, 1 Jan 2014 10:51:05 +0530
From: Haider Abbas <haiderabbasphy at gmail.com>
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] rate of a reaction
Message-ID:
	<CAO+nnti1fDSY+i59Fa4ioQzwVF+k77OPUDLC=jHJ5m_zt-4P_g at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear all user,

Could you please let me know how to calculate reaction rate of a barrierless
chemical reaction in gas phase by chimera.

with regards
Haider Abbas
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------------------------------

Message: 2
Date: Thu, 02 Jan 2014 12:38:20 +0530
From: Isha <isha1520 at imtech.res.in>
To: chimera-dev at cgl.ucsf.edu, chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] Error in generating sqm for FAD
Message-ID: <62a2958cbbacd17e544ff5fa5d04bae9 at imtech.res.in>
Content-Type: text/plain; charset="utf-8"

 

Dear Sir/Mam 

 I used antechamber in chimera to add charges to ligand "FAD" using am-bcc,
amber ffo3r.1 and +5 charge (as depicted by chimera). The procedure was
Tools > structure editing > add H and then add charge. The error shown is : 

Charge model: AMBER ff03.r1
Assigning partial charges to residue FAD (net charge +1) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/Chimera
1.8.1/bin/amber12/binantechamber -ek qm_theory='AM1', -i
c:usersamehtaappdatalocaltemptmpjjpoaqante.in.mol2 -fi mol2 -o
c:usersamehtaappdatalocaltemptmpjjpoaqante.out.mol2 -fo mol2 -c bcc -nc
1 -j 5 -s 2
(FAD) 

(FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/bondtype"
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac 

(FAD) 

(FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/atomtype"
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff 

(FAD) Total number of electrons: 412; net charge: 1 

(FAD) 

(FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i
sqm.in -o sqm.out 

(FAD) Error: cannot run ""C:/Program Files/Chimera
1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c
properly, exit 

Failure running ANTECHAMBER for residue FAD

Please help as it is very urgent. Hope for your reply. I have also attached
the ligand. Please find the attachment. 

With Regards,
Isha
C/O Dr. Raman Parkesh
Protein Science & Engg.
Institute of Microbial Technology
Sector 39A, Chandigarh 160036
Ext: 0172-6665489
 
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------------------------------

Message: 3
Date: Thu, 2 Jan 2014 10:21:54 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Haider Abbas <haiderabbasphy at gmail.com>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] rate of a reaction
Message-ID: <A04B11CC-DDB2-4A49-BE14-1ACE6AC7F97B at cgl.ucsf.edu>
Content-Type: text/plain; charset=iso-8859-1

Dear Haider Abbas,
Sorry, Chimera does not do that type of calculation. You have to use some
other program.
Regards,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of
Pharmaceutical Chemistry University of California, San Francisco

On Dec 31, 2013, at 9:21 PM, Haider Abbas <haiderabbasphy at gmail.com> wrote:

> Dear all user,
> 
> Could you please let me know how to calculate reaction rate of a
barrierless chemical reaction in gas phase by chimera.
> 
> with regards
> Haider Abbas




------------------------------

_______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


End of Chimera-users Digest, Vol 129, Issue 1
*********************************************




From meng at cgl.ucsf.edu  Fri Jan  3 13:25:27 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 3 Jan 2014 13:25:27 -0800
Subject: [Chimera-users] How to measure the radius of density map
In-Reply-To: <000001cf08b7$37a596b0$a6f0c410$@psu.edu>
References: <000001cf08b7$37a596b0$a6f0c410$@psu.edu>
Message-ID: <78C4F5ED-36AD-4EF6-964D-63DE4C2CC7F6@cgl.ucsf.edu>

Hi Jian,
Well, this idea is also partly manual: using Volume Tracer to place two markers (fake atoms) on the surface and then measuring the distance between them.

(1) use Volume Tracer to place "markers" on the density map isosurface (Volume Tracer menu: Mouse... Place markers on surfaces, turn off other Mouse options).  The manual part is where you click on the surface, and it might be tricky to put the markers where you want them.  Maybe clip the surface so that it is cut across where you want to measure it, then try to put the markers on opposite sides of the rim.

Volume Tracer:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>

(2) measure distance between the two markers, just like for atoms, e.g. Ctrl-click one, Shift-Ctrl-doubleclick on the other, choose "show distance" from the resulting context menu.

Happy New Year to you too,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 3, 2014, at 11:08 AM, Jian Guan wrote:

> Hi all,
> I have density map of virus (mrc format) and want to measure the radius of
> it. I tried measure command, High-order structure-->Icosahedron surface.
> Both of them need me to measure it manually by eye. Are there any tools to
> measure the radius by chimera, so we can get more accurate result? Or does
> anybody know how to measure it accurately? Thank you so much.
> Sincerely yours,
> Happy New Year.
> Jian




From goddard at sonic.net  Fri Jan  3 14:17:51 2014
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 3 Jan 2014 14:17:51 -0800
Subject: [Chimera-users] How to measure the radius of density map
In-Reply-To: <78C4F5ED-36AD-4EF6-964D-63DE4C2CC7F6@cgl.ucsf.edu>
References: <000001cf08b7$37a596b0$a6f0c410$@psu.edu>
	<78C4F5ED-36AD-4EF6-964D-63DE4C2CC7F6@cgl.ucsf.edu>
Message-ID: <2DD87177-79B7-4B04-9820-15E8BAB69B0C@sonic.net>

Another approach is to use the Measure and Color Blobs.  You can click on the virus surface and it will draw a box around it and report the exact dimensions of the box.

The tricky part of this problem is deciding how you want to define "radius".  Radius to a 5-fold vertex may be larger than radius along a 3-fold symmetry axis.  And where do you define the surface of the virus, or do you measure to a maximum in density within the virus capsid along a radial line.  I'm not sure what the commonly used definitions of virus radius are -- probably everyone does something different so the numbers are only meaningful to within maybe 5%.

	Tom


On Jan 3, 2014, at 1:25 PM, Elaine Meng  wrote:

> Hi Jian,
> Well, this idea is also partly manual: using Volume Tracer to place two markers (fake atoms) on the surface and then measuring the distance between them.
> 
> (1) use Volume Tracer to place "markers" on the density map isosurface (Volume Tracer menu: Mouse... Place markers on surfaces, turn off other Mouse options).  The manual part is where you click on the surface, and it might be tricky to put the markers where you want them.  Maybe clip the surface so that it is cut across where you want to measure it, then try to put the markers on opposite sides of the rim.
> 
> Volume Tracer:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>
> 
> (2) measure distance between the two markers, just like for atoms, e.g. Ctrl-click one, Shift-Ctrl-doubleclick on the other, choose "show distance" from the resulting context menu.
> 
> Happy New Year to you too,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Jan 3, 2014, at 11:08 AM, Jian Guan wrote:
> 
>> Hi all,
>> I have density map of virus (mrc format) and want to measure the radius of
>> it. I tried measure command, High-order structure-->Icosahedron surface.
>> Both of them need me to measure it manually by eye. Are there any tools to
>> measure the radius by chimera, so we can get more accurate result? Or does
>> anybody know how to measure it accurately? Thank you so much.
>> Sincerely yours,
>> Happy New Year.
>> Jian
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From lilipeng at gmail.com  Sun Jan  5 23:42:17 2014
From: lilipeng at gmail.com (Lili Peng)
Date: Sun, 5 Jan 2014 23:42:17 -0800
Subject: [Chimera-users] General question about Chimera
Message-ID: <CAHUiwNbAoh_2xXE_F3D=f_-kejAMpKhSUHdn3YQGSGQaKBpZRA@mail.gmail.com>

Hi,

When I load a structure of a protein into Chimera, the structure is
automatically rendered in ribbon mode, with select atoms being rendered in
stick mode.  I am curious as to why certain atoms are rendered as sticks,
and other are not.  What is the selection criteria?

Thank you,
Lili
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From meng at cgl.ucsf.edu  Mon Jan  6 09:24:35 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 6 Jan 2014 09:24:35 -0800
Subject: [Chimera-users] General question about Chimera
In-Reply-To: <CAHUiwNbAoh_2xXE_F3D=f_-kejAMpKhSUHdn3YQGSGQaKBpZRA@mail.gmail.com>
References: <CAHUiwNbAoh_2xXE_F3D=f_-kejAMpKhSUHdn3YQGSGQaKBpZRA@mail.gmail.com>
Message-ID: <ED9F5A4D-BE42-4623-A791-3F3488E1A118@cgl.ucsf.edu>

Hi Lili,
The default "smart initial display" uses rules similar to the ribbons preset, including showing residues within 3.6 A of residues classified as ligand or metal ions.  The ribbons preset (e.g. menu: Preset... Interactive 1 (ribbons)) is described in more detail here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>

... ligand and ions classification here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats>

... and the smart initial display is a setting in the New Molecules category of Preferences.  You can change various preferences in that category if you want a different initial appearance.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules>
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 5, 2014, at 11:42 PM, Lili Peng wrote:

> Hi,
> When I load a structure of a protein into Chimera, the structure is automatically rendered in ribbon mode, with select atoms being rendered in stick mode.  I am curious as to why certain atoms are rendered as sticks, and other are not.  What is the selection criteria?
> Thank you,
> Lili




From YZHANG56 at mgh.harvard.edu  Mon Jan  6 10:20:36 2014
From: YZHANG56 at mgh.harvard.edu (Zhang, Yinghui)
Date: Mon, 6 Jan 2014 18:20:36 +0000
Subject: [Chimera-users] the old Mac OX 10.4 can not run Chimera
Message-ID: <607150D615F12C478D98B3A53CACE54C3F87B7F2@PHSX10MB24.partners.org>

Dear Sir/Madam,

This is Yinghui Zhang from Massachusetts General Hospital. I am a postdoc here and my project requires me to use the Chimera often. However, the desktop I used is some old and I can not update and use Chimera right now. The Chimera installed is 1.2 version but cannot be started. The specifics of computer is as follows:

Apple PowerMac G5 chip, duo core and 3G memory. The OS is Mac OX 10.4.11.

The operating system very probably cannot be updated because of chip version problem. Could you please give us some information if there is some alternative we can install executable Chimera on this computer?

Thank you very much!

Yinghui Zhang
EDR 514, Dept. of Anesthesia
MGH
Boston, MA 02148


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From pett at cgl.ucsf.edu  Mon Jan  6 15:51:03 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 6 Jan 2014 15:51:03 -0800
Subject: [Chimera-users] the old Mac OX 10.4 can not run Chimera
In-Reply-To: <607150D615F12C478D98B3A53CACE54C3F87B7F2@PHSX10MB24.partners.org>
References: <607150D615F12C478D98B3A53CACE54C3F87B7F2@PHSX10MB24.partners.org>
Message-ID: <F1FA746C-4099-473F-9231-3DCC84D8F403@cgl.ucsf.edu>

On Jan 6, 2014, at 10:20 AM, "Zhang, Yinghui" <YZHANG56 at mgh.harvard.edu> wrote:

> Dear Sir/Madam,
>  
> This is Yinghui Zhang from Massachusetts General Hospital. I am a postdoc here and my project requires me to use the Chimera often. However, the desktop I used is some old and I can not update and use Chimera right now. The Chimera installed is 1.2 version but cannot be started. The specifics of computer is as follows:
>  
> Apple PowerMac G5 chip, duo core and 3G memory. The OS is Mac OX 10.4.11.
>  
> The operating system very probably cannot be updated because of chip version problem. Could you please give us some information if there is some alternative we can install executable Chimera on this computer?
>  
> Thank you very much!

Hi Yinghui,
	The last version of Chimera that should run on OS X 10.4 is version 1.4.1.  You can download that version and try it by going to the Chimera download page and clicking on the "Old releases" link (one of the links right under the "Download Chimera" text near the top of the page).  Scroll quite aways down the table on the old releases page to get to the 1.4.1 version.  The "Notes" section of that table notes what OS versions that version of Chimera works on.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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From lawrence at wehi.EDU.AU  Mon Jan  6 18:16:03 2014
From: lawrence at wehi.EDU.AU (Mike Lawrence)
Date: Tue, 7 Jan 2014 13:16:03 +1100 (EST)
Subject: [Chimera-users] Updating coordinates without having to regenerate
 the depiction of an atomic model
In-Reply-To: <1396024521.60275637.1389060660716.JavaMail.root@wehi.edu.au>
Message-ID: <1303734856.60276865.1389060963876.JavaMail.root@wehi.edu.au>

Hi,

Within Chimera is there any way in which the underlying coordinates of an atomic model can be updated in order to yield the same depiction but based on the new coordinates, or (equivalently) can the attributes of one model be transferred to another, assuming of course that they have the same underlying protein sequence, etc.

thanks

Mike Lawrence
Walter + Eliza Hall Institute of Medical Research
Parkville
Australia


______________________________________________________________________
The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.
______________________________________________________________________


From meng at cgl.ucsf.edu  Tue Jan  7 10:30:26 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 7 Jan 2014 10:30:26 -0800
Subject: [Chimera-users] Updating coordinates without having to
	regenerate the depiction of an atomic model
In-Reply-To: <1303734856.60276865.1389060963876.JavaMail.root@wehi.edu.au>
References: <1303734856.60276865.1389060963876.JavaMail.root@wehi.edu.au>
Message-ID: <D37C2076-286C-487E-8BB2-67A030C59D5F@cgl.ucsf.edu>

Hi Mike,
Take a look at the "mcopy" command -- I think that's what you want.  It doesn't handle all attributes, but you could copy depiction/colors from one model to another, or (opposite direction) the atomic coordinates.

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

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

On Jan 6, 2014, at 6:16 PM, Mike Lawrence <lawrence at wehi.EDU.AU> wrote:

> Hi,
> Within Chimera is there any way in which the underlying coordinates of an atomic model can be updated in order to yield the same depiction but based on the new coordinates, or (equivalently) can the attributes of one model be transferred to another, assuming of course that they have the same underlying protein sequence, etc.
> thanks
> 
> Mike Lawrence
> Walter + Eliza Hall Institute of Medical Research
> Parkville
> Australia




From darrellh at niaid.nih.gov  Tue Jan  7 11:55:16 2014
From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E])
Date: Tue, 7 Jan 2014 19:55:16 +0000
Subject: [Chimera-users] BioPython in a Chimera Python script; PDBio?
Message-ID: <CEF1C5D2.A14F%darrellh@niaid.nih.gov>

Hi Chimera friends,

I've been trying to install BioPython into the Python interpreter embedded within Chimera. I've been following the guidelines posted a couple of years ago:
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000807.html

This works up to a point for me. I'm using Mac OS X 10.8.5 with MacPorts installed. I'm trying to install BioPython 1.63:
http://biopython.org/wiki/Download#Installation_Instructions

The "build" process starts to work, but gets hung up with the error "xcrun: Error: failed to exec real xcrun. (No such file or directory)". It seems to be referencing "/Developer/SDKs/MacOSX10.6.sdk", which does not exist in recent versions of Xcode. I've been able to install the 10.6 frameworks into both Xcode 4.6.2 and Xcode 5.x, but that still doesn't work. I manually installed the MacOSX10.6.sdk from Xcode 4.2 into the appropriate location, but still no luck.

I'm using BioPython because I want to pull some information out of the PDB headers. I was able to use PDBio as described in this discussion:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001291.html

But the "dictionary" entries "keyed by record type" need additional cleanup/parsing before I can use them (which is why I wanted to use BioPython).

Is this just a case of Apple not building in enough backwards compatibility? Or is it something that Chimera needs to fix?

Do you have any additional suggestions for me about "PDBio"? The fields I want are the DOI and title information.

Finally, is there an analogous "EMDBio" for EMDB records?

Thanks,
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559
Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<https://twitter.com/niaidbioit>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.



From pett at cgl.ucsf.edu  Tue Jan  7 16:08:11 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 7 Jan 2014 16:08:11 -0800
Subject: [Chimera-users] BioPython in a Chimera Python script; PDBio?
In-Reply-To: <CEF1C5D2.A14F%darrellh@niaid.nih.gov>
References: <CEF1C5D2.A14F%darrellh@niaid.nih.gov>
Message-ID: <4D5AC3F0-1F5F-4BB0-9456-8A7567F28EAC@cgl.ucsf.edu>

Hi Darrell,
	You're right; due to the way we compile Chimera to maintain compatibility with older systems makes it tough to compile BioPython with newer Macs since it is a bear to get/use the 10.6 SDK on them (I've never gotten that to work).  So though BioPython compiles easily with my source-code installation of Chimera, I run aground on the same rocks you do using the distributed version of Chimera.
	On the other hand, for the task you describe I don't think using BioPython is going to help you any.  With the BioPython I installed, this is the value of the BioPython 'journal' header record for 1gcn:

	AUTH K.SASAKI,S.DOCKERILL,D.A.ADAMIAK,I.J.TICKLE,AUTH 2 T.BLUNDELLTITL X-RAY ANALYSIS OF GLUCAGON AND ITS RELATIONSHIP TOTITL 2 RECEPTOR BINDING.REF NATURE V. 257 751 1975REFN ISSN 0028-0836PMID 171582DOI 10.1038/257751A0

You can see that you'd have some tricky parsing on your hands anyway!  So if you have to do some parsing anyway you might as well stick with Chimera.
	So here's some code that will parse out the title and DOI from the JRNL records:

from chimera import openModels, Molecule
for m in openModels.list(modelTypes=[Molecule]):
	if hasattr(m, 'pdbHeaders') and 'JRNL' in m.pdbHeaders:
		title = doi = None
		for line in m.pdbHeaders['JRNL']:
			if line[12:16] == "TITL":
				if title:
					title += " " + line[19:].strip()
				else:
					title = line[19:].strip()
			if line[12:15] == "DOI":
				if doi:
					doi += " " + line[19:].strip()
				else:
					doi = line[19:].strip()
		print m.name, "Title:", title
		print m.name, "DOI:", doi
	else:
		print m.name, "has no JRNL header records"

I haven't tested the above code but it should work, modulo a typo or two.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 7, 2014, at 11:55 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh at niaid.nih.gov> wrote:

> Hi Chimera friends,
> 
> I've been trying to install BioPython into the Python interpreter embedded within Chimera. I've been following the guidelines posted a couple of years ago:
> http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000807.html
> 
> This works up to a point for me. I'm using Mac OS X 10.8.5 with MacPorts installed. I'm trying to install BioPython 1.63:
> http://biopython.org/wiki/Download#Installation_Instructions
> 
> The "build" process starts to work, but gets hung up with the error "xcrun: Error: failed to exec real xcrun. (No such file or directory)". It seems to be referencing "/Developer/SDKs/MacOSX10.6.sdk", which does not exist in recent versions of Xcode. I've been able to install the 10.6 frameworks into both Xcode 4.6.2 and Xcode 5.x, but that still doesn't work. I manually installed the MacOSX10.6.sdk from Xcode 4.2 into the appropriate location, but still no luck.
> 
> I'm using BioPython because I want to pull some information out of the PDB headers. I was able to use PDBio as described in this discussion:
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001291.html
> 
> But the "dictionary" entries "keyed by record type" need additional cleanup/parsing before I can use them (which is why I wanted to use BioPython).
> 
> Is this just a case of Apple not building in enough backwards compatibility? Or is it something that Chimera needs to fix?
> 
> Do you have any additional suggestions for me about "PDBio"? The fields I want are the DOI and title information.
> 
> Finally, is there an analogous "EMDBio" for EMDB records?
> 
> Thanks,
> Darrell
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office: 301-402-0095
> Mobile: 301-758-3559
> Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
> 
> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users







From goddard at sonic.net  Tue Jan  7 16:15:26 2014
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 7 Jan 2014 16:15:26 -0800
Subject: [Chimera-users] BioPython in a Chimera Python script; PDBio?
In-Reply-To: <CEF1C5D2.A14F%darrellh@niaid.nih.gov>
References: <CEF1C5D2.A14F%darrellh@niaid.nih.gov>
Message-ID: <AB457243-17B4-4D39-8375-316B11DEC991@sonic.net>

Hi Darrell,

  Chimera is compiled on Mac OS 10.6.  The compilation explicitly specifies MacOSX10.6.sdk and that setting gets put into the Chimera Python configuration files.   So when you try to install a Python module using the Chimera Python and it requires compiling some C or C++ code it attempts to use the same compiler and same settings that Python itself was compiled with to assure that the new compiled module will work with Python.  But as you point out Mac OS 10.8 (and 10.9) don't have the Mac 10.6 SDK files.  And in fact Apple changed the location where SDK files live.  I have encountered this and on my Mac 10.8 system use a symbollic link

  /Developer/SDKs -> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs

so that when I recompile parts of Chimera on my Mac 10.8 machine that were originally compiled on Mac 10.6 it can find the 10.6 SDKs.

  It seems you already figured out all of the above.  Your error says it cannot find "xcrun".  xcrun is in /usr/bin on my Mac 10.8 system

$ locate xcrun
/Applications/Xcode.app/Contents/Developer/usr/bin/xcrun
/Applications/Xcode.app/Contents/Developer/usr/share/man/man1/xcrun.1
/usr/bin/xcrun
/usr/share/man/man1/xcrun.1

and on our Mac 10.6 build machine it is also in /usr/bin

$ locate xcrun
/Developer/usr/share/man/man1/xcrun.1
/private/var/db/receipts/com.apple.pkg.xcrunLeo.bom
/private/var/db/receipts/com.apple.pkg.xcrunLeo.plist
/usr/bin/xcrun
/usr/share/man/man1/xcrun.1

Is xcrun in /usr/bin on your computer?

If your goal is to get title and doi info from PDB files, it would be much easier to do the minor parsing needed on the records obtained from Chimera.  Installing BioPython just to do that is hitting a needle with a sledgehammer.  But maybe you have other reasons for wanting BioPython in Chimera.

  I'm not sure what you mean by "EMDB records".  If you mean the XML meta data file provided by EMDB, Chimera does not fetch that because it doesn't need any data it contains currently.  I used it many years ago to find the PDB entries fit to an EMDB map but switched that to use and EMDB web service instead of the XML file.  If instead you mean you want the header values of the EMDB CCP4 binary map files, Chimera reads those and I can tell you how to get them if you are interested.

	Tom



On Jan 7, 2014, at 11:55 AM, "Hurt, Darrell (NIH/NIAID) [E]"  wrote:

> Hi Chimera friends,
> 
> I've been trying to install BioPython into the Python interpreter embedded within Chimera. I've been following the guidelines posted a couple of years ago:
> http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000807.html
> 
> This works up to a point for me. I'm using Mac OS X 10.8.5 with MacPorts installed. I'm trying to install BioPython 1.63:
> http://biopython.org/wiki/Download#Installation_Instructions
> 
> The "build" process starts to work, but gets hung up with the error "xcrun: Error: failed to exec real xcrun. (No such file or directory)". It seems to be referencing "/Developer/SDKs/MacOSX10.6.sdk", which does not exist in recent versions of Xcode. I've been able to install the 10.6 frameworks into both Xcode 4.6.2 and Xcode 5.x, but that still doesn't work. I manually installed the MacOSX10.6.sdk from Xcode 4.2 into the appropriate location, but still no luck.
> 
> I'm using BioPython because I want to pull some information out of the PDB headers. I was able to use PDBio as described in this discussion:
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001291.html
> 
> But the "dictionary" entries "keyed by record type" need additional cleanup/parsing before I can use them (which is why I wanted to use BioPython).
> 
> Is this just a case of Apple not building in enough backwards compatibility? Or is it something that Chimera needs to fix?
> 
> Do you have any additional suggestions for me about "PDBio"? The fields I want are the DOI and title information.
> 
> Finally, is there an analogous "EMDBio" for EMDB records?
> 
> Thanks,
> Darrell
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office: 301-402-0095
> Mobile: 301-758-3559
> Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
> 
> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From pett at cgl.ucsf.edu  Thu Jan  9 10:59:13 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 9 Jan 2014 10:59:13 -0800
Subject: [Chimera-users] running wild with Chimera :-)
Message-ID: <F9220BED-0934-435D-B52F-03F445D681B7@cgl.ucsf.edu>

New Year Cards in 3D
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From meng at cgl.ucsf.edu  Thu Jan  9 13:38:53 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 9 Jan 2014 13:38:53 -0800
Subject: [Chimera-users] rna and set shadows commands
In-Reply-To: <CAHXR=Oo--KQepS_gy7fS4jXHAFVxb6+KdH_6qzjxApSZwXGzHw@mail.gmail.com>
References: <CAHXR=Oo--KQepS_gy7fS4jXHAFVxb6+KdH_6qzjxApSZwXGzHw@mail.gmail.com>
Message-ID: <EE60E80D-F321-4B82-BC49-3F5F860C5BE3@cgl.ucsf.edu>

On Jan 9, 2014, at 12:07 PM, "pythonchemia Gazeta.pl" <pythonchemia at gazeta.pl> wrote:
> 
> Hello Elaine C. Meng
> 
> Thank you very much for your reply and sorry that I answer only now.
> When it comes to command rna  path and rna model  your tips helped me. :)
> Although I do not know how to define the path for the command operations rna duplex. : (
> 
> Unfortunately for me the system WinXP / Chimera 1.8 - 32bit shadows set command does not work. : (
> Chimera returns this message:
> 
> - Unable to turn on shadows (shadows not supported)
> 
> After opening the Chimera Reply log returns this message:
> 
> Disabled programs because the GPU and graphics driver bug
> you encountered while compiling a vertex shader.
> -------------------------------------------------- -----------
> 
> Maybe my graphics card is inappropriate?
> 
> The User's Guide about the Build Structure writes that the helical DNA / RNA (not yet Implemented )
> and this option is disabled.
> 
> Sincerely, Janusz Grabowski

Hi Janusz,
The message suggests your computer can't do the shadows.  It might help to update your graphics driver, but I don't know for certain.  However, other "set" options should work,  for example:

set bgColor white

As mentioned in the "rna duplex" description, the path file is created using the command "rna path":
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#duplex>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#path>

Also, as mentioned in an earlier message you have to get a daily build (version 1.9), also available from our download page, to use the "helical DNA/RNA" option in Build Structure.
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009497.html>

It is recommended to send chimera questions to chimera-users at cgl.ucsf.edu instead of to me directly.
Thanks,
Elaine





From bala.biophysics at gmail.com  Fri Jan 10 02:26:50 2014
From: bala.biophysics at gmail.com (Bala subramanian)
Date: Fri, 10 Jan 2014 11:26:50 +0100
Subject: [Chimera-users] displaying electrostatic field
Message-ID: <CA+WPOVPUYfENpp9rT6kS14eTNcLhiUsaT6+9E_WXRvyyk+R2Jg@mail.gmail.com>

Friends,

Kindly see the following link (Fig 22, left panel).

http://www.bioscience.org/2009/v14/af/3398/fulltext.php?bframe=figures.htm

Has anyone tried making the display of electric field in Chimera. Is there
any way i can make the same in chimera.

Thanks,
Bala

-- 
C. Balasubramanian
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From meng at cgl.ucsf.edu  Fri Jan 10 09:58:13 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 10 Jan 2014 09:58:13 -0800
Subject: [Chimera-users] displaying electrostatic field
In-Reply-To: <CA+WPOVPUYfENpp9rT6kS14eTNcLhiUsaT6+9E_WXRvyyk+R2Jg@mail.gmail.com>
References: <CA+WPOVPUYfENpp9rT6kS14eTNcLhiUsaT6+9E_WXRvyyk+R2Jg@mail.gmail.com>
Message-ID: <87CD9B0E-888C-4344-BF50-27728C42BB41@cgl.ucsf.edu>

Hi Bala,
There is no option to show cones like in the left panel of Fig 22, but for the electric field lines in the right panel, see command "measure fieldLines":
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#fieldLines>

There is an example image in the Chimera Image Gallery:
<http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/fieldlines/fieldlines.html>

Showing field lines requires already having an electrostatic potential map, which can be calculated in other programs outside of Chimera, or via Chimera with the PDB2PQR and APBS tools as in the last section of the "surface properties" image tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#esp2>

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

On Jan 10, 2014, at 2:26 AM, Bala subramanian wrote:

> Friends,
> Kindly see the following link (Fig 22, left panel). 
> 
> http://www.bioscience.org/2009/v14/af/3398/fulltext.php?bframe=figures.htm
> 
> Has anyone tried making the display of electric field in Chimera. Is there any way i can make the same in chimera.
> Thanks,
> Bala




From boissel at uni-mainz.de  Mon Jan 13 01:30:40 2014
From: boissel at uni-mainz.de (Jean-Paul Boissel)
Date: Mon, 13 Jan 2014 10:30:40 +0100
Subject: [Chimera-users] Registration ?
Message-ID: <CEF970D0.89E4%boissel@uni-mainz.de>

Just downloaded the new dally build. At opening got the message:
Registration file "/Users/JPB/.chimera/registration" has expired.
Do we have to register again for 2014
Thanks

> 
> Dr. Jean-Paul Boissel, Team Leader
> Solute Transport Through Biological Membranes/ Ellen I. Closs' group
> Department of Pharmacology
> University Medical Center of the Johannes Gutenberg-University
> Obere Zahlbacher Strasse 67, D-55101 Mainz
> Tel.:    +49 6131-17 9189
> FAX:   +49 6131-17 9329
> e-mail: boissel at uni-mainz.de
> http://www.unimedizin-mainz.de/pharmakologie/research/solute-transport-through
> -biological-membranes.html?L=1
> This e-mail contains confidential information and may also be legally
> privileged. If you are not the intended recipient or received this mail by
> mistake, please inform the sender immediately and delete the mail. Any
> un-authorized use, copying, disclosure or forwarding of this mail and of
> information contained therein is prohibited.



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From pett at cgl.ucsf.edu  Mon Jan 13 11:08:06 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 13 Jan 2014 11:08:06 -0800
Subject: [Chimera-users] Registration ?
In-Reply-To: <CEF970D0.89E4%boissel@uni-mainz.de>
References: <CEF970D0.89E4%boissel@uni-mainz.de>
Message-ID: <5DA55578-A95B-4DAC-84B8-2AFEEDB91321@cgl.ucsf.edu>

On Jan 13, 2014, at 1:30 AM, Jean-Paul Boissel wrote:

> Just downloaded the new dally build. At opening got the message:
> Registration file "/Users/JPB/.chimera/registration" has expired.
> Do we have to register again for 2014
> Thanks

It isn't "for 2014" per se, but whenever it's been more than a year since your last registration.  This is so we can give our funding agency, the NIH, some kind of feel for how many people are currently using Chimera -- so thanks for registering!

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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From jqewt2 at mail.umkc.edu  Sat Jan 11 13:58:41 2014
From: jqewt2 at mail.umkc.edu (Jay Eifler)
Date: Sat, 11 Jan 2014 13:58:41 -0800
Subject: [Chimera-users] batch writing of attributes
Message-ID: <201401112158.s0BLwfr1051929@plato.cgl.ucsf.edu>


I'm trying to automate saving the areaSAS for a bunch
of models. I've got no problem loading the models, etc.
The problem is simply how do I use command line
arguments to save the areaSAS. I've tried writesel.  This
works all fine in Render/Select by attribute simply
because it has a feature to save the areaSAS to a file.
Thanks.


From goddard at sonic.net  Mon Jan 13 13:53:09 2014
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 13 Jan 2014 13:53:09 -0800
Subject: [Chimera-users] Computing solvent accessible area without internal
	cavities
In-Reply-To: <160512F9DE0B5F478413FB7608F255828856F77510@EXCMSMBX02.ad.bcm.edu>
References: <160512F9DE0B5F478413FB7608F255828856F77510@EXCMSMBX02.ad.bcm.edu>
Message-ID: <A17009EB-118F-4319-8D2A-0C995DE6F89B@sonic.net>

Hi Numan,

  Chimera uses the MSMS program to compute solvent accessible surface area, and MSMS has an option to only compute for the outside surface component without internal cavities.  So I think this is just what you want.  Although you could script it in Chimera you might find it easier to write a script that uses the standalone program directly from Michel Sanner

	http://mgl.scripps.edu/people/sanner/html/msms_home.html
 
The one trouble you may run into is the calculation failing on some molecules due to numerical instabilities.  The older version of the MSMS library we use in Chimera often fails to compute the surfaces and areas for molecules larger than 10,000 atoms, and sometimes fails for much smaller molecules.  The standalone program from Michel failed much less often in tests I did a few years ago, probably because it used some newer more reliable code.

	Tom


On Jan 13, 2014, at 11:13 AM, "Oezguen, Numan"  wrote:

> Dear Tom,
>  
> I am facing a problem that you have most probably already have solved and hoping you could help me out. I need to identify atoms that are solvent accessible. For this I used the program Getarea from Werner Braun?s group in Galveston Texas. It works fine, however it lists also internal cavity surface atoms as solvent exposed. Technically it is correct? but I am interested only in those surface areas that are not internal i.e. surface areas that are accessible to molecules approaching it from outside.
>  
> Do you know of any commercial or free (preferably) program that can do this. Ideally it should be possible to call it from scripts (shell or Perl).
>  
> Thank you very much for you time and help,
> Numan
>  
>  
> Numan Oezguen, Dr. rer. nat.
> Instructor of Pathology & Immunology
> Texas Children?s Microbiome Center
> Feigin Center, Suite 830
> 1102 Bates Avenue
> Houston, TX 77030

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From pett at cgl.ucsf.edu  Mon Jan 13 14:05:41 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 13 Jan 2014 14:05:41 -0800
Subject: [Chimera-users] batch writing of attributes
In-Reply-To: <201401112158.s0BLwfr1051929@plato.cgl.ucsf.edu>
References: <201401112158.s0BLwfr1051929@plato.cgl.ucsf.edu>
Message-ID: <D77ABE32-FAF2-4EF4-AD99-2F12066232FD@cgl.ucsf.edu>

On Jan 11, 2014, at 1:58 PM, Jay Eifler <jqewt2 at mail.umkc.edu> wrote:

> 
> I'm trying to automate saving the areaSAS for a bunch
> of models. I've got no problem loading the models, etc.
> The problem is simply how do I use command line
> arguments to save the areaSAS. I've tried writesel.  This
> works all fine in Render/Select by attribute simply
> because it has a feature to save the areaSAS to a file.
> Thanks.

Hi Jay,
	Do you really need the values on a per-atom basis?  If you just need the grand total, it's reported in the reply log so you could just open and surface your structures one by one via a script (one by one to avoid possibly running out of memory) and then afterward save the reply log contents to a file manually (there's a "Save" button on the reply log).

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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From thrabe at sanfordburnham.org  Mon Jan 13 17:18:50 2014
From: thrabe at sanfordburnham.org (Thomas Hrabe)
Date: Tue, 14 Jan 2014 01:18:50 +0000
Subject: [Chimera-users] Problem with HEADER keyword in PDBs
Message-ID: <0E63ED67-CE36-48CE-ACF1-CB94505B31F8@sanfordburnham.org>

Hi everyone,

I believe I found a problem with the >HEADER< keyword in PDB files.
Some programs may create pdbs with the header keyword specifying the origin or a name of a chain or other metadata with the coordinates below.
PyMol understands this keyword and colors chains that have identical chain ID (see example attached) in multiple colors while chimera interprets all as one chain.


Thanks,
Thomas

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From cantini at cerm.unifi.it  Tue Jan 14 07:10:36 2014
From: cantini at cerm.unifi.it (cantini at cerm.unifi.it)
Date: Tue, 14 Jan 2014 16:10:36 +0100
Subject: [Chimera-users] RMSD per residue NMR structure
Message-ID: <20140114161036.96896nnojrekomck@alpha.cerm.unifi.it>

Dear users

Does anyone knows how to calculate through CHIMERA the backbone rmsd  
per residue of a NMR ensembles of protein structures ?

thank a lot

Francesca Cantini

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.



From meng at cgl.ucsf.edu  Tue Jan 14 08:51:26 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 14 Jan 2014 08:51:26 -0800
Subject: [Chimera-users] Problem with HEADER keyword in PDBs
In-Reply-To: <0E63ED67-CE36-48CE-ACF1-CB94505B31F8@sanfordburnham.org>
References: <0E63ED67-CE36-48CE-ACF1-CB94505B31F8@sanfordburnham.org>
Message-ID: <54D562A9-5E55-4CCF-93E7-6461122A5702@cgl.ucsf.edu>

Hi Thomas,
Well, I wouldn't call it a problem? it just happens that Pymol does one thing and Chimera does another.  Chimera "knows" they are multiple chains, however.  If you want the chains in different colors, for example, you could use the command:  

rainbow chain

You can also specify the colors to use in this command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html>

It doesn't have anything to do with the HEADER.  This file only has one HEADER line, and it just contains the name of a PDB file.  The chain IDs are in the ATOM lines.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 13, 2014, at 5:18 PM, Thomas Hrabe <thrabe at sanfordburnham.org> wrote:

> Hi everyone,
> I believe I found a problem with the >HEADER< keyword in PDB files.
> Some programs may create pdbs with the header keyword specifying the origin or a name of a chain or other metadata with the coordinates below.
> PyMol understands this keyword and colors chains that have identical chain ID (see example attached) in multiple colors while chimera interprets all as one chain.
> Thanks,
> Thomas




From meng at cgl.ucsf.edu  Tue Jan 14 09:46:31 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 14 Jan 2014 09:46:31 -0800
Subject: [Chimera-users] RMSD per residue NMR structure
In-Reply-To: <20140114161036.96896nnojrekomck@alpha.cerm.unifi.it>
References: <20140114161036.96896nnojrekomck@alpha.cerm.unifi.it>
Message-ID: <96A49723-AF88-459C-8767-E2FF6327793F@cgl.ucsf.edu>

Hi Francesca,
The per-residue RMSD (from CA atoms only) can be calculated easily by associating all of the structures to a single sequence:

(1) open the NMR ensemble ensemble, then show the sequence for any one of the ensemble members, it doesn't matter which one.  You can show the sequence with menu: Favorites? Sequence and choosing which to show, or command, for example: sequence #0.1
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>

(2) in the sequence window menu, choose "Structure? Associations," and in the resulting dialog change the association of every model (every ensemble member) from "none" to that same sequence, then click OK.

(3) in the sequence window menu, choose "Headers? RMSD."  A histogram of the per-residue RMSDs will be shown above the sequence.

So far I have assumed the structures are already superimposed on each other.  If they are not, the RMSDs will be high because they are calculated from the current positions.  If the structures are not superimposed, however, you can easily superimpose them.  One way is to choose from the sequence window menu  "Structure? Match".  You could try using all the positions of the sequence (no match options checked) or starting with all positions but turning on the option to iterate the fit, perhaps with cutoff 2 A.  You can try the matching several times to see what looks good to you.  Once you have gotten the structures matched (superimposed) the way you like, then you could go ahead with further steps.

(4) if you just want to show the per-residue RMSDs with color and/or "worm" fatness on one of the structures, you can just do that with Render by Attribute (in menu under Tools? Structure Analysis), in which you would choose the residue attribute named mavRMSD.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>

(5) if you want to write out the values, you can also do that with Render by Attribute, with "File? Save Attributes" in its menu, again choosing the residue attribute named mavRMSD.  You would just do that for one of the structues, because all of the structures would have the same values as each other.

Again, these RMSDs are based on the CA atoms only.   If you only had 2 structures in the ensemble, it would just be the CA-CA distance at each position.  There is no simple (nonprogramming) way to use all the backbone atoms.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 14, 2014, at 7:10 AM, cantini at cerm.unifi.it wrote:

> Dear users
> Does anyone knows how to calculate through CHIMERA the backbone rmsd per residue of a NMR ensembles of protein structures ?
> thank a lot
> Francesca Cantini




From ipark.c at gmail.com  Mon Jan 13 17:18:46 2014
From: ipark.c at gmail.com (inhee park)
Date: Mon, 13 Jan 2014 17:18:46 -0800
Subject: [Chimera-users] MD trajectory play by commandline
Message-ID: <CAK1CK_5kBPWXGcq83kRKVO8G_gOVaLPDCRD6QpEpD5kooOJ3EA@mail.gmail.com>

Dear Chimera developers and users:


I am using Chimera (production version 1.8 (build 38824) 2013-06-07
21:09:20 UTC).

I wanted to process MD trajectories to extract their detailed H-bond
information.
To do so, I would like to process by script with Hbond.py file.
$ chimera --script Hbond.py

#---[Hbond.py]
from chimera import runCommand

# pr trajectory movie
with open("metafile", 'w') as m:
    meta_input = """amber
mypdb.prmtop
pr_dry_netcdf.crd
"""
    print >> m, meta_input
#
runCommand("open movie:metafile")
runCommand("alias ^myhb hbond relax true savefile hbond.$1")
runCommand("perframe myhb")
runCommand("coordset #0 1,1000,10; wait 100")
#-----------------------

As I have many MD trajectories to be processed, I was looking for a
commandline
in lieu of actually clicking buttons in MD movie GUI to play.
I thought that "coordset #0 1,10000,10; wait 100" may operate like
automatically
starting the MD movie to load frame 1 to 1000 at every 100 interval.
But resulting saved H-bond files contain same information all about the
first frame
(because graphically displayed was the first frame without any update
unless clicking the button in MD movie GUI).

Is there a way to achieve an automatic play via commandline?

Thank you,
  inhee park
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From meng at cgl.ucsf.edu  Tue Jan 14 11:06:27 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 14 Jan 2014 11:06:27 -0800
Subject: [Chimera-users] MD trajectory play by commandline
In-Reply-To: <CAK1CK_5kBPWXGcq83kRKVO8G_gOVaLPDCRD6QpEpD5kooOJ3EA@mail.gmail.com>
References: <CAK1CK_5kBPWXGcq83kRKVO8G_gOVaLPDCRD6QpEpD5kooOJ3EA@mail.gmail.com>
Message-ID: <08CA94CE-37E9-4357-B913-42B47A5F5DA1@cgl.ucsf.edu>

Dear Inhee Park,
A big limitation of the "coordset" command is that most formats of MD trajectory would have to be played through entirely using the graphical interface before it would work to use "coordset", as mentioned here:

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

In other words, probably the frame is not updating when you use coordset.  Another thing that confuses me in your script is the use of "wait".  I don't think it is needed.  Assuming "coordset" is working, I'd use something like

perframe myhb; coordset #0 1,1000,10
~perframe

Sorry about that limitation.  Maybe someone else can suggest how to use python to play the trajectory.
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Jan 13, 2014, at 5:18 PM, inhee park <ipark.c at gmail.com> wrote:

> Dear Chimera developers and users:
> 
> 
> I am using Chimera (production version 1.8 (build 38824) 2013-06-07 21:09:20 UTC).
> 
> I wanted to process MD trajectories to extract their detailed H-bond information.
> To do so, I would like to process by script with Hbond.py file.
> $ chimera --script Hbond.py
> 
> #---[Hbond.py] 
> from chimera import runCommand
> 
> # pr trajectory movie
> with open("metafile", 'w') as m:
>     meta_input = """amber
> mypdb.prmtop
> pr_dry_netcdf.crd
> """
>     print >> m, meta_input
> #
> runCommand("open movie:metafile")
> runCommand("alias ^myhb hbond relax true savefile hbond.$1")
> runCommand("perframe myhb")
> runCommand("coordset #0 1,1000,10; wait 100")
> #-----------------------
> 
> As I have many MD trajectories to be processed, I was looking for a commandline 
> in lieu of actually clicking buttons in MD movie GUI to play.
> I thought that "coordset #0 1,10000,10; wait 100" may operate like automatically 
> starting the MD movie to load frame 1 to 1000 at every 100 interval.
> But resulting saved H-bond files contain same information all about the first frame
> (because graphically displayed was the first frame without any update
> unless clicking the button in MD movie GUI).
> 
> Is there a way to achieve an automatic play via commandline?
> 
> Thank you,
>   inhee park
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From pett at cgl.ucsf.edu  Tue Jan 14 11:13:41 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 14 Jan 2014 11:13:41 -0800
Subject: [Chimera-users] MD trajectory play by commandline
In-Reply-To: <08CA94CE-37E9-4357-B913-42B47A5F5DA1@cgl.ucsf.edu>
References: <CAK1CK_5kBPWXGcq83kRKVO8G_gOVaLPDCRD6QpEpD5kooOJ3EA@mail.gmail.com>
	<08CA94CE-37E9-4357-B913-42B47A5F5DA1@cgl.ucsf.edu>
Message-ID: <F63B8097-5028-4FEF-B06A-CE253352F4EE@cgl.ucsf.edu>

Yes, as Elaine says you need all the frames loaded.  Since you are using a Python script it is not hard to do this with a few additional lines before your coordset command:

from chimera import openModels, Molecule
m = openModels.list(modelTypes=[Molecule])[0]
m.loadAllFrames()

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 14, 2014, at 11:06 AM, Elaine Meng wrote:

> Dear Inhee Park,
> A big limitation of the "coordset" command is that most formats of MD trajectory would have to be played through entirely using the graphical interface before it would work to use "coordset", as mentioned here:
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
> 
> In other words, probably the frame is not updating when you use coordset.  Another thing that confuses me in your script is the use of "wait".  I don't think it is needed.  Assuming "coordset" is working, I'd use something like
> 
> perframe myhb; coordset #0 1,1000,10
> ~perframe
> 
> Sorry about that limitation.  Maybe someone else can suggest how to use python to play the trajectory.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> On Jan 13, 2014, at 5:18 PM, inhee park wrote:
> 
>> Dear Chimera developers and users:
>> 
>> 
>> I am using Chimera (production version 1.8 (build 38824) 2013-06-07 21:09:20 UTC).
>> 
>> I wanted to process MD trajectories to extract their detailed H-bond information.
>> To do so, I would like to process by script with Hbond.py file.
>> $ chimera --script Hbond.py
>> 
>> #---[Hbond.py] 
>> from chimera import runCommand
>> 
>> # pr trajectory movie
>> with open("metafile", 'w') as m:
>>    meta_input = """amber
>> mypdb.prmtop
>> pr_dry_netcdf.crd
>> """
>>    print >> m, meta_input
>> #
>> runCommand("open movie:metafile")
>> runCommand("alias ^myhb hbond relax true savefile hbond.$1")
>> runCommand("perframe myhb")
>> runCommand("coordset #0 1,1000,10; wait 100")
>> #-----------------------
>> 
>> As I have many MD trajectories to be processed, I was looking for a commandline 
>> in lieu of actually clicking buttons in MD movie GUI to play.
>> I thought that "coordset #0 1,10000,10; wait 100" may operate like automatically 
>> starting the MD movie to load frame 1 to 1000 at every 100 interval.
>> But resulting saved H-bond files contain same information all about the first frame
>> (because graphically displayed was the first frame without any update
>> unless clicking the button in MD movie GUI).
>> 
>> Is there a way to achieve an automatic play via commandline?
>> 
>> Thank you,
>>  inhee park
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users






From pett at cgl.ucsf.edu  Tue Jan 14 11:25:24 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 14 Jan 2014 11:25:24 -0800
Subject: [Chimera-users] Problem with HEADER keyword in PDBs
In-Reply-To: <0E63ED67-CE36-48CE-ACF1-CB94505B31F8@sanfordburnham.org>
References: <0E63ED67-CE36-48CE-ACF1-CB94505B31F8@sanfordburnham.org>
Message-ID: <4342AC78-6F41-43B9-91F7-E3642F342643@cgl.ucsf.edu>

On Jan 13, 2014, at 5:18 PM, Thomas Hrabe wrote:

> Hi everyone,
> 
> I believe I found a problem with the >HEADER< keyword in PDB files.
> Some programs may create pdbs with the header keyword specifying the origin or a name of a chain or other metadata with the coordinates below.
> PyMol understands this keyword and colors chains that have identical chain ID (see example attached) in multiple colors while chimera interprets all as one chain.

Yeah, Chimera basically ignores the (non-standard) second and third HEADER records.  As Elaine said, Chimera knows they are different chains (which you can see by showing their sequences) but you are going to have trouble using commands in some cases because there are two :110.a for instance.  You probably want the chains in different models for this reason.  You can do that either by typing "split" in the command line, or by editing your PDB file and changing the two TER records to END records.

--Eric






From goddard at sonic.net  Tue Jan 14 11:27:31 2014
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 14 Jan 2014 11:27:31 -0800
Subject: [Chimera-users] MD trajectory play by commandline
In-Reply-To: <08CA94CE-37E9-4357-B913-42B47A5F5DA1@cgl.ucsf.edu>
References: <CAK1CK_5kBPWXGcq83kRKVO8G_gOVaLPDCRD6QpEpD5kooOJ3EA@mail.gmail.com>
	<08CA94CE-37E9-4357-B913-42B47A5F5DA1@cgl.ucsf.edu>
Message-ID: <DA1957BC-A507-4C7A-BCBD-E4C9B8113F18@sonic.net>

Hi Inhee,

  I think the "wait 100" command is needed after the "coordset" command because the coordset command does not wait for the 100 frames to be shown before going on to the next command.  This weird behavior is for making animations where you want to start coordset, and maybe start spinning the model at the same time.

	Tom


On Jan 14, 2014, at 11:06 AM, Elaine Meng wrote:

> Dear Inhee Park,
> A big limitation of the "coordset" command is that most formats of MD trajectory would have to be played through entirely using the graphical interface before it would work to use "coordset", as mentioned here:
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
> 
> In other words, probably the frame is not updating when you use coordset.  Another thing that confuses me in your script is the use of "wait".  I don't think it is needed.  Assuming "coordset" is working, I'd use something like
> 
> perframe myhb; coordset #0 1,1000,10
> ~perframe
> 
> Sorry about that limitation.  Maybe someone else can suggest how to use python to play the trajectory.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> On Jan 13, 2014, at 5:18 PM, inhee park <ipark.c at gmail.com> wrote:
> 
>> Dear Chimera developers and users:
>> 
>> 
>> I am using Chimera (production version 1.8 (build 38824) 2013-06-07 21:09:20 UTC).
>> 
>> I wanted to process MD trajectories to extract their detailed H-bond information.
>> To do so, I would like to process by script with Hbond.py file.
>> $ chimera --script Hbond.py
>> 
>> #---[Hbond.py] 
>> from chimera import runCommand
>> 
>> # pr trajectory movie
>> with open("metafile", 'w') as m:
>>    meta_input = """amber
>> mypdb.prmtop
>> pr_dry_netcdf.crd
>> """
>>    print >> m, meta_input
>> #
>> runCommand("open movie:metafile")
>> runCommand("alias ^myhb hbond relax true savefile hbond.$1")
>> runCommand("perframe myhb")
>> runCommand("coordset #0 1,1000,10; wait 100")
>> #-----------------------
>> 
>> As I have many MD trajectories to be processed, I was looking for a commandline 
>> in lieu of actually clicking buttons in MD movie GUI to play.
>> I thought that "coordset #0 1,10000,10; wait 100" may operate like automatically 
>> starting the MD movie to load frame 1 to 1000 at every 100 interval.
>> But resulting saved H-bond files contain same information all about the first frame
>> (because graphically displayed was the first frame without any update
>> unless clicking the button in MD movie GUI).
>> 
>> Is there a way to achieve an automatic play via commandline?
>> 
>> Thank you,
>>  inhee park
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From pett at cgl.ucsf.edu  Tue Jan 14 11:50:47 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 14 Jan 2014 11:50:47 -0800
Subject: [Chimera-users] batch writing of attributes
In-Reply-To: <C5EA912FC8226E49961CEFDAA97DE3B229F28C3D@CO1PRD0113MB747.prod.exchangelabs.com>
References: <201401112158.s0BLwfr1051929@plato.cgl.ucsf.edu>,
	<D77ABE32-FAF2-4EF4-AD99-2F12066232FD@cgl.ucsf.edu>
	<C5EA912FC8226E49961CEFDAA97DE3B229F28C3D@CO1PRD0113MB747.prod.exchangelabs.com>
Message-ID: <3D56DA88-F72C-405D-9D27-D73199863697@cgl.ucsf.edu>

Hi Jay,
	We thought as much really.  Well, you are going to have to use a Python script.  The good news is that it's a really simple Python script.  Put the following in a file whose name ends in ".py":

from chimera import openModels, Molecule
for m in openModels.list(modelTypes=[Molecule]):
	from OpenSave import osOpen
	f = osOpen("~/surfData/%s.data" % m.name, "w")
	for a in m.atoms:
		print>>f, a, getattr(a, "areaSES", 0.0)
	f.close()

The indentation matters, so make sure to preserve it.
	Then once you open your model and surface it, you can run the above script simply by opening it with the "open" command.  It will create a file with a list of atoms and corresponding surface areas.  The file will be named <model name>.data and it will be in the "surfData" folder in your home directory, so make sure that folder exists beforehand or modify the script to have it go to another location.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 14, 2014, at 5:56 AM, "Eifler, Jay Q. (UMKC-Student)" wrote:

> Actually I'm doing ab-initio quantum mechanical calculations and need
> to analyze on a atom and residue basis.  I've already been able to
> save the atom and residue results but can't figure out how to automate
> it since you have got to click buttons in the render/select attribute. The
> Chimera notes seem to imply it should be possible to save attributes to
> file. However, areaSAS is supposed to be an attribute but doesn't seem
> to belong to the model attributes.
> From: Eric Pettersen
> Sent: Monday, January 13, 2014 4:05 PM
> To: Eifler, Jay Q. (UMKC-Student)
> Cc: <Chimera-users at cgl.ucsf.edu> List
> Subject: Re: [Chimera-users] batch writing of attributes
> 
> On Jan 11, 2014, at 1:58 PM, Jay Eifler wrote:
> 
>> 
>> I'm trying to automate saving the areaSAS for a bunch
>> of models. I've got no problem loading the models, etc.
>> The problem is simply how do I use command line
>> arguments to save the areaSAS. I've tried writesel.  This
>> works all fine in Render/Select by attribute simply
>> because it has a feature to save the areaSAS to a file.
>> Thanks.
> 
> Hi Jay,
> Do you really need the values on a per-atom basis?  If you just need the grand total, it's reported in the reply log so you could just open and surface your structures one by one via a script (one by one to avoid possibly running out of memory) and then afterward save the reply log contents to a file manually (there's a "Save" button on the reply log).
> 
> --Eric
> 
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu



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From ipark.c at gmail.com  Tue Jan 14 11:24:42 2014
From: ipark.c at gmail.com (inhee park)
Date: Tue, 14 Jan 2014 11:24:42 -0800
Subject: [Chimera-users] MD trajectory play by commandline
In-Reply-To: <08CA94CE-37E9-4357-B913-42B47A5F5DA1@cgl.ucsf.edu>
References: <CAK1CK_5kBPWXGcq83kRKVO8G_gOVaLPDCRD6QpEpD5kooOJ3EA@mail.gmail.com>
	<08CA94CE-37E9-4357-B913-42B47A5F5DA1@cgl.ucsf.edu>
Message-ID: <CAK1CK_4=_nSXwFQiq8Sn6pWWwBmdGBHeEz07R6UxO946GeuO2g@mail.gmail.com>

Dear Elaine and Eric:

Thank you for your help.
Actually the following previous posts were directly helpful to accomplish
what I wanted to do, i.e. utilizing MoveDialog.
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2013/000968.html
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-August/006634.html

Now hbond information seems properly saved upon updated frame with
LoadFrame.

Thanks a lot!

#chimera --script Hbond.py
#
from chimera import runCommand
from Movie.gui import MovieDialog
from chimera.extension import manager

# pr trajectory movie open by metafile
meta = open("metafile", 'w')
meta_input = """ amber
mypdb.prmtop
pr.crd
"""
meta.write(meta_input)
meta.close()
#####
def findMDMovie():
    mdms = [inst for inst in manager.instances if isinstance(inst,
MovieDialog)]
    if not mdms:
        raise AssertionError("No MD Movie Instances!")
    return mdms[-1]
#####
runCommand("open movie:metafile; sel protein")
mdm = findMDMovie()
for x in range(1,1000+1,5):
    frame = x
    mdm.LoadFrame(x)
    runCommand("hbond selRestrict any relax true savefile hbond.%s" % x)
    runCommand("wait")
runCommand("stop") # move onto next MD trajectory


On Tue, Jan 14, 2014 at 11:06 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Inhee Park,
> A big limitation of the "coordset" command is that most formats of MD
> trajectory would have to be played through entirely using the graphical
> interface before it would work to use "coordset", as mentioned here:
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
>
> In other words, probably the frame is not updating when you use coordset.
>  Another thing that confuses me in your script is the use of "wait".  I
> don't think it is needed.  Assuming "coordset" is working, I'd use
> something like
>
> perframe myhb; coordset #0 1,1000,10
> ~perframe
>
> Sorry about that limitation.  Maybe someone else can suggest how to use
> python to play the trajectory.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Jan 13, 2014, at 5:18 PM, inhee park <ipark.c at gmail.com> wrote:
>
> > Dear Chimera developers and users:
> >
> >
> > I am using Chimera (production version 1.8 (build 38824) 2013-06-07
> 21:09:20 UTC).
> >
> > I wanted to process MD trajectories to extract their detailed H-bond
> information.
> > To do so, I would like to process by script with Hbond.py file.
> > $ chimera --script Hbond.py
> >
> > #---[Hbond.py]
> > from chimera import runCommand
> >
> > # pr trajectory movie
> > with open("metafile", 'w') as m:
> >     meta_input = """amber
> > mypdb.prmtop
> > pr_dry_netcdf.crd
> > """
> >     print >> m, meta_input
> > #
> > runCommand("open movie:metafile")
> > runCommand("alias ^myhb hbond relax true savefile hbond.$1")
> > runCommand("perframe myhb")
> > runCommand("coordset #0 1,1000,10; wait 100")
> > #-----------------------
> >
> > As I have many MD trajectories to be processed, I was looking for a
> commandline
> > in lieu of actually clicking buttons in MD movie GUI to play.
> > I thought that "coordset #0 1,10000,10; wait 100" may operate like
> automatically
> > starting the MD movie to load frame 1 to 1000 at every 100 interval.
> > But resulting saved H-bond files contain same information all about the
> first frame
> > (because graphically displayed was the first frame without any update
> > unless clicking the button in MD movie GUI).
> >
> > Is there a way to achieve an automatic play via commandline?
> >
> > Thank you,
> >   inhee park
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>


-- 
_________
inhee park
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From pythonchemia at gazeta.pl  Thu Jan 16 10:11:04 2014
From: pythonchemia at gazeta.pl (pythonchemia Gazeta.pl)
Date: Thu, 16 Jan 2014 19:11:04 +0100
Subject: [Chimera-users] rna and set shadows commands
In-Reply-To: <EE60E80D-F321-4B82-BC49-3F5F860C5BE3@cgl.ucsf.edu>
References: <CAHXR=Oo--KQepS_gy7fS4jXHAFVxb6+KdH_6qzjxApSZwXGzHw@mail.gmail.com>
	<EE60E80D-F321-4B82-BC49-3F5F860C5BE3@cgl.ucsf.edu>
Message-ID: <CAHXR=OqibL190it8E1k-WAp162t05rWnONRdXSw34o4giWpFRw@mail.gmail.com>

Dear Elaine Meng

Thank you very much for your help. I have Chimere in alpha version and RNA /
DNA Build Structure  works.I Experiment with the rna duplex command.
I'm sorry that I addressed questions to you - I did it automatically.
In the future, I'll send questions to chimera-users at cgl.ucsf.edu

Sincerely, Janusz Grabowsk



2014/1/9 Elaine Meng <meng at cgl.ucsf.edu>

> On Jan 9, 2014, at 12:07 PM, "pythonchemia Gazeta.pl" <
> pythonchemia at gazeta.pl> wrote:
> >
> > Hello Elaine C. Meng
> >
> > Thank you very much for your reply and sorry that I answer only now.
> > When it comes to command rna  path and rna model  your tips helped me. :)
> > Although I do not know how to define the path for the command operations
> rna duplex. : (
> >
> > Unfortunately for me the system WinXP / Chimera 1.8 - 32bit shadows set
> command does not work. : (
> > Chimera returns this message:
> >
> > - Unable to turn on shadows (shadows not supported)
> >
> > After opening the Chimera Reply log returns this message:
> >
> > Disabled programs because the GPU and graphics driver bug
> > you encountered while compiling a vertex shader.
> > -------------------------------------------------- -----------
> >
> > Maybe my graphics card is inappropriate?
> >
> > The User's Guide about the Build Structure writes that the helical DNA /
> RNA (not yet Implemented )
> > and this option is disabled.
> >
> > Sincerely, Janusz Grabowski
>
> Hi Janusz,
> The message suggests your computer can't do the shadows.  It might help to
> update your graphics driver, but I don't know for certain.  However, other
> "set" options should work,  for example:
>
> set bgColor white
>
> As mentioned in the "rna duplex" description, the path file is created
> using the command "rna path":
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#duplex>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#path>
>
> Also, as mentioned in an earlier message you have to get a daily build
> (version 1.9), also available from our download page, to use the "helical
> DNA/RNA" option in Build Structure.
> <
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009497.html
> >
>
> It is recommended to send chimera questions to chimera-users at cgl.ucsf.eduinstead of to me directly.
> Thanks,
> Elaine
>
>
>
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From craigmdana at berkeley.edu  Thu Jan 16 14:27:18 2014
From: craigmdana at berkeley.edu (Craig Dana)
Date: Thu, 16 Jan 2014 14:27:18 -0800
Subject: [Chimera-users] pyroglutamate distorted in 3PFJ
Message-ID: <201401162227.s0GMRIaU074343@plato.cgl.ucsf.edu>

I'm looking at the N-terminal pyroglutamate residue in PDB: 3PFJ. It is clearly distorted, but when I open the same PDB file in VMD, the pyroglutamate is not distorted.



From jupiter.hce at gmail.com  Fri Jan 17 00:56:58 2014
From: jupiter.hce at gmail.com (jupiter)
Date: Fri, 17 Jan 2014 19:56:58 +1100
Subject: [Chimera-users] Failed to start chimera
Message-ID: <CAA=hcWQTeNcPyhqbwVyMs-UpK=UrxBM93XOxMbGBMMjo2xViJg@mail.gmail.com>

Hi,

I installed Chimera 1.7 on CentOS 6.4. I can run any opengl
applications, but failed to run chimera , it got following error
message. Appreciate any tips to fix this issue.

X Error of failed request:  BadMatch (invalid parameter attributes)
  Major opcode of failed request:  72 (X_PutImage)
  Serial number of failed request:  34
  Current serial number in output stream:  37


From jupiter.hce at gmail.com  Fri Jan 17 02:26:04 2014
From: jupiter.hce at gmail.com (jupiter)
Date: Fri, 17 Jan 2014 21:26:04 +1100
Subject: [Chimera-users] Failed to start chimera
In-Reply-To: <CAA=hcWQTeNcPyhqbwVyMs-UpK=UrxBM93XOxMbGBMMjo2xViJg@mail.gmail.com>
References: <CAA=hcWQTeNcPyhqbwVyMs-UpK=UrxBM93XOxMbGBMMjo2xViJg@mail.gmail.com>
Message-ID: <CAA=hcWRdtsQ5fQCnMJ299+zy-huGyWJz7hUMUE4MetW12TWiWw@mail.gmail.com>

Please ignore it, it is not Chimera issue but X installation issue.

Sorry about it.

Kind regards,

-j

On 1/17/14, jupiter <jupiter.hce at gmail.com> wrote:
> Hi,
>
> I installed Chimera 1.7 on CentOS 6.4. I can run any opengl
> applications, but failed to run chimera , it got following error
> message. Appreciate any tips to fix this issue.
>
> X Error of failed request:  BadMatch (invalid parameter attributes)
>   Major opcode of failed request:  72 (X_PutImage)
>   Serial number of failed request:  34
>   Current serial number in output stream:  37
>


From mpeters at vcu.edu  Fri Jan 17 07:53:59 2014
From: mpeters at vcu.edu (Michael H Peters)
Date: Fri, 17 Jan 2014 10:53:59 -0500
Subject: [Chimera-users] how to display coordinate axes
Message-ID: <CA+Wdjv27JVYe339p3iwbb_KxUtkQ6n9R6i7YwJS-G5eyTAv7cw@mail.gmail.com>

Hi:  I have a simple question - How do I display the lab or fixed frame
coordinate axes?  I am using the windows 32 bit UCSF Chimera on my desktop.
 In rasmol the command is "axes on".  I cannot find anything similar in
Chimera.

Thanks for your help.  An axes display is critical if you need to know the
spatial orientation wrt the lab frame.

Best wishes, Michael


Dr. Michael H. Peters
mpeters at vcu.edu
804-828-7790
www.engineering.vcu.edu/proteinengineering
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From meng at cgl.ucsf.edu  Fri Jan 17 10:09:08 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 17 Jan 2014 10:09:08 -0800
Subject: [Chimera-users] pyroglutamate distorted in 3PFJ
In-Reply-To: <201401162227.s0GMRIaU074343@plato.cgl.ucsf.edu>
References: <201401162227.s0GMRIaU074343@plato.cgl.ucsf.edu>
Message-ID: <9B211E2E-1EFC-4385-A47D-60F661A649FB@cgl.ucsf.edu>

Hi Craig,
This is an artifact from the ribbon smoothing, where by default (only when ribbon is shown) the apparent positions of peptide backbone atoms are adjusted to fall along the smoothed ribbon path. The real positions are used for any measurements.  The real positions are apparent if you just hide ribbon for that residue, e.g. with command:

~ribbon :1

(or ribbon and atoms can be shown simultaneously after you use command "ribbackbone").  The issue is described in more depth here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>

Another possibility is to use a different method with less smoothing to calculate the ribbon path, e.g. command:

ribspline cardinal
...or...
ribspline cardinal smooth strand

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

On Jan 16, 2014, at 2:27 PM, Craig Dana wrote:

> I'm looking at the N-terminal pyroglutamate residue in PDB: 3PFJ. It is clearly distorted, but when I open the same PDB file in VMD, the pyroglutamate is not distorted.




From meng at cgl.ucsf.edu  Fri Jan 17 10:17:53 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 17 Jan 2014 10:17:53 -0800
Subject: [Chimera-users] how to display coordinate axes
In-Reply-To: <CA+Wdjv27JVYe339p3iwbb_KxUtkQ6n9R6i7YwJS-G5eyTAv7cw@mail.gmail.com>
References: <CA+Wdjv27JVYe339p3iwbb_KxUtkQ6n9R6i7YwJS-G5eyTAv7cw@mail.gmail.com>
Message-ID: <588F528F-6091-4E7D-9D86-612C3300ECC2@cgl.ucsf.edu>

Hi Michael,
If you mean axes that will move along with your structures and show how their current coordinate system(s) are oriented, there isn't a built-in option, but you can open the attached BILD object file in Chimera to display such axes. It shows the axes (X red, Y yellow, Z blue). The file should be named with the suffix .bild to be recognized automatically.

The BILD text file is very small and simple.  You can edit the colors, 
scale, offset etc. as desired.  The format is described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>

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


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On Jan 17, 2014, at 7:53 AM, Michael H Peters wrote:

> Hi:  I have a simple question - How do I display the lab or fixed frame coordinate axes?  I am using the windows 32 bit UCSF Chimera on my desktop.  In rasmol the command is "axes on".  I cannot find anything similar in Chimera.
> 
> Thanks for your help.  An axes display is critical if you need to know the spatial orientation wrt the lab frame.
> 
> Best wishes, Michael


From mpeters at vcu.edu  Fri Jan 17 10:22:00 2014
From: mpeters at vcu.edu (Dr. Michael Peters)
Date: Fri, 17 Jan 2014 13:22:00 -0500
Subject: [Chimera-users] how to display coordinate axes
In-Reply-To: <588F528F-6091-4E7D-9D86-612C3300ECC2@cgl.ucsf.edu>
References: <CA+Wdjv27JVYe339p3iwbb_KxUtkQ6n9R6i7YwJS-G5eyTAv7cw@mail.gmail.com>
	<588F528F-6091-4E7D-9D86-612C3300ECC2@cgl.ucsf.edu>
Message-ID: <BCFA3E3C-B617-4B76-96CC-58B3C8128172@vcu.edu>

Thanks - I?ll try that.

M.P.
Dr. Michael Peters
mpeters at vcu.edu
804-828-7790




On Jan 17, 2014, at 1:17 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Michael,
> If you mean axes that will move along with your structures and show how their current coordinate system(s) are oriented, there isn't a built-in option, but you can open the attached BILD object file in Chimera to display such axes. It shows the axes (X red, Y yellow, Z blue). The file should be named with the suffix .bild to be recognized automatically.
> 
> The BILD text file is very small and simple.  You can edit the colors, 
> scale, offset etc. as desired.  The format is described here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> On Jan 17, 2014, at 7:53 AM, Michael H Peters wrote:
> 
>> Hi:  I have a simple question - How do I display the lab or fixed frame coordinate axes?  I am using the windows 32 bit UCSF Chimera on my desktop.  In rasmol the command is "axes on".  I cannot find anything similar in Chimera.
>> 
>> Thanks for your help.  An axes display is critical if you need to know the spatial orientation wrt the lab frame.
>> 
>> Best wishes, Michael
> 

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From pett at cgl.ucsf.edu  Fri Jan 17 11:30:08 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 17 Jan 2014 11:30:08 -0800
Subject: [Chimera-users] [Chimera] #12778: failure assigning charges to
	FAD (was: Chimera bug report submission)
In-Reply-To: <045.6292fc707727b0266350f975715f9c90@cgl.ucsf.edu>
References: <030.74ccfcf16b89898dc86d3c49f9ffe1cd@cgl.ucsf.edu>
	<045.6292fc707727b0266350f975715f9c90@cgl.ucsf.edu>
Message-ID: <00E89824-FFD1-474C-9871-A1D8C5440CA8@cgl.ucsf.edu>

Hi Will,
	The underlying program that Chimera uses to compute charges, antechamber/sqm from AmberTools, frequently fails for molecules with regions of concentrated negative charge, such as the central phosphate connector of FAD.  It not really something I can do much about.  Nonetheless, the failure not only depends on the charge density but also on the specific atomic geometry.  So for instance, I can compute the charges for the FAD in 4kpu, though it does take a long time (about 10 minutes).  This means that there is kind of a work around.  Compute the charges in a structure that works and then transfer them to your structure.  You do this by bringing up the Render by Attribute tool after successfully computing charges and using it's File->Save Attributes menu entry to save the charges to a file.  You should select the FAD and then restrict the save to selected atoms.  Edit the resulting file and change the residue name and chain ID (in this case 401.A) to FAD so that it can be applied to all FADs in your structure.  Then in the Chimera with your structure open, read in the charge-attribute file with the Define Attributes tool.  To save you a lot of the effort here, I've attached the edited charge-attribute file I saved from 4kpu.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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From craigmdana at gmail.com  Fri Jan 17 10:16:49 2014
From: craigmdana at gmail.com (Craig Dana)
Date: Fri, 17 Jan 2014 10:16:49 -0800
Subject: [Chimera-users] pyroglutamate distorted in 3PFJ
In-Reply-To: <9B211E2E-1EFC-4385-A47D-60F661A649FB@cgl.ucsf.edu>
References: <201401162227.s0GMRIaU074343@plato.cgl.ucsf.edu>
	<9B211E2E-1EFC-4385-A47D-60F661A649FB@cgl.ucsf.edu>
Message-ID: <CAJZCFWmGmgmLj+U=pb5E3T6YYq-0NrFpUc5P2t5jbJFrdfADyg@mail.gmail.com>

Much better - that's the ring shape I recognize.  That was very helpful!

I appreciate it.

Best,
Craig


On Fri, Jan 17, 2014 at 10:09 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Craig,
> This is an artifact from the ribbon smoothing, where by default (only when
> ribbon is shown) the apparent positions of peptide backbone atoms are
> adjusted to fall along the smoothed ribbon path. The real positions are
> used for any measurements.  The real positions are apparent if you just
> hide ribbon for that residue, e.g. with command:
>
> ~ribbon :1
>
> (or ribbon and atoms can be shown simultaneously after you use command
> "ribbackbone").  The issue is described in more depth here:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset
> >
>
> Another possibility is to use a different method with less smoothing to
> calculate the ribbon path, e.g. command:
>
> ribspline cardinal
> ...or...
> ribspline cardinal smooth strand
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Jan 16, 2014, at 2:27 PM, Craig Dana wrote:
>
> > I'm looking at the N-terminal pyroglutamate residue in PDB: 3PFJ. It is
> clearly distorted, but when I open the same PDB file in VMD, the
> pyroglutamate is not distorted.
>
>
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From naismith at st-andrews.ac.uk  Mon Jan 20 05:17:32 2014
From: naismith at st-andrews.ac.uk (James Naismith)
Date: Mon, 20 Jan 2014 13:17:32 +0000
Subject: [Chimera-users] Morphing
In-Reply-To: <D5A0DCB2-B119-4E2E-98D9-2FDB0C702783@st-and.ac.uk>
References: <D5A0DCB2-B119-4E2E-98D9-2FDB0C702783@st-and.ac.uk>
Message-ID: <3DCEB4AD-7E95-487F-A664-430C8513064D@st-andrews.ac.uk>

I am experimenting with the morphing feature. I know I am being very stupid but I cannot get the analysis to work.

I am using a MAC OSX latest version.

I have created my morph which is running nicely.

What I would like to do is analyse the morph for VDW clashes.
(That is in going from structure 1 to structure 2, what residues would have to move).


First problem is when I run cluster (under analysis in MD movie) then generate residue interaction for cluster, up pop a new dialogue with warnings but seems to ask about calculations

When I click OK or apply I get a new box residue interaction contact parameters

This always generates an error ?No atoms designated for clash detection?
I seem only to have four options 
themselves
all others atoms (default)
other atoms in same model 
second set of designated atoms


Any help gratefully received

(Ps I have installed the latest cytoscope but it does not have the structure.viz plugin; I keep getting errors trying to install older version)

best
Jim


Jim Naismith


The University of St Andrews is a charity registered in Scotland : No SC013532


From meng at cgl.ucsf.edu  Mon Jan 20 13:25:44 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 20 Jan 2014 13:25:44 -0800
Subject: [Chimera-users] Morphing
In-Reply-To: <3DCEB4AD-7E95-487F-A664-430C8513064D@st-andrews.ac.uk>
References: <D5A0DCB2-B119-4E2E-98D9-2FDB0C702783@st-and.ac.uk>
	<3DCEB4AD-7E95-487F-A664-430C8513064D@st-andrews.ac.uk>
Message-ID: <C92E71DB-F056-43D1-A675-F18FE769E167@cgl.ucsf.edu>

Hi Jim,
If using the Find Clashes/Contacts dialog, you have to first "select" the atoms and then click the "Designate" button to designate them.  If you click the Help button on the dialog, it will show you its manual page, or you can see the same page on our website here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
There are lots of ways to select atoms, for example command "select protein" if you want to select all protein atoms:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

This tutorial has a step-by-step example of using Find Clashes/Contacts:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

However, two things come to mind based on your description:

(1) Find Clashes won't tell you what is changing across your morph per se; instead it will just find the clashes at each point (at each frame of the morph trajectory).  Not sure if that is what you wanted.  If you just want to see where the CA atoms deviate from each other when the structures are superimposed, you could superimpose them with MatchMaker with the option to show the sequence alignment turned on, and then in the resulting sequence alignment menu, choose Headers... RMSD.

(2) since you may want to calculate clashes for each point in your morph trajectory, it may be more convenient to use the command "findclash" instead of the GUI.  Then the atoms would be specified in the command instead of as a selection. The MD Movie dialog that is showing your morph allows defining a per-frame script, that is, one or more commands to be run at each frame of the trajectory.  See "per-frame scripts" in the MD Movie manual page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

This tutorial has an example of defining a per-frame script.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>

I don't know if structureViz is available for Cytoscape 3.  At least for Cytoscape 2.x, one would use the Plugins menu to get various plugins including structureViz.

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

On Jan 20, 2014, at 5:17 AM, James Naismith wrote:

> I am experimenting with the morphing feature. I know I am being very stupid but I cannot get the analysis to work.
> 
> I am using a MAC OSX latest version.
> 
> I have created my morph which is running nicely.
> 
> What I would like to do is analyse the morph for VDW clashes.
> (That is in going from structure 1 to structure 2, what residues would have to move).
> 
> 
> First problem is when I run cluster (under analysis in MD movie) then generate residue interaction for cluster, up pop a new dialogue with warnings but seems to ask about calculations
> 
> When I click OK or apply I get a new box residue interaction contact parameters
> 
> This always generates an error ?No atoms designated for clash detection?
> I seem only to have four options 
> themselves
> all others atoms (default)
> other atoms in same model 
> second set of designated atoms
> 
> Any help gratefully received
> 
> (Ps I have installed the latest cytoscope but it does not have the structure.viz plugin; I keep getting errors trying to install older version)
> 
> best
> Jim




From meng at cgl.ucsf.edu  Mon Jan 20 13:35:09 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 20 Jan 2014 13:35:09 -0800
Subject: [Chimera-users] Morphing
In-Reply-To: <C92E71DB-F056-43D1-A675-F18FE769E167@cgl.ucsf.edu>
References: <D5A0DCB2-B119-4E2E-98D9-2FDB0C702783@st-and.ac.uk>
	<3DCEB4AD-7E95-487F-A664-430C8513064D@st-andrews.ac.uk>
	<C92E71DB-F056-43D1-A675-F18FE769E167@cgl.ucsf.edu>
Message-ID: <C216A683-1852-4563-BBCE-0D712535189A@cgl.ucsf.edu>

Hi Jim,
One more thing...
I didn't understand your mention of clustering.  Clustering doesn't really make sense for a morph trajectory; it is mainly for grouping similar conformations in an NMR ensemble or similar frames from molecular dynamics simulations.  It doesn't calculate or use residue interactions, it just compares the trajectory frames with one another.
Best,
Elaine

On Jan 20, 2014, at 1:25 PM, Elaine Meng wrote:

> Hi Jim,
> If using the Find Clashes/Contacts dialog, you have to first "select" the atoms and then click the "Designate" button to designate them.  If you click the Help button on the dialog, it will show you its manual page, or you can see the same page on our website here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
> There are lots of ways to select atoms, for example command "select protein" if you want to select all protein atoms:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
> 
> This tutorial has a step-by-step example of using Find Clashes/Contacts:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
> 
> However, two things come to mind based on your description:
> 
> (1) Find Clashes won't tell you what is changing across your morph per se; instead it will just find the clashes at each point (at each frame of the morph trajectory).  Not sure if that is what you wanted.  If you just want to see where the CA atoms deviate from each other when the structures are superimposed, you could superimpose them with MatchMaker with the option to show the sequence alignment turned on, and then in the resulting sequence alignment menu, choose Headers... RMSD.
> 
> (2) since you may want to calculate clashes for each point in your morph trajectory, it may be more convenient to use the command "findclash" instead of the GUI.  Then the atoms would be specified in the command instead of as a selection. The MD Movie dialog that is showing your morph allows defining a per-frame script, that is, one or more commands to be run at each frame of the trajectory.  See "per-frame scripts" in the MD Movie manual page:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
> 
> This tutorial has an example of defining a per-frame script.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>
> 
> I don't know if structureViz is available for Cytoscape 3.  At least for Cytoscape 2.x, one would use the Plugins menu to get various plugins including structureViz.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Jan 20, 2014, at 5:17 AM, James Naismith wrote:
> 
>> I am experimenting with the morphing feature. I know I am being very stupid but I cannot get the analysis to work.
>> 
>> I am using a MAC OSX latest version.
>> 
>> I have created my morph which is running nicely.
>> 
>> What I would like to do is analyse the morph for VDW clashes.
>> (That is in going from structure 1 to structure 2, what residues would have to move).
>> 
>> 
>> First problem is when I run cluster (under analysis in MD movie) then generate residue interaction for cluster, up pop a new dialogue with warnings but seems to ask about calculations
>> 
>> When I click OK or apply I get a new box residue interaction contact parameters
>> 
>> This always generates an error ?No atoms designated for clash detection?
>> I seem only to have four options 
>> themselves
>> all others atoms (default)
>> other atoms in same model 
>> second set of designated atoms
>> 
>> Any help gratefully received
>> 
>> (Ps I have installed the latest cytoscope but it does not have the structure.viz plugin; I keep getting errors trying to install older version)
>> 
>> best
>> Jim
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From xyuwan at gmail.com  Sat Jan 18 13:03:29 2014
From: xyuwan at gmail.com (Wenda Wang)
Date: Sat, 18 Jan 2014 16:03:29 -0500
Subject: [Chimera-users] movie recode
Message-ID: <CABv_XiSNyO9i94rKNLQsaM=f0EbozgCLc3TO6K5+o0hgaZmj3w@mail.gmail.com>

Dear List,

I am trying to use UCSF chimera to make a movie after TEM reconstruction
using IMOD. But an error message always pops out, even I use the script in
the examples. Belows shows the error messages in the Reply Log. Can anyone
take a look and give me some clue where the problem is?

Thank you.
-----------------------------
C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i
c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -vf
crop=(in_w/2)*2:(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -vb 200.0k
C:\Users\Public\Desktop\rock.mp4
An error occurred during encoding. See Reply Log for details.

Error during MPEG encoding:
-----------------------------
Exit value:    1
Error message:

-----------------------------
C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i
c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -y -vcodec libvpx -f
webm -vb 200.0k C:\Users\Public\Desktop\rock.webm
An error occurred during encoding. See Reply Log for details.

Error during MPEG encoding:
-----------------------------
Exit value:    1
Error message:

-----------------------------
C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i
c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -y -vcodec libtheora
-f ogg -vb 200.0k C:\Users\Public\Desktop\rock.ogv
An error occurred during encoding. See Reply Log for details.

Error during MPEG encoding:
-----------------------------
Exit value:    1
Error message:


Thank you very much,
Wenda

Wenda Wang,
PhD candidate
Department of Materials Sciences and Engineering,
Drexel University, Philadelphia, PA
215-6883348
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From goddard at sonic.net  Tue Jan 21 10:35:05 2014
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 21 Jan 2014 10:35:05 -0800
Subject: [Chimera-users] movie recode
In-Reply-To: <CABv_XiSNyO9i94rKNLQsaM=f0EbozgCLc3TO6K5+o0hgaZmj3w@mail.gmail.com>
References: <CABv_XiSNyO9i94rKNLQsaM=f0EbozgCLc3TO6K5+o0hgaZmj3w@mail.gmail.com>
Message-ID: <BF645C6F-27E0-4FDB-83DB-6717713471BA@sonic.net>

Hi Wenda,

  My guess is that you don't have permission to write the movie output file to /Users/Public/Desktop or perhaps that directory does not exist.  If that is not the issue use Chimera menu Help / Report a Bug? and we will investigate.

	Tom


On Jan 18, 2014, at 1:03 PM, Wenda Wang  wrote:

> Dear List,
> 
> I am trying to use UCSF chimera to make a movie after TEM reconstruction using IMOD. But an error message always pops out, even I use the script in the examples. Belows shows the error messages in the Reply Log. Can anyone take a look and give me some clue where the problem is?
> 
> Thank you.
> -----------------------------
> C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -vf crop=(in_w/2)*2:(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -vb 200.0k C:\Users\Public\Desktop\rock.mp4
> An error occurred during encoding. See Reply Log for details.
> 
> Error during MPEG encoding:
> -----------------------------
> Exit value:    1
> Error message: 
> 
> -----------------------------
> C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -y -vcodec libvpx -f webm -vb 200.0k C:\Users\Public\Desktop\rock.webm
> An error occurred during encoding. See Reply Log for details.
> 
> Error during MPEG encoding:
> -----------------------------
> Exit value:    1
> Error message: 
> 
> -----------------------------
> C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -y -vcodec libtheora -f ogg -vb 200.0k C:\Users\Public\Desktop\rock.ogv
> An error occurred during encoding. See Reply Log for details.
> 
> Error during MPEG encoding:
> -----------------------------
> Exit value:    1
> Error message: 
> 
> 
> Thank you very much,
> Wenda
> 
> Wenda Wang,
> PhD candidate
> Department of Materials Sciences and Engineering,
> Drexel University, Philadelphia, PA
> 215-6883348
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From royassis at mail.tau.ac.il  Tue Jan 21 10:29:29 2014
From: royassis at mail.tau.ac.il (Roy Assis)
Date: Tue, 21 Jan 2014 20:29:29 +0200
Subject: [Chimera-users] Chimera Issues
Message-ID: <CAF_Lh3HP5kaZCnKPSLzsqnW_cBJCiJFxVh4WUDETP33FRL4czg@mail.gmail.com>

Hello !

For some time i've been using chimera, but for some reason a week ago, when
I try to lunch chimera, I get an error message (attached).


Please help
Roy Assis
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From pett at cgl.ucsf.edu  Tue Jan 21 17:37:44 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 21 Jan 2014 17:37:44 -0800
Subject: [Chimera-users] Chimera Issues
In-Reply-To: <CAF_Lh3HP5kaZCnKPSLzsqnW_cBJCiJFxVh4WUDETP33FRL4czg@mail.gmail.com>
References: <CAF_Lh3HP5kaZCnKPSLzsqnW_cBJCiJFxVh4WUDETP33FRL4czg@mail.gmail.com>
Message-ID: <6E1386DD-F490-481B-B918-FA270CB3858C@cgl.ucsf.edu>

On Jan 21, 2014, at 10:29 AM, Roy Assis <royassis at mail.tau.ac.il> wrote:

> Hello !
> 
> For some time i've been using chimera, but for some reason a week ago, when I try to lunch chimera, I get an error message (attached).

So this keeps happening upon launch for you?  I can get it to happen once, but then it starts working.  It has to do with a custom preset directory either no longer existing, or being unreadable for some reason.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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From agnel-praveen.joseph at stfc.ac.uk  Thu Jan 23 05:04:44 2014
From: agnel-praveen.joseph at stfc.ac.uk (agnel-praveen.joseph at stfc.ac.uk)
Date: Thu, 23 Jan 2014 13:04:44 +0000
Subject: [Chimera-users] Segger : command line
Message-ID: <458CD614B3712C42AF18F2A40F2D57240754A3AD@EXCHMBX03.fed.cclrc.ac.uk>

Hi,

I would like to automate watershed segmentation (Segger) on a set of volumes. Given that I have the details on the volume threshold, number of smoothing steps and minimum voxels in each region, is there a way to automate segmentation with different parameter inputs?

Many Thanks.

-- 
Scanned by iCritical.

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From goddard at sonic.net  Thu Jan 23 18:51:10 2014
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 23 Jan 2014 18:51:10 -0800
Subject: [Chimera-users] Segger : command line
In-Reply-To: <458CD614B3712C42AF18F2A40F2D57240754A3AD@EXCHMBX03.fed.cclrc.ac.uk>
References: <458CD614B3712C42AF18F2A40F2D57240754A3AD@EXCHMBX03.fed.cclrc.ac.uk>
Message-ID: <5D4298E0-1BE2-4B07-ACC4-6F9F7B440F65@sonic.net>

There is no Chimera command to run Segger so you would need to use Python code to automate it on a set of volumes.  The Segger Python code is very messy so this will be difficult.  If you are an experienced Python programmer then your aim would be to write a Python script that runs within Chimera opens the first map, creates a Segmentation instance from the class defined in

	chimera/share/Segger/regions.py

calls the smooth_and_group(steps, sdev) method, and writes out the resulting segmentation with the write_segmentation() routine in

	chimera/share/Segger/segfile.py

or the writing could be done with the Chimera "segment" command to export a mask file

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/segment.html

The Segger code is complicated with lots of code that was testing experimental features, so if you are not an experienced Python programmer I'm afraid it will not be possible to automate processing using it.

It would be nice if the Chimera segment command let you run the Segger algorithm -- then your processing of many maps would be much easier.  We will keep that in mind for the next generation of Chimera which we are currently working on.

	Tom


On Jan 23, 2014, at 5:04 AM, wrote:

> Hi,
>  
> I would like to automate watershed segmentation (Segger) on a set of volumes. Given that I have the details on the volume threshold, number of smoothing steps and minimum voxels in each region, is there a way to automate segmentation with different parameter inputs?
>  
> Many Thanks.
> 
> -- 
> Scanned by iCritical.
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From agnel-praveen.joseph at stfc.ac.uk  Fri Jan 24 02:51:18 2014
From: agnel-praveen.joseph at stfc.ac.uk (agnel-praveen.joseph at stfc.ac.uk)
Date: Fri, 24 Jan 2014 10:51:18 +0000
Subject: [Chimera-users] Segger : command line
In-Reply-To: <5D4298E0-1BE2-4B07-ACC4-6F9F7B440F65@sonic.net>
References: <458CD614B3712C42AF18F2A40F2D57240754A3AD@EXCHMBX03.fed.cclrc.ac.uk>
	<5D4298E0-1BE2-4B07-ACC4-6F9F7B440F65@sonic.net>
Message-ID: <458CD614B3712C42AF18F2A40F2D57240754C43F@EXCHMBX03.fed.cclrc.ac.uk>

Many thanks. I will have a look at the scripts and extract the required functions and classes. This is very helpful.

From: Tom Goddard [mailto:goddard at sonic.net]
Sent: 24 January 2014 02:51
To: Joseph, Agnel Praveen (STFC,RAL,SC)
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Segger : command line

There is no Chimera command to run Segger so you would need to use Python code to automate it on a set of volumes.  The Segger Python code is very messy so this will be difficult.  If you are an experienced Python programmer then your aim would be to write a Python script that runs within Chimera opens the first map, creates a Segmentation instance from the class defined in

            chimera/share/Segger/regions.py

calls the smooth_and_group(steps, sdev) method, and writes out the resulting segmentation with the write_segmentation() routine in

            chimera/share/Segger/segfile.py

or the writing could be done with the Chimera "segment" command to export a mask file

            http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/segment.html

The Segger code is complicated with lots of code that was testing experimental features, so if you are not an experienced Python programmer I'm afraid it will not be possible to automate processing using it.

It would be nice if the Chimera segment command let you run the Segger algorithm -- then your processing of many maps would be much easier.  We will keep that in mind for the next generation of Chimera which we are currently working on.

            Tom


On Jan 23, 2014, at 5:04 AM, wrote:


Hi,

I would like to automate watershed segmentation (Segger) on a set of volumes. Given that I have the details on the volume threshold, number of smoothing steps and minimum voxels in each region, is there a way to automate segmentation with different parameter inputs?

Many Thanks.


--
Scanned by iCritical.

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


-- 
Scanned by iCritical.

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From sarah.l.keasey.ctr at mail.mil  Fri Jan 24 07:59:57 2014
From: sarah.l.keasey.ctr at mail.mil (Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US))
Date: Fri, 24 Jan 2014 15:59:57 +0000
Subject: [Chimera-users] Multialign Viewer Header Definition File
	(UNCLASSIFIED)
Message-ID: <26617189835EAE44AB08964093BB5DEC2505C9EA@umechphh.easf.csd.disa.mil>

Classification: UNCLASSIFIED
Caveats: NONE

Hello,

I would like to generate a Header Definition File to load in to Multialign Viewer. I am unclear on the format of the file though, I keep getting errors when I try to load the file in and I think it has something to do with the way I am formatting the file. Would you be able to provide an example Header Definition file?

Thank you in advance,
Sarah Keasey
Graduate Student
University of Maryland, Baltimore County
ORISE participant, USAMRIID, Fort Detrick MD 

Classification: UNCLASSIFIED
Caveats: NONE





From meng at cgl.ucsf.edu  Fri Jan 24 11:17:52 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 24 Jan 2014 11:17:52 -0800
Subject: [Chimera-users] Multialign Viewer Header Definition File
	(UNCLASSIFIED)
In-Reply-To: <26617189835EAE44AB08964093BB5DEC2505C9EA@umechphh.easf.csd.disa.mil>
References: <26617189835EAE44AB08964093BB5DEC2505C9EA@umechphh.easf.csd.disa.mil>
Message-ID: <10C12382-AB9E-424C-B7F6-33EFCBEC259E@cgl.ucsf.edu>

Hi Sarah,
Sure thing - this may be more than you wanted, but here are a couple of examples of alignments and header files that go with them (4 files attached).  First open the alignment and then from the alignment window menu, choose "Headers... Load" and open the corresponding header file.

(1) alignment file 1bzm-others.afa and header file 1bzm-stars.hdr
This is an example with symbols.  It shows one header line named "Zn++ binding" with yellow stars in 3 positions.

(2) alignment file HIV1_REF_2008_ENV_PRO-norecomb.fasta and header file alascan-HIV1ref-cools.hdr
This is an example with quantitative values shown as histogram bar heights.  It shows two header lines with values only at certain positions.  If I remember correctly, this is the same data I used for the "Log..." headers in the figure here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavpref-analysis>

Header format description:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat>

It should just be plain text.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 24, 2014, at 7:59 AM, Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US) wrote:
> 
> Hello,
> I would like to generate a Header Definition File to load in to Multialign Viewer. I am unclear on the format of the file though, I keep getting errors when I try to load the file in and I think it has something to do with the way I am formatting the file. Would you be able to provide an example Header Definition file?
> 
> Thank you in advance,
> Sarah Keasey
> Graduate Student
> University of Maryland, Baltimore County
> ORISE participant, USAMRIID, Fort Detrick MD 
> 
> Classification: UNCLASSIFIED
> Caveats: NONE
> 
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From meng at cgl.ucsf.edu  Fri Jan 24 11:23:27 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 24 Jan 2014 11:23:27 -0800
Subject: [Chimera-users] Multialign Viewer Header Definition File
	(UNCLASSIFIED)
In-Reply-To: <10C12382-AB9E-424C-B7F6-33EFCBEC259E@cgl.ucsf.edu>
References: <26617189835EAE44AB08964093BB5DEC2505C9EA@umechphh.easf.csd.disa.mil>
	<10C12382-AB9E-424C-B7F6-33EFCBEC259E@cgl.ucsf.edu>
Message-ID: <C9C85F6D-98ED-4D1F-9178-BBC4F08F591F@cgl.ucsf.edu>

Oops, here's the correct link for the figure showing alignment headers:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers>

Elaine

On Jan 24, 2014, at 11:17 AM, Elaine Meng wrote:

> If I remember correctly, this is the same data I used for the "Log..." headers in the figure here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavpref-analysis>




From sarah.l.keasey.ctr at mail.mil  Fri Jan 24 13:37:44 2014
From: sarah.l.keasey.ctr at mail.mil (Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US))
Date: Fri, 24 Jan 2014 21:37:44 +0000
Subject: [Chimera-users] Multialign Viewer Header Definition File
 (UNCLASSIFIED)
In-Reply-To: <C9C85F6D-98ED-4D1F-9178-BBC4F08F591F@cgl.ucsf.edu>
References: <26617189835EAE44AB08964093BB5DEC2505C9EA@umechphh.easf.csd.disa.mil>
	<10C12382-AB9E-424C-B7F6-33EFCBEC259E@cgl.ucsf.edu>
	<C9C85F6D-98ED-4D1F-9178-BBC4F08F591F@cgl.ucsf.edu>
Message-ID: <26617189835EAE44AB08964093BB5DEC2505CBC1@umechphh.easf.csd.disa.mil>

Classification: UNCLASSIFIED
Caveats: NONE

Elaine,

Thank you for your response. It is now working, I had extra tabs at the end of my data lines and I think that might have been causing the problem.

Have a great weekend!

Sarah

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Friday, January 24, 2014 2:23 PM
To: Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US)
Cc: chimera-users at cgl.ucsf.edu List
Subject: Re: [Chimera-users] Multialign Viewer Header Definition File (UNCLASSIFIED)

Oops, here's the correct link for the figure showing alignment headers:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers>

Elaine

On Jan 24, 2014, at 11:17 AM, Elaine Meng wrote:

> If I remember correctly, this is the same data I used for the "Log..." headers in the figure here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavpref-analysis>


Classification: UNCLASSIFIED
Caveats: NONE





From htm211 at nyu.edu  Sun Jan 26 20:52:41 2014
From: htm211 at nyu.edu (Haresh Tukaram More)
Date: Sun, 26 Jan 2014 23:52:41 -0500
Subject: [Chimera-users] Need help in Coulombic surface coloring
Message-ID: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>

Hi,

I tried to get the Coulombic surface coloring for one of the protein that I
modified by removing certain residue at the C-termini and then mutated some
residues to the non-natural amino acid 5,5,5-trifluoroleucine using
Swisssidechin option. I am getting this error which I am not able to
understand.

Disabled GPU programs because a graphics driver bug
  was encountered while compiling a vertex shader.

#0, chain A: COMP
#0, chain B: COMP
#0, chain C: COMP
#0, chain D: COMP
#0, chain E: COMP
C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
MSMSLIB 1.3 started on Local PC
Copyright M.F. Sanner (March 2000)
Compilation flags

Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2
  22 connected surface components
  Total solvent excluded surface area = 10393.6
    component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059, 54.8894,
54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549, 37.0513,
35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319, 26.9429
  Total solvent accessible surface area = 10372
    component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165, 4.12717,
3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737, 0.962375,
0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394, 0.0674059,
0.0311705
No SEQRES records for combination (#-2147483648.-2147483648) chain A;
guessing terminii instead
No SEQRES records for combination (#-2147483648.-2147483648) chain B;
guessing terminii instead
No SEQRES records for combination (#-2147483648.-2147483648) chain C;
guessing terminii instead
No SEQRES records for combination (#-2147483648.-2147483648) chain D;
guessing terminii instead
No SEQRES records for combination (#-2147483648.-2147483648) chain E;
guessing terminii instead
Chain-initial residues that are actual N terminii: #-2147483648.-2147483648
MET 27.A, #-2147483648.-2147483648 MET 27.B, #-2147483648.-2147483648 MET
27.C, #-2147483648.-2147483648 MET 27.D, #-2147483648.-2147483648 MET 27.E
Chain-initial residues that are not actual N terminii:
Chain-final residues that are actual C terminii: #-2147483648.-2147483648
TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B, #-2147483648.-2147483648
TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D, #-2147483648.-2147483648
TFLE 67.E
Chain-final residues that are not actual C terminii:
424 hydrogen bonds
Hydrogens added
Charge model: AMBER ff12SB
Assigning partial charges to residue TFLE+TFLE (net charge +0) with am1-bcc
method
Running ANTECHAMBER command: C:/Program Files/Chimera
1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i
c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o
c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2
-c bcc -nc 0 -j 5 -s 2
(TFLE+TFLE)

Cannot automatically determine charges for residue TFLE+TFLE;
Run AddCharge tool manually to add charges and then rerun ESP

Can someone please tell me a step by step procedure to make this work.

Thanks & Regards,
Haresh
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From meng at cgl.ucsf.edu  Mon Jan 27 09:28:44 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 27 Jan 2014 09:28:44 -0800
Subject: [Chimera-users] Need help in Coulombic surface coloring
In-Reply-To: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
Message-ID: <7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>

Hi Haresh,
The Reply Log message (see the bottom part of what you sent) says there was a problem calculating the charges of your mutated residues and that you should try running Add Charge first, so that's what I would recommend.  Add Charge is in the menu under Tools.. Structure Editing, or can be run with command "addcharge".  It has two options for calculating the charges of nonstandard residues: AM1-BCC or Gasteiger.  Since the message shows there was a problem calculating using the AM1-BCC method on your mutated residues, I would try the Gasteiger method instead.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>

Then, after you run Add Charge successfully, you can run Coulombic again.  It will automatically detect that the charges have already been calculated, and use those charges for calculating the ESP and coloring the surface.

Actually I tried calculating charges for a single 5,5,5-trifluoroleucine residue by itself (in Chimera, can use "open pubchem:259832" to fetch it by PubChem CID) 
<http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs>
...and both methods, AM1-BCC and Gasteiger, worked fine; however maybe the calculation is more difficult in your structure where it sounds like the two mutated residues are treated together.

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

On Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:

> Hi,
> I tried to get the Coulombic surface coloring for one of the protein that I modified by removing certain residue at the C-termini and then mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine using Swisssidechin option. I am getting this error which I am not able to understand.
> 
> Disabled GPU programs because a graphics driver bug
>   was encountered while compiling a vertex shader.
> 
> #0, chain A: COMP
> #0, chain B: COMP
> #0, chain C: COMP
> #0, chain D: COMP
> #0, chain E: COMP
> C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
> MSMSLIB 1.3 started on Local PC
> Copyright M.F. Sanner (March 2000)
> Compilation flags  
> 
> Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2
>   22 connected surface components
>   Total solvent excluded surface area = 10393.6
>     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059, 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549, 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319, 26.9429
>   Total solvent accessible surface area = 10372
>     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165, 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737, 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394, 0.0674059, 0.0311705
> No SEQRES records for combination (#-2147483648.-2147483648) chain A; guessing terminii instead
> No SEQRES records for combination (#-2147483648.-2147483648) chain B; guessing terminii instead
> No SEQRES records for combination (#-2147483648.-2147483648) chain C; guessing terminii instead
> No SEQRES records for combination (#-2147483648.-2147483648) chain D; guessing terminii instead
> No SEQRES records for combination (#-2147483648.-2147483648) chain E; guessing terminii instead
> Chain-initial residues that are actual N terminii: #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B, #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D, #-2147483648.-2147483648 MET 27.E
> Chain-initial residues that are not actual N terminii: 
> Chain-final residues that are actual C terminii: #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B, #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D, #-2147483648.-2147483648 TFLE 67.E
> Chain-final residues that are not actual C terminii: 
> 424 hydrogen bonds
> Hydrogens added
> Charge model: AMBER ff12SB
> Assigning partial charges to residue TFLE+TFLE (net charge +0) with am1-bcc method
> Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2
> (TFLE+TFLE) 
> 
> Cannot automatically determine charges for residue TFLE+TFLE;
> Run AddCharge tool manually to add charges and then rerun ESP
> 
> Can someone please tell me a step by step procedure to make this work. 
> Thanks & Regards,
> Haresh




From pollack.1 at osu.edu  Mon Jan 27 09:39:58 2014
From: pollack.1 at osu.edu (Pollack, J)
Date: Mon, 27 Jan 2014 17:39:58 +0000
Subject: [Chimera-users] Need help in Coulombic surface coloring
In-Reply-To: <7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
Message-ID: <24E32E0182934B4BBFD71A8018107736900CA6D8@CIO-TNC-D1MBX10.osuad.osu.edu>

This ain't my problem, wow...that is, if I have one #12798 .....Thanks, regards, Den (JDennis Pollack)

-----Original Message-----
From: chimera-users-bounces at cgl.ucsf.edu [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Elaine Meng
Sent: Monday, January 27, 2014 12:29 PM
To: Haresh Tukaram More
Cc: Chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Need help in Coulombic surface coloring

Hi Haresh,
The Reply Log message (see the bottom part of what you sent) says there was a problem calculating the charges of your mutated residues and that you should try running Add Charge first, so that's what I would recommend.  Add Charge is in the menu under Tools.. Structure Editing, or can be run with command "addcharge".  It has two options for calculating the charges of nonstandard residues: AM1-BCC or Gasteiger.  Since the message shows there was a problem calculating using the AM1-BCC method on your mutated residues, I would try the Gasteiger method instead.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>

Then, after you run Add Charge successfully, you can run Coulombic again.  It will automatically detect that the charges have already been calculated, and use those charges for calculating the ESP and coloring the surface.

Actually I tried calculating charges for a single 5,5,5-trifluoroleucine residue by itself (in Chimera, can use "open pubchem:259832" to fetch it by PubChem CID) <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs>
...and both methods, AM1-BCC and Gasteiger, worked fine; however maybe the calculation is more difficult in your structure where it sounds like the two mutated residues are treated together.

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

On Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:

> Hi,
> I tried to get the Coulombic surface coloring for one of the protein that I modified by removing certain residue at the C-termini and then mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine using Swisssidechin option. I am getting this error which I am not able to understand.
> 
> Disabled GPU programs because a graphics driver bug
>   was encountered while compiling a vertex shader.
> 
> #0, chain A: COMP
> #0, chain B: COMP
> #0, chain C: COMP
> #0, chain D: COMP
> #0, chain E: COMP
> C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1 
> MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) 
> Compilation flags
> 
> Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2
>   22 connected surface components
>   Total solvent excluded surface area = 10393.6
>     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059, 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549, 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319, 26.9429
>   Total solvent accessible surface area = 10372
>     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165, 
> 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737, 
> 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394, 
> 0.0674059, 0.0311705 No SEQRES records for combination 
> (#-2147483648.-2147483648) chain A; guessing terminii instead No 
> SEQRES records for combination (#-2147483648.-2147483648) chain B; 
> guessing terminii instead No SEQRES records for combination 
> (#-2147483648.-2147483648) chain C; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain D; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain E; guessing terminii instead Chain-initial residues that are actual N terminii: #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B, #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D, #-2147483648.-2147483648 MET 27.E Chain-initial residues that are not actual N terminii:
> Chain-final residues that are actual C terminii: 
> #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B, #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D, #-2147483648.-2147483648 TFLE 67.E Chain-final residues that are not actual C terminii:
> 424 hydrogen bonds
> Hydrogens added
> Charge model: AMBER ff12SB
> Assigning partial charges to residue TFLE+TFLE (net charge +0) with 
> am1-bcc method Running ANTECHAMBER command: C:/Program Files/Chimera 
> 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i 
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi 
> mol2 -o 
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo 
> mol2 -c bcc -nc 0 -j 5 -s 2
> (TFLE+TFLE)
> 
> Cannot automatically determine charges for residue TFLE+TFLE; Run 
> AddCharge tool manually to add charges and then rerun ESP
> 
> Can someone please tell me a step by step procedure to make this work. 
> Thanks & Regards,
> Haresh


_______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users





From htm211 at nyu.edu  Mon Jan 27 18:56:31 2014
From: htm211 at nyu.edu (Haresh Tukaram More)
Date: Mon, 27 Jan 2014 21:56:31 -0500
Subject: [Chimera-users] Need help in Coulombic surface coloring
In-Reply-To: <7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
Message-ID: <CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>

Thanks a lot Elaine. I will try to work on it now and see if I can get any
results.

Regards,
Haresh


On Mon, Jan 27, 2014 at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Haresh,
> The Reply Log message (see the bottom part of what you sent) says there
> was a problem calculating the charges of your mutated residues and that you
> should try running Add Charge first, so that's what I would recommend.  Add
> Charge is in the menu under Tools.. Structure Editing, or can be run with
> command "addcharge".  It has two options for calculating the charges of
> nonstandard residues: AM1-BCC or Gasteiger.  Since the message shows there
> was a problem calculating using the AM1-BCC method on your mutated
> residues, I would try the Gasteiger method instead.
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html
> >
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
>
> Then, after you run Add Charge successfully, you can run Coulombic again.
>  It will automatically detect that the charges have already been
> calculated, and use those charges for calculating the ESP and coloring the
> surface.
>
> Actually I tried calculating charges for a single 5,5,5-trifluoroleucine
> residue by itself (in Chimera, can use "open pubchem:259832" to fetch it by
> PubChem CID)
> <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs
> >
> ...and both methods, AM1-BCC and Gasteiger, worked fine; however maybe the
> calculation is more difficult in your structure where it sounds like the
> two mutated residues are treated together.
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
>
> > Hi,
> > I tried to get the Coulombic surface coloring for one of the protein
> that I modified by removing certain residue at the C-termini and then
> mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine
> using Swisssidechin option. I am getting this error which I am not able to
> understand.
> >
> > Disabled GPU programs because a graphics driver bug
> >   was encountered while compiling a vertex shader.
> >
> > #0, chain A: COMP
> > #0, chain B: COMP
> > #0, chain C: COMP
> > #0, chain D: COMP
> > #0, chain E: COMP
> > C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
> > MSMSLIB 1.3 started on Local PC
> > Copyright M.F. Sanner (March 2000)
> > Compilation flags
> >
> > Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2
> >   22 connected surface components
> >   Total solvent excluded surface area = 10393.6
> >     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059,
> 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549,
> 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319,
> 26.9429
> >   Total solvent accessible surface area = 10372
> >     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165,
> 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737,
> 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394,
> 0.0674059, 0.0311705
> > No SEQRES records for combination (#-2147483648.-2147483648) chain A;
> guessing terminii instead
> > No SEQRES records for combination (#-2147483648.-2147483648) chain B;
> guessing terminii instead
> > No SEQRES records for combination (#-2147483648.-2147483648) chain C;
> guessing terminii instead
> > No SEQRES records for combination (#-2147483648.-2147483648) chain D;
> guessing terminii instead
> > No SEQRES records for combination (#-2147483648.-2147483648) chain E;
> guessing terminii instead
> > Chain-initial residues that are actual N terminii:
> #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B,
> #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D,
> #-2147483648.-2147483648 MET 27.E
> > Chain-initial residues that are not actual N terminii:
> > Chain-final residues that are actual C terminii:
> #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B,
> #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D,
> #-2147483648.-2147483648 TFLE 67.E
> > Chain-final residues that are not actual C terminii:
> > 424 hydrogen bonds
> > Hydrogens added
> > Charge model: AMBER ff12SB
> > Assigning partial charges to residue TFLE+TFLE (net charge +0) with
> am1-bcc method
> > Running ANTECHAMBER command: C:/Program Files/Chimera
> 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2
> -c bcc -nc 0 -j 5 -s 2
> > (TFLE+TFLE)
> >
> > Cannot automatically determine charges for residue TFLE+TFLE;
> > Run AddCharge tool manually to add charges and then rerun ESP
> >
> > Can someone please tell me a step by step procedure to make this work.
> > Thanks & Regards,
> > Haresh
>
>
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From meng at cgl.ucsf.edu  Tue Jan 28 09:27:11 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 28 Jan 2014 09:27:11 -0800
Subject: [Chimera-users] Need help in Coulombic surface coloring
In-Reply-To: <CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
	<CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
Message-ID: <F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>

Hi Haresh,
There is another issue you may wish to consider:  Add Charge will require adding hydrogens first, but then the molecular surface will be more "craggy" due to the additional small atoms. Here are instructions if you want to show the Coulombic ESP coloring on the less rugged surface calculated without hydrogens (as is usually done; radii automatically adjust to compensate):

After adding hydrogens and charges:
(1) when you use the Coulombic Surface Coloring tool, turn on the option to "Compute grid?"  (in my test just now I took the defaults for the other grid options)

(2) delete the hydrogens, e.g. command: del H

(3) use the "Surface Color" dialog that automatically appeared when you created the grid to color the main surface by electrostatic potential using the potential file (grid) you just created.  If you don't see that dialog, you can raise it using menu: Tools? Surface/Binding Analysis? Electrostatic Surface Coloring. The default name of that grid is Coulombic ESP.  (Do not use the Coulombic Surface Coloring dialog for coloring!  After the hydrogens with many positive charges have been deleted, mostly negative charges will be left, and you will get an incorrect very red surface using the Coulombic Surface Coloring dialog.)

Normally the protein wouldn't have strange residues that require a separate charge calculation, and this circuitous process wouldn't be required.
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 27, 2014, at 6:56 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:

> Thanks a lot Elaine. I will try to work on it now and see if I can get any results.
> 
> Regards,
> Haresh
> 
> 
> On Mon, Jan 27, 2014 at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Haresh,
> The Reply Log message (see the bottom part of what you sent) says there was a problem calculating the charges of your mutated residues and that you should try running Add Charge first, so that's what I would recommend.  Add Charge is in the menu under Tools.. Structure Editing, or can be run with command "addcharge".  It has two options for calculating the charges of nonstandard residues: AM1-BCC or Gasteiger.  Since the message shows there was a problem calculating using the AM1-BCC method on your mutated residues, I would try the Gasteiger method instead.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> 
> Then, after you run Add Charge successfully, you can run Coulombic again.  It will automatically detect that the charges have already been calculated, and use those charges for calculating the ESP and coloring the surface.
> 
> Actually I tried calculating charges for a single 5,5,5-trifluoroleucine residue by itself (in Chimera, can use "open pubchem:259832" to fetch it by PubChem CID)
> <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs>
> ...and both methods, AM1-BCC and Gasteiger, worked fine; however maybe the calculation is more difficult in your structure where it sounds like the two mutated residues are treated together.
> 
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> 
> > Hi,
> > I tried to get the Coulombic surface coloring for one of the protein that I modified by removing certain residue at the C-termini and then mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine using Swisssidechin option. I am getting this error which I am not able to understand.
> >
> > Disabled GPU programs because a graphics driver bug
> >   was encountered while compiling a vertex shader.
> >
> > #0, chain A: COMP
> > #0, chain B: COMP
> > #0, chain C: COMP
> > #0, chain D: COMP
> > #0, chain E: COMP
> > C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
> > MSMSLIB 1.3 started on Local PC
> > Copyright M.F. Sanner (March 2000)
> > Compilation flags
> >
> > Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2
> >   22 connected surface components
> >   Total solvent excluded surface area = 10393.6
> >     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059, 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549, 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319, 26.9429
> >   Total solvent accessible surface area = 10372
> >     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165, 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737, 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394, 0.0674059, 0.0311705
> > No SEQRES records for combination (#-2147483648.-2147483648) chain A; guessing terminii instead
> > No SEQRES records for combination (#-2147483648.-2147483648) chain B; guessing terminii instead
> > No SEQRES records for combination (#-2147483648.-2147483648) chain C; guessing terminii instead
> > No SEQRES records for combination (#-2147483648.-2147483648) chain D; guessing terminii instead
> > No SEQRES records for combination (#-2147483648.-2147483648) chain E; guessing terminii instead
> > Chain-initial residues that are actual N terminii: #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B, #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D, #-2147483648.-2147483648 MET 27.E
> > Chain-initial residues that are not actual N terminii:
> > Chain-final residues that are actual C terminii: #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B, #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D, #-2147483648.-2147483648 TFLE 67.E
> > Chain-final residues that are not actual C terminii:
> > 424 hydrogen bonds
> > Hydrogens added
> > Charge model: AMBER ff12SB
> > Assigning partial charges to residue TFLE+TFLE (net charge +0) with am1-bcc method
> > Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2
> > (TFLE+TFLE)
> >
> > Cannot automatically determine charges for residue TFLE+TFLE;
> > Run AddCharge tool manually to add charges and then rerun ESP
> >
> > Can someone please tell me a step by step procedure to make this work.
> > Thanks & Regards,
> > Haresh
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From carter_jjc at hotmail.com  Mon Jan 27 23:32:58 2014
From: carter_jjc at hotmail.com (Joshua Carter)
Date: Tue, 28 Jan 2014 01:32:58 -0600
Subject: [Chimera-users] Surface Transparency Command Issues
Message-ID: <BAY178-W43AB652C0178D81135C6F6E0AD0@phx.gbl>

Hello,
I'm having trouble getting the surface transparency command to work correctly.  I'm currently making a movie about the formation of a protein complex and I want the subunits to be shown as ribbons while they dock and then after they dock the electrostatic surface to appear.  I have the script written and the surface generated but when I use either the surftransp or transparency command nothing happens.  The command is correct, if I use it to change the transparency of a ribbon or atom it does so, but if I try to make the surface appear after docking nothing changes.  In addition, if I go to the Actions menu and change the surface transparency from there it also works.
If you could help me figure out why the command won't work that would be extremely helpful.
Thanks,Josh 		 	   		  
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From meng at cgl.ucsf.edu  Tue Jan 28 10:05:29 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 28 Jan 2014 10:05:29 -0800
Subject: [Chimera-users] Overlay structures in Chimera (UNCLASSIFIED)
In-Reply-To: <26617189835EAE44AB08964093BB5DEC25060FBA@umechphg.easf.csd.disa.mil>
References: <26617189835EAE44AB08964093BB5DEC25060FBA@umechphg.easf.csd.disa.mil>
Message-ID: <CAFD9563-9D23-4482-AB33-4F59F2F3D914@cgl.ucsf.edu>

On Jan 28, 2014, at 9:45 AM, "Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US)" <sarah.l.keasey.ctr at mail.mil> wrote:

> Elaine,
> 
> I have a new question regarding overlaying structures using Chimera.
> 
> I have opened two structures in Chimera. I am trying to move them so that they are overlaid. It appears as though I should be able to inactivate one of the structures in order to freely move the other, but this doesn't work for me and I'm not sure where I am going wrong. When I inactivate one structure, I can freely rotate the other, but not move it from one place to another. I have watched the youtube video here: http://www.youtube.com/watch?v=6VGYo1pRRZ8 which deals with merging two structures, and also watched the "Sequential Fitting" video on the "Videos" page of the UCSF Chimera site.
> 
> Any suggestions for what I am doing wrong? I apologize for such elementary questions, I am a new Chimera user.
> 
> Thanks in advance,
> Sarah Keasey

Hi Sarah,
(we generally ask everyone to send questions to chimera-users at cgl.ucsf.edu, CC'd here, so that everybody can benefit, unless the data are private)

Those videos aren't that relevant to your situation.  More relevant is the manual page discussing the various ways to superimpose structures.   The Chimera User's Guide can be searched or browsed from the Help menu, or you can see the same thing on our website, e.g.:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

If using the mouse to move one structure, what you did is exactly correct: inactivate the other structure.   The mouse should continue to work exactly the same for the movable structure as when everything was movable (both rotation and translation).   The default control for XY-translation is middle mouse button, if you have one.  For touchpad or mouse with fewer buttons, see here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html>

However, more often one doesn't use the tedious approach of trying to do it by hand, and instead uses one of the other superposition methods.  The easiest is usually MatchMaker (in the menu under Tools? Structure Comparison), so I would try that first.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>

To help you become more familiar with Chimera, there are several tutorials in the User's Guide (again also available from Help menu), ranging from "getting started" to more advanced.
<http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html>

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




From emarquez at ualberta.ca  Tue Jan 28 10:07:42 2014
From: emarquez at ualberta.ca (Elsa Marquez)
Date: Tue, 28 Jan 2014 11:07:42 -0700
Subject: [Chimera-users] adding GalNac moiety on Threonine residue
Message-ID: <CALzMobi+rsi+muwCXYuiTY=eX=v8v_BS84Mej0xTL40n+zgnSA@mail.gmail.com>

Hi there!
Do you guys know if I can add or somehow draw a carbohydrate moiety such as
GalNac to a single Threonine in a protein complex?
Thanks!
Elsa Marquez
University of Alberta
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From meng at cgl.ucsf.edu  Tue Jan 28 10:20:54 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 28 Jan 2014 10:20:54 -0800
Subject: [Chimera-users] Surface Transparency Command Issues
In-Reply-To: <BAY178-W43AB652C0178D81135C6F6E0AD0@phx.gbl>
References: <BAY178-W43AB652C0178D81135C6F6E0AD0@phx.gbl>
Message-ID: <CDFD6858-9169-4760-B0CF-0B89821B3AF2@cgl.ucsf.edu>

Hi Josh,
I really can't tell from that description.  If you can provide a series of commands that demonstrates the problem (or a session at the point when you try the command + the exact command you then tried), you could use Help? Report a Bug and put that in the description field and/or attach the session file.  Be sure to include your email address if you want a response. 

The only vague idea I had is that maybe there are multiple transparent layers but have single-layer transparency turned on, which would only show the topmost transparent layer (and not any additional transparent things below it)? but it doesn't make any sense to me that the Actions? Surface menu would work (or did you mean to say that it didn't work??) and the command wouldn't.  Single-layer vs. multi-layer transparency can be toggled with the command "set singleLayer" / "~set singleLayer" (or in the Effects tool), but again, I'm skeptical that that is the issue.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#singlelayer>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#transparency>

Thanks,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 27, 2014, at 11:32 PM, Joshua Carter <carter_jjc at hotmail.com> wrote:

> Hello,
> 
> I'm having trouble getting the surface transparency command to work correctly.  I'm currently making a movie about the formation of a protein complex and I want the subunits to be shown as ribbons while they dock and then after they dock the electrostatic surface to appear.  I have the script written and the surface generated but when I use either the surftransp or transparency command nothing happens.  The command is correct, if I use it to change the transparency of a ribbon or atom it does so, but if I try to make the surface appear after docking nothing changes.  In addition, if I go to the Actions menu and change the surface transparency from there it also works.
> 
> If you could help me figure out why the command won't work that would be extremely helpful.
> 
> Thanks,
> Josh




From htm211 at nyu.edu  Tue Jan 28 10:29:45 2014
From: htm211 at nyu.edu (Haresh Tukaram More)
Date: Tue, 28 Jan 2014 13:29:45 -0500
Subject: [Chimera-users] Need help in Coulombic surface coloring
In-Reply-To: <F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
	<CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
	<F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>
Message-ID: <CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>

HI Elaine,

I tried to do that, but not able to add charges manually. I have attached a
PDB filer here with TFLE mutations. Can you please see if you can add
charges on it. I am unable to give charge to TFLE as all the time the
process stop at antechamber.exe and abruptly closes the chimera.

Thanks & Regards,
Haresh


On Tue, Jan 28, 2014 at 12:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Haresh,
> There is another issue you may wish to consider:  Add Charge will require
> adding hydrogens first, but then the molecular surface will be more
> "craggy" due to the additional small atoms. Here are instructions if you
> want to show the Coulombic ESP coloring on the less rugged surface
> calculated without hydrogens (as is usually done; radii automatically
> adjust to compensate):
>
> After adding hydrogens and charges:
> (1) when you use the Coulombic Surface Coloring tool, turn on the option
> to "Compute grid..."  (in my test just now I took the defaults for the other
> grid options)
>
> (2) delete the hydrogens, e.g. command: del H
>
> (3) use the "Surface Color" dialog that automatically appeared when you
> created the grid to color the main surface by electrostatic potential using
> the potential file (grid) you just created.  If you don't see that dialog,
> you can raise it using menu: Tools... Surface/Binding Analysis... Electrostatic
> Surface Coloring. The default name of that grid is Coulombic ESP.  (Do not
> use the Coulombic Surface Coloring dialog for coloring!  After the
> hydrogens with many positive charges have been deleted, mostly negative
> charges will be left, and you will get an incorrect very red surface using
> the Coulombic Surface Coloring dialog.)
>
> Normally the protein wouldn't have strange residues that require a
> separate charge calculation, and this circuitous process wouldn't be
> required.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Jan 27, 2014, at 6:56 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
>
> > Thanks a lot Elaine. I will try to work on it now and see if I can get
> any results.
> >
> > Regards,
> > Haresh
> >
> >
> > On Mon, Jan 27, 2014 at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Haresh,
> > The Reply Log message (see the bottom part of what you sent) says there
> was a problem calculating the charges of your mutated residues and that you
> should try running Add Charge first, so that's what I would recommend.  Add
> Charge is in the menu under Tools.. Structure Editing, or can be run with
> command "addcharge".  It has two options for calculating the charges of
> nonstandard residues: AM1-BCC or Gasteiger.  Since the message shows there
> was a problem calculating using the AM1-BCC method on your mutated
> residues, I would try the Gasteiger method instead.
> >
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html
> >
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> >
> > Then, after you run Add Charge successfully, you can run Coulombic
> again.  It will automatically detect that the charges have already been
> calculated, and use those charges for calculating the ESP and coloring the
> surface.
> >
> > Actually I tried calculating charges for a single 5,5,5-trifluoroleucine
> residue by itself (in Chimera, can use "open pubchem:259832" to fetch it by
> PubChem CID)
> > <
> http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs>
> > ...and both methods, AM1-BCC and Gasteiger, worked fine; however maybe
> the calculation is more difficult in your structure where it sounds like
> the two mutated residues are treated together.
> >
> > I hope this helps,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > On Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> >
> > > Hi,
> > > I tried to get the Coulombic surface coloring for one of the protein
> that I modified by removing certain residue at the C-termini and then
> mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine
> using Swisssidechin option. I am getting this error which I am not able to
> understand.
> > >
> > > Disabled GPU programs because a graphics driver bug
> > >   was encountered while compiling a vertex shader.
> > >
> > > #0, chain A: COMP
> > > #0, chain B: COMP
> > > #0, chain C: COMP
> > > #0, chain D: COMP
> > > #0, chain E: COMP
> > > C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
> > > MSMSLIB 1.3 started on Local PC
> > > Copyright M.F. Sanner (March 2000)
> > > Compilation flags
> > >
> > > Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2
> > >   22 connected surface components
> > >   Total solvent excluded surface area = 10393.6
> > >     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059,
> 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549,
> 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319,
> 26.9429
> > >   Total solvent accessible surface area = 10372
> > >     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165,
> 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737,
> 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394,
> 0.0674059, 0.0311705
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain A;
> guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain B;
> guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain C;
> guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain D;
> guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain E;
> guessing terminii instead
> > > Chain-initial residues that are actual N terminii:
> #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B,
> #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D,
> #-2147483648.-2147483648 MET 27.E
> > > Chain-initial residues that are not actual N terminii:
> > > Chain-final residues that are actual C terminii:
> #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B,
> #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D,
> #-2147483648.-2147483648 TFLE 67.E
> > > Chain-final residues that are not actual C terminii:
> > > 424 hydrogen bonds
> > > Hydrogens added
> > > Charge model: AMBER ff12SB
> > > Assigning partial charges to residue TFLE+TFLE (net charge +0) with
> am1-bcc method
> > > Running ANTECHAMBER command: C:/Program Files/Chimera
> 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2
> -c bcc -nc 0 -j 5 -s 2
> > > (TFLE+TFLE)
> > >
> > > Cannot automatically determine charges for residue TFLE+TFLE;
> > > Run AddCharge tool manually to add charges and then rerun ESP
> > >
> > > Can someone please tell me a step by step procedure to make this work.
> > > Thanks & Regards,
> > > Haresh
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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From meng at cgl.ucsf.edu  Tue Jan 28 10:41:30 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 28 Jan 2014 10:41:30 -0800
Subject: [Chimera-users] adding GalNac moiety on Threonine residue
In-Reply-To: <CALzMobi+rsi+muwCXYuiTY=eX=v8v_BS84Mej0xTL40n+zgnSA@mail.gmail.com>
References: <CALzMobi+rsi+muwCXYuiTY=eX=v8v_BS84Mej0xTL40n+zgnSA@mail.gmail.com>
Message-ID: <AA4FB6F0-C1F1-4814-B007-91C5D4171C6F@cgl.ucsf.edu>

Hi Elsa,
(A) One way would be to open some additional PDB entry that has a GalNac in it, deleting all the other atoms in that structure except for one GalNac, and then using the Join Models section of Build Structure (in menu under Tools? Structure Editing) to stick the GalNac onto the threonine in your protein complex structure.  You may need to add hydrogens first. Join Models also requires you to enter the desired attachment bond length and angles, which you could determine by measuring them in some example glycosylated structure.  You could open yet another glycosylated structure in the same Chimera and temporarily hide the other stuff while you do the measurements, then close that example structure and unhide the others, or just start another instance of Chimera to open and measure the example structure.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#structuremeas>

(B) Another way would be to again open an additional PDB entry that has a GalNac glycosylation, deleting all but the GalNac and the attached residue, superimposing that on the threonine in your structure, deleting the attached residue, and then merging the two structures.  The tricky part might be superimposing the structures adequately, and approaches for that could include the "match" command and specifying exactly which atoms to fit and/or manual positioning.  These methods are mentioned in the superposition page:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
Merging can be done with "copy/combine" in the Model Panel (under Favorites in the menu) or the command "combine":
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
Then you would still need to add the bond with the "bond" command or the Adjust Bonds section of Build Structure (in menu under Tools? Structure Editing).

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

On Jan 28, 2014, at 10:07 AM, Elsa Marquez <emarquez at ualberta.ca> wrote:

> Hi there! 
> Do you guys know if I can add or somehow draw a carbohydrate moiety such as GalNac to a single Threonine in a protein complex? 
> Thanks! 
> Elsa Marquez 
> University of Alberta




From meng at cgl.ucsf.edu  Tue Jan 28 10:44:25 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 28 Jan 2014 10:44:25 -0800
Subject: [Chimera-users] Need help in Coulombic surface coloring
In-Reply-To: <CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
	<CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
	<F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>
	<CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>
Message-ID: <6A125701-E7A2-451F-A765-CC079D07E12C@cgl.ucsf.edu>

Hi Haresh,
If you use "Gasteiger" instead of "AM1-BCC" in the Add Charge dialog as suggested in my first reply, it works (at least for me, but I'm pretty sure it will for you too)!
Elaine

On Jan 28, 2014, at 10:29 AM, Haresh Tukaram More <htm211 at nyu.edu> wrote:

> HI Elaine,
> 
> I tried to do that, but not able to add charges manually. I have attached a PDB filer here with TFLE mutations. Can you please see if you can add charges on it. I am unable to give charge to TFLE as all the time the process stop at antechamber.exe and abruptly closes the chimera.
> 
> Thanks & Regards,
> Haresh
> 
> 
> On Tue, Jan 28, 2014 at 12:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Haresh,
> There is another issue you may wish to consider:  Add Charge will require adding hydrogens first, but then the molecular surface will be more "craggy" due to the additional small atoms. Here are instructions if you want to show the Coulombic ESP coloring on the less rugged surface calculated without hydrogens (as is usually done; radii automatically adjust to compensate):
> 
> After adding hydrogens and charges:
> (1) when you use the Coulombic Surface Coloring tool, turn on the option to "Compute grid?"  (in my test just now I took the defaults for the other grid options)
> 
> (2) delete the hydrogens, e.g. command: del H
> 
> (3) use the "Surface Color" dialog that automatically appeared when you created the grid to color the main surface by electrostatic potential using the potential file (grid) you just created.  If you don't see that dialog, you can raise it using menu: Tools? Surface/Binding Analysis? Electrostatic Surface Coloring. The default name of that grid is Coulombic ESP.  (Do not use the Coulombic Surface Coloring dialog for coloring!  After the hydrogens with many positive charges have been deleted, mostly negative charges will be left, and you will get an incorrect very red surface using the Coulombic Surface Coloring dialog.)
> 
> Normally the protein wouldn't have strange residues that require a separate charge calculation, and this circuitous process wouldn't be required.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Jan 27, 2014, at 6:56 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> 
> > Thanks a lot Elaine. I will try to work on it now and see if I can get any results.
> >
> > Regards,
> > Haresh
> >
> >
> > On Mon, Jan 27, 2014 at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Haresh,
> > The Reply Log message (see the bottom part of what you sent) says there was a problem calculating the charges of your mutated residues and that you should try running Add Charge first, so that's what I would recommend.  Add Charge is in the menu under Tools.. Structure Editing, or can be run with command "addcharge".  It has two options for calculating the charges of nonstandard residues: AM1-BCC or Gasteiger.  Since the message shows there was a problem calculating using the AM1-BCC method on your mutated residues, I would try the Gasteiger method instead.
> >
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> >
> > Then, after you run Add Charge successfully, you can run Coulombic again.  It will automatically detect that the charges have already been calculated, and use those charges for calculating the ESP and coloring the surface.
> >
> > Actually I tried calculating charges for a single 5,5,5-trifluoroleucine residue by itself (in Chimera, can use "open pubchem:259832" to fetch it by PubChem CID)
> > <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs>
> > ...and both methods, AM1-BCC and Gasteiger, worked fine; however maybe the calculation is more difficult in your structure where it sounds like the two mutated residues are treated together.
> >
> > I hope this helps,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > On Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> >
> > > Hi,
> > > I tried to get the Coulombic surface coloring for one of the protein that I modified by removing certain residue at the C-termini and then mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine using Swisssidechin option. I am getting this error which I am not able to understand.
> > >
> > > Disabled GPU programs because a graphics driver bug
> > >   was encountered while compiling a vertex shader.
> > >
> > > #0, chain A: COMP
> > > #0, chain B: COMP
> > > #0, chain C: COMP
> > > #0, chain D: COMP
> > > #0, chain E: COMP
> > > C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
> > > MSMSLIB 1.3 started on Local PC
> > > Copyright M.F. Sanner (March 2000)
> > > Compilation flags
> > >
> > > Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2
> > >   22 connected surface components
> > >   Total solvent excluded surface area = 10393.6
> > >     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059, 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549, 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319, 26.9429
> > >   Total solvent accessible surface area = 10372
> > >     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165, 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737, 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394, 0.0674059, 0.0311705
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain A; guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain B; guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain C; guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain D; guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain E; guessing terminii instead
> > > Chain-initial residues that are actual N terminii: #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B, #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D, #-2147483648.-2147483648 MET 27.E
> > > Chain-initial residues that are not actual N terminii:
> > > Chain-final residues that are actual C terminii: #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B, #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D, #-2147483648.-2147483648 TFLE 67.E
> > > Chain-final residues that are not actual C terminii:
> > > 424 hydrogen bonds
> > > Hydrogens added
> > > Charge model: AMBER ff12SB
> > > Assigning partial charges to residue TFLE+TFLE (net charge +0) with am1-bcc method
> > > Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2
> > > (TFLE+TFLE)
> > >
> > > Cannot automatically determine charges for residue TFLE+TFLE;
> > > Run AddCharge tool manually to add charges and then rerun ESP
> > >
> > > Can someone please tell me a step by step procedure to make this work.
> > > Thanks & Regards,
> > > Haresh
> >
> >



From pett at cgl.ucsf.edu  Tue Jan 28 11:26:20 2014
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 28 Jan 2014 11:26:20 -0800
Subject: [Chimera-users] Need help in Coulombic surface coloring
In-Reply-To: <CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
	<CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
	<F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>
	<CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>
Message-ID: <B1A26B95-55BA-470C-8DF0-0921DF960FFD@cgl.ucsf.edu>

Hi Haresh,
	I was able to add charges / ESP color the surface for your structure without any problem on both my Mac and a Windows machine.  I will be sending you a session file in a separate mail with the colored surface.
	On a Windows machine, while the charge calculation is ongoing a second window pops up (with 'antechamber.exe' at the end of its title).  Do not close that window.  Closing that window will cause the charge calculation to stop/fail.  The calculation takes several minutes, so be patient.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 28, 2014, at 10:29 AM, Haresh Tukaram More <htm211 at nyu.edu> wrote:

> HI Elaine,
> 
> I tried to do that, but not able to add charges manually. I have attached a PDB filer here with TFLE mutations. Can you please see if you can add charges on it. I am unable to give charge to TFLE as all the time the process stop at antechamber.exe and abruptly closes the chimera.
> 
> Thanks & Regards,
> Haresh
> 
> 
> On Tue, Jan 28, 2014 at 12:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Haresh,
> There is another issue you may wish to consider:  Add Charge will require adding hydrogens first, but then the molecular surface will be more "craggy" due to the additional small atoms. Here are instructions if you want to show the Coulombic ESP coloring on the less rugged surface calculated without hydrogens (as is usually done; radii automatically adjust to compensate):
> 
> After adding hydrogens and charges:
> (1) when you use the Coulombic Surface Coloring tool, turn on the option to "Compute grid?"  (in my test just now I took the defaults for the other grid options)
> 
> (2) delete the hydrogens, e.g. command: del H
> 
> (3) use the "Surface Color" dialog that automatically appeared when you created the grid to color the main surface by electrostatic potential using the potential file (grid) you just created.  If you don't see that dialog, you can raise it using menu: Tools? Surface/Binding Analysis? Electrostatic Surface Coloring. The default name of that grid is Coulombic ESP.  (Do not use the Coulombic Surface Coloring dialog for coloring!  After the hydrogens with many positive charges have been deleted, mostly negative charges will be left, and you will get an incorrect very red surface using the Coulombic Surface Coloring dialog.)
> 
> Normally the protein wouldn't have strange residues that require a separate charge calculation, and this circuitous process wouldn't be required.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Jan 27, 2014, at 6:56 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> 
> > Thanks a lot Elaine. I will try to work on it now and see if I can get any results.
> >
> > Regards,
> > Haresh
> >
> >
> > On Mon, Jan 27, 2014 at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Haresh,
> > The Reply Log message (see the bottom part of what you sent) says there was a problem calculating the charges of your mutated residues and that you should try running Add Charge first, so that's what I would recommend.  Add Charge is in the menu under Tools.. Structure Editing, or can be run with command "addcharge".  It has two options for calculating the charges of nonstandard residues: AM1-BCC or Gasteiger.  Since the message shows there was a problem calculating using the AM1-BCC method on your mutated residues, I would try the Gasteiger method instead.
> >
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> >
> > Then, after you run Add Charge successfully, you can run Coulombic again.  It will automatically detect that the charges have already been calculated, and use those charges for calculating the ESP and coloring the surface.
> >
> > Actually I tried calculating charges for a single 5,5,5-trifluoroleucine residue by itself (in Chimera, can use "open pubchem:259832" to fetch it by PubChem CID)
> > <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs>
> > ...and both methods, AM1-BCC and Gasteiger, worked fine; however maybe the calculation is more difficult in your structure where it sounds like the two mutated residues are treated together.
> >
> > I hope this helps,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > On Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> >
> > > Hi,
> > > I tried to get the Coulombic surface coloring for one of the protein that I modified by removing certain residue at the C-termini and then mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine using Swisssidechin option. I am getting this error which I am not able to understand.
> > >
> > > Disabled GPU programs because a graphics driver bug
> > >   was encountered while compiling a vertex shader.
> > >
> > > #0, chain A: COMP
> > > #0, chain B: COMP
> > > #0, chain C: COMP
> > > #0, chain D: COMP
> > > #0, chain E: COMP
> > > C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
> > > MSMSLIB 1.3 started on Local PC
> > > Copyright M.F. Sanner (March 2000)
> > > Compilation flags
> > >
> > > Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2
> > >   22 connected surface components
> > >   Total solvent excluded surface area = 10393.6
> > >     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059, 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549, 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319, 26.9429
> > >   Total solvent accessible surface area = 10372
> > >     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165, 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737, 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394, 0.0674059, 0.0311705
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain A; guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain B; guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain C; guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain D; guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain E; guessing terminii instead
> > > Chain-initial residues that are actual N terminii: #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B, #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D, #-2147483648.-2147483648 MET 27.E
> > > Chain-initial residues that are not actual N terminii:
> > > Chain-final residues that are actual C terminii: #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B, #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D, #-2147483648.-2147483648 TFLE 67.E
> > > Chain-final residues that are not actual C terminii:
> > > 424 hydrogen bonds
> > > Hydrogens added
> > > Charge model: AMBER ff12SB
> > > Assigning partial charges to residue TFLE+TFLE (net charge +0) with am1-bcc method
> > > Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2
> > > (TFLE+TFLE)
> > >
> > > Cannot automatically determine charges for residue TFLE+TFLE;
> > > Run AddCharge tool manually to add charges and then rerun ESP
> > >
> > > Can someone please tell me a step by step procedure to make this work.
> > > Thanks & Regards,
> > > Haresh
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> <TFLE protein.pdb>_______________________________________________
> Chimera-users mailing list
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From htm211 at nyu.edu  Tue Jan 28 11:37:35 2014
From: htm211 at nyu.edu (Haresh Tukaram More)
Date: Tue, 28 Jan 2014 14:37:35 -0500
Subject: [Chimera-users] Need help in Coulombic surface coloring
In-Reply-To: <6A125701-E7A2-451F-A765-CC079D07E12C@cgl.ucsf.edu>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
	<CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
	<F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>
	<CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>
	<6A125701-E7A2-451F-A765-CC079D07E12C@cgl.ucsf.edu>
Message-ID: <CACWQECRSRQOVGtp0jx_74G_Fwoe-wNrZ39XZox5m3A6m2AjHMg@mail.gmail.com>

Hi Elaine,

Finally!! it worked. In the reply log it shows following

Charges for residue TFLE determined
Assigning partial charges to residue CL (net charge -1) with gasteiger
method
Total charge for #0: 9.000

So i should use +9 charge for TFLE and TFLE+TFLE? I did that and now able
to get the electrostatic surface potential. The way I did is as follows

1. AddH
2. Add charge
3. Select surface of protein
4. Select coulombic surface coloring command and selected the grid option.
5. Next the surface color box opened and I selected color option.
6. Once it is done I removed hydrogen by del H

and I got the protein with electrostatic surface potential.

I hope now this is correct.

Regards,
Haresh


On Tue, Jan 28, 2014 at 1:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Haresh,
> If you use "Gasteiger" instead of "AM1-BCC" in the Add Charge dialog as
> suggested in my first reply, it works (at least for me, but I'm pretty sure
> it will for you too)!
> Elaine
>
> On Jan 28, 2014, at 10:29 AM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
>
> > HI Elaine,
> >
> > I tried to do that, but not able to add charges manually. I have
> attached a PDB filer here with TFLE mutations. Can you please see if you
> can add charges on it. I am unable to give charge to TFLE as all the time
> the process stop at antechamber.exe and abruptly closes the chimera.
> >
> > Thanks & Regards,
> > Haresh
> >
> >
> > On Tue, Jan 28, 2014 at 12:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Haresh,
> > There is another issue you may wish to consider:  Add Charge will
> require adding hydrogens first, but then the molecular surface will be more
> "craggy" due to the additional small atoms. Here are instructions if you
> want to show the Coulombic ESP coloring on the less rugged surface
> calculated without hydrogens (as is usually done; radii automatically
> adjust to compensate):
> >
> > After adding hydrogens and charges:
> > (1) when you use the Coulombic Surface Coloring tool, turn on the option
> to "Compute grid..."  (in my test just now I took the defaults for the other
> grid options)
> >
> > (2) delete the hydrogens, e.g. command: del H
> >
> > (3) use the "Surface Color" dialog that automatically appeared when you
> created the grid to color the main surface by electrostatic potential using
> the potential file (grid) you just created.  If you don't see that dialog,
> you can raise it using menu: Tools... Surface/Binding Analysis... Electrostatic
> Surface Coloring. The default name of that grid is Coulombic ESP.  (Do not
> use the Coulombic Surface Coloring dialog for coloring!  After the
> hydrogens with many positive charges have been deleted, mostly negative
> charges will be left, and you will get an incorrect very red surface using
> the Coulombic Surface Coloring dialog.)
> >
> > Normally the protein wouldn't have strange residues that require a
> separate charge calculation, and this circuitous process wouldn't be
> required.
> > Best,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > On Jan 27, 2014, at 6:56 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> >
> > > Thanks a lot Elaine. I will try to work on it now and see if I can get
> any results.
> > >
> > > Regards,
> > > Haresh
> > >
> > >
> > > On Mon, Jan 27, 2014 at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu>
> wrote:
> > > Hi Haresh,
> > > The Reply Log message (see the bottom part of what you sent) says
> there was a problem calculating the charges of your mutated residues and
> that you should try running Add Charge first, so that's what I would
> recommend.  Add Charge is in the menu under Tools.. Structure Editing, or
> can be run with command "addcharge".  It has two options for calculating
> the charges of nonstandard residues: AM1-BCC or Gasteiger.  Since the
> message shows there was a problem calculating using the AM1-BCC method on
> your mutated residues, I would try the Gasteiger method instead.
> > >
> > > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html
> >
> > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html
> >
> > >
> > > Then, after you run Add Charge successfully, you can run Coulombic
> again.  It will automatically detect that the charges have already been
> calculated, and use those charges for calculating the ESP and coloring the
> surface.
> > >
> > > Actually I tried calculating charges for a single
> 5,5,5-trifluoroleucine residue by itself (in Chimera, can use "open
> pubchem:259832" to fetch it by PubChem CID)
> > > <
> http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs>
> > > ...and both methods, AM1-BCC and Gasteiger, worked fine; however maybe
> the calculation is more difficult in your structure where it sounds like
> the two mutated residues are treated together.
> > >
> > > I hope this helps,
> > > Elaine
> > > ----------
> > > Elaine C. Meng, Ph.D.
> > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > > Department of Pharmaceutical Chemistry
> > > University of California, San Francisco
> > >
> > > On Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu>
> wrote:
> > >
> > > > Hi,
> > > > I tried to get the Coulombic surface coloring for one of the protein
> that I modified by removing certain residue at the C-termini and then
> mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine
> using Swisssidechin option. I am getting this error which I am not able to
> understand.
> > > >
> > > > Disabled GPU programs because a graphics driver bug
> > > >   was encountered while compiling a vertex shader.
> > > >
> > > > #0, chain A: COMP
> > > > #0, chain B: COMP
> > > > #0, chain C: COMP
> > > > #0, chain D: COMP
> > > > #0, chain E: COMP
> > > > C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
> > > > MSMSLIB 1.3 started on Local PC
> > > > Copyright M.F. Sanner (March 2000)
> > > > Compilation flags
> > > >
> > > > Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density
> 2
> > > >   22 connected surface components
> > > >   Total solvent excluded surface area = 10393.6
> > > >     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059,
> 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549,
> 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319,
> 26.9429
> > > >   Total solvent accessible surface area = 10372
> > > >     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165,
> 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737,
> 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394,
> 0.0674059, 0.0311705
> > > > No SEQRES records for combination (#-2147483648.-2147483648) chain
> A; guessing terminii instead
> > > > No SEQRES records for combination (#-2147483648.-2147483648) chain
> B; guessing terminii instead
> > > > No SEQRES records for combination (#-2147483648.-2147483648) chain
> C; guessing terminii instead
> > > > No SEQRES records for combination (#-2147483648.-2147483648) chain
> D; guessing terminii instead
> > > > No SEQRES records for combination (#-2147483648.-2147483648) chain
> E; guessing terminii instead
> > > > Chain-initial residues that are actual N terminii:
> #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B,
> #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D,
> #-2147483648.-2147483648 MET 27.E
> > > > Chain-initial residues that are not actual N terminii:
> > > > Chain-final residues that are actual C terminii:
> #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B,
> #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D,
> #-2147483648.-2147483648 TFLE 67.E
> > > > Chain-final residues that are not actual C terminii:
> > > > 424 hydrogen bonds
> > > > Hydrogens added
> > > > Charge model: AMBER ff12SB
> > > > Assigning partial charges to residue TFLE+TFLE (net charge +0) with
> am1-bcc method
> > > > Running ANTECHAMBER command: C:/Program Files/Chimera
> 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2
> -c bcc -nc 0 -j 5 -s 2
> > > > (TFLE+TFLE)
> > > >
> > > > Cannot automatically determine charges for residue TFLE+TFLE;
> > > > Run AddCharge tool manually to add charges and then rerun ESP
> > > >
> > > > Can someone please tell me a step by step procedure to make this
> work.
> > > > Thanks & Regards,
> > > > Haresh
> > >
> > >
>
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From meng at cgl.ucsf.edu  Tue Jan 28 11:46:59 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 28 Jan 2014 11:46:59 -0800
Subject: [Chimera-users] Need help in Coulombic surface coloring
In-Reply-To: <CACWQECRSRQOVGtp0jx_74G_Fwoe-wNrZ39XZox5m3A6m2AjHMg@mail.gmail.com>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
	<CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
	<F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>
	<CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>
	<6A125701-E7A2-451F-A765-CC079D07E12C@cgl.ucsf.edu>
	<CACWQECRSRQOVGtp0jx_74G_Fwoe-wNrZ39XZox5m3A6m2AjHMg@mail.gmail.com>
Message-ID: <00646B58-7EF6-489E-B4F3-CE36A8491494@cgl.ucsf.edu>

No, don't use 9 for the charge of TFLE!  Total charge is including the whole protein.  Presumably TFLE  charge is 0, i.e., it is not a charged sidechain.

Also you should delete hydrogens and then use Surface Color,  as in my previous instructions.
Elaine

On Jan 28, 2014, at 11:37 AM, Haresh Tukaram More <htm211 at nyu.edu> wrote:

> Hi Elaine,
> 
> Finally!! it worked. In the reply log it shows following
> 
> Charges for residue TFLE determined
> Assigning partial charges to residue CL (net charge -1) with gasteiger method
> Total charge for #0: 9.000
> 
> So i should use +9 charge for TFLE and TFLE+TFLE? I did that and now able to get the electrostatic surface potential. The way I did is as follows
> 
> 1. AddH
> 2. Add charge
> 3. Select surface of protein
> 4. Select coulombic surface coloring command and selected the grid option.
> 5. Next the surface color box opened and I selected color option.
> 6. Once it is done I removed hydrogen by del H
> 
> and I got the protein with electrostatic surface potential.
> 
> I hope now this is correct.
> 
> Regards,
> Haresh
> 
> 
> On Tue, Jan 28, 2014 at 1:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Haresh,
> If you use "Gasteiger" instead of "AM1-BCC" in the Add Charge dialog as suggested in my first reply, it works (at least for me, but I'm pretty sure it will for you too)!
> Elaine
> 
> On Jan 28, 2014, at 10:29 AM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> 
> > HI Elaine,
> >
> > I tried to do that, but not able to add charges manually. I have attached a PDB filer here with TFLE mutations. Can you please see if you can add charges on it. I am unable to give charge to TFLE as all the time the process stop at antechamber.exe and abruptly closes the chimera.
> >
> > Thanks & Regards,
> > Haresh
> >
> >
> > On Tue, Jan 28, 2014 at 12:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Haresh,
> > There is another issue you may wish to consider:  Add Charge will require adding hydrogens first, but then the molecular surface will be more "craggy" due to the additional small atoms. Here are instructions if you want to show the Coulombic ESP coloring on the less rugged surface calculated without hydrogens (as is usually done; radii automatically adjust to compensate):
> >
> > After adding hydrogens and charges:
> > (1) when you use the Coulombic Surface Coloring tool, turn on the option to "Compute grid?"  (in my test just now I took the defaults for the other grid options)
> >
> > (2) delete the hydrogens, e.g. command: del H
> >
> > (3) use the "Surface Color" dialog that automatically appeared when you created the grid to color the main surface by electrostatic potential using the potential file (grid) you just created.  If you don't see that dialog, you can raise it using menu: Tools? Surface/Binding Analysis? Electrostatic Surface Coloring. The default name of that grid is Coulombic ESP.  (Do not use the Coulombic Surface Coloring dialog for coloring!  After the hydrogens with many positive charges have been deleted, mostly negative charges will be left, and you will get an incorrect very red surface using the Coulombic Surface Coloring dialog.)
> >
> > Normally the protein wouldn't have strange residues that require a separate charge calculation, and this circuitous process wouldn't be required.
> > Best,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > On Jan 27, 2014, at 6:56 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> >
> > > Thanks a lot Elaine. I will try to work on it now and see if I can get any results.
> > >
> > > Regards,
> > > Haresh
> > >
> > >
> > > On Mon, Jan 27, 2014 at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > > Hi Haresh,
> > > The Reply Log message (see the bottom part of what you sent) says there was a problem calculating the charges of your mutated residues and that you should try running Add Charge first, so that's what I would recommend.  Add Charge is in the menu under Tools.. Structure Editing, or can be run with command "addcharge".  It has two options for calculating the charges of nonstandard residues: AM1-BCC or Gasteiger.  Since the message shows there was a problem calculating using the AM1-BCC method on your mutated residues, I would try the Gasteiger method instead.
> > >
> > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>
> > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> > >
> > > Then, after you run Add Charge successfully, you can run Coulombic again.  It will automatically detect that the charges have already been calculated, and use those charges for calculating the ESP and coloring the surface.
> > >
> > > Actually I tried calculating charges for a single 5,5,5-trifluoroleucine residue by itself (in Chimera, can use "open pubchem:259832" to fetch it by PubChem CID)
> > > <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs>
> > > ...and both methods, AM1-BCC and Gasteiger, worked fine; however maybe the calculation is more difficult in your structure where it sounds like the two mutated residues are treated together.
> > >
> > > I hope this helps,
> > > Elaine
> > > ----------
> > > Elaine C. Meng, Ph.D.
> > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > > Department of Pharmaceutical Chemistry
> > > University of California, San Francisco
> > >
> > > On Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> > >
> > > > Hi,
> > > > I tried to get the Coulombic surface coloring for one of the protein that I modified by removing certain residue at the C-termini and then mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine using Swisssidechin option. I am getting this error which I am not able to understand.
> > > >
> > > > Disabled GPU programs because a graphics driver bug
> > > >   was encountered while compiling a vertex shader.
> > > >
> > > > #0, chain A: COMP
> > > > #0, chain B: COMP
> > > > #0, chain C: COMP
> > > > #0, chain D: COMP
> > > > #0, chain E: COMP
> > > > C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
> > > > MSMSLIB 1.3 started on Local PC
> > > > Copyright M.F. Sanner (March 2000)
> > > > Compilation flags
> > > >
> > > > Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2
> > > >   22 connected surface components
> > > >   Total solvent excluded surface area = 10393.6
> > > >     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059, 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549, 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319, 26.9429
> > > >   Total solvent accessible surface area = 10372
> > > >     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165, 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737, 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394, 0.0674059, 0.0311705
> > > > No SEQRES records for combination (#-2147483648.-2147483648) chain A; guessing terminii instead
> > > > No SEQRES records for combination (#-2147483648.-2147483648) chain B; guessing terminii instead
> > > > No SEQRES records for combination (#-2147483648.-2147483648) chain C; guessing terminii instead
> > > > No SEQRES records for combination (#-2147483648.-2147483648) chain D; guessing terminii instead
> > > > No SEQRES records for combination (#-2147483648.-2147483648) chain E; guessing terminii instead
> > > > Chain-initial residues that are actual N terminii: #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B, #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D, #-2147483648.-2147483648 MET 27.E
> > > > Chain-initial residues that are not actual N terminii:
> > > > Chain-final residues that are actual C terminii: #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B, #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D, #-2147483648.-2147483648 TFLE 67.E
> > > > Chain-final residues that are not actual C terminii:
> > > > 424 hydrogen bonds
> > > > Hydrogens added
> > > > Charge model: AMBER ff12SB
> > > > Assigning partial charges to residue TFLE+TFLE (net charge +0) with am1-bcc method
> > > > Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2
> > > > (TFLE+TFLE)
> > > >
> > > > Cannot automatically determine charges for residue TFLE+TFLE;
> > > > Run AddCharge tool manually to add charges and then rerun ESP
> > > >
> > > > Can someone please tell me a step by step procedure to make this work.
> > > > Thanks & Regards,
> > > > Haresh
> > >
> > >
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From htm211 at nyu.edu  Tue Jan 28 14:43:37 2014
From: htm211 at nyu.edu (Haresh Tukaram More)
Date: Tue, 28 Jan 2014 17:43:37 -0500
Subject: [Chimera-users] Need help in Coulombic surface coloring
In-Reply-To: <00646B58-7EF6-489E-B4F3-CE36A8491494@cgl.ucsf.edu>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
	<CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
	<F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>
	<CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>
	<6A125701-E7A2-451F-A765-CC079D07E12C@cgl.ucsf.edu>
	<CACWQECRSRQOVGtp0jx_74G_Fwoe-wNrZ39XZox5m3A6m2AjHMg@mail.gmail.com>
	<00646B58-7EF6-489E-B4F3-CE36A8491494@cgl.ucsf.edu>
Message-ID: <CACWQECSCFqTaeuCoYNw8w9MFkyA2OLs0Y0MPBwVqSyvA-ZjnYw@mail.gmail.com>

Hi Elaine,

Yes I did exactly the way you explained and it is working now.

I have another question. I need to add some 14 residues on N-termius of the
protein which I did using the addaa command. However, I am unable to
simulate its secondary structure using ksdssp. I am not sure how to run
this command in command line. Or am I doing something wrong in terms of
predicting the structures.

Can you please let me know what do I need to do in terms of getting the
structure of protein after addsing residues on N-terminus.

Thanks,
Haresh


On Tue, Jan 28, 2014 at 2:46 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> No, don't use 9 for the charge of TFLE!  Total charge is including the
> whole protein.  Presumably TFLE  charge is 0, i.e., it is not a charged
> sidechain.
>
> Also you should delete hydrogens and then use Surface Color,  as in my
> previous instructions.
> Elaine
>
> On Jan 28, 2014, at 11:37 AM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
>
> > Hi Elaine,
> >
> > Finally!! it worked. In the reply log it shows following
> >
> > Charges for residue TFLE determined
> > Assigning partial charges to residue CL (net charge -1) with gasteiger
> method
> > Total charge for #0: 9.000
> >
> > So i should use +9 charge for TFLE and TFLE+TFLE? I did that and now
> able to get the electrostatic surface potential. The way I did is as follows
> >
> > 1. AddH
> > 2. Add charge
> > 3. Select surface of protein
> > 4. Select coulombic surface coloring command and selected the grid
> option.
> > 5. Next the surface color box opened and I selected color option.
> > 6. Once it is done I removed hydrogen by del H
> >
> > and I got the protein with electrostatic surface potential.
> >
> > I hope now this is correct.
> >
> > Regards,
> > Haresh
> >
> >
> > On Tue, Jan 28, 2014 at 1:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Haresh,
> > If you use "Gasteiger" instead of "AM1-BCC" in the Add Charge dialog as
> suggested in my first reply, it works (at least for me, but I'm pretty sure
> it will for you too)!
> > Elaine
> >
> > On Jan 28, 2014, at 10:29 AM, Haresh Tukaram More <htm211 at nyu.edu>
> wrote:
> >
> > > HI Elaine,
> > >
> > > I tried to do that, but not able to add charges manually. I have
> attached a PDB filer here with TFLE mutations. Can you please see if you
> can add charges on it. I am unable to give charge to TFLE as all the time
> the process stop at antechamber.exe and abruptly closes the chimera.
> > >
> > > Thanks & Regards,
> > > Haresh
> > >
> > >
> > > On Tue, Jan 28, 2014 at 12:27 PM, Elaine Meng <meng at cgl.ucsf.edu>
> wrote:
> > > Hi Haresh,
> > > There is another issue you may wish to consider:  Add Charge will
> require adding hydrogens first, but then the molecular surface will be more
> "craggy" due to the additional small atoms. Here are instructions if you
> want to show the Coulombic ESP coloring on the less rugged surface
> calculated without hydrogens (as is usually done; radii automatically
> adjust to compensate):
> > >
> > > After adding hydrogens and charges:
> > > (1) when you use the Coulombic Surface Coloring tool, turn on the
> option to "Compute grid..."  (in my test just now I took the defaults for the
> other grid options)
> > >
> > > (2) delete the hydrogens, e.g. command: del H
> > >
> > > (3) use the "Surface Color" dialog that automatically appeared when
> you created the grid to color the main surface by electrostatic potential
> using the potential file (grid) you just created.  If you don't see that
> dialog, you can raise it using menu: Tools... Surface/Binding Analysis...
> Electrostatic Surface Coloring. The default name of that grid is Coulombic
> ESP.  (Do not use the Coulombic Surface Coloring dialog for coloring!
>  After the hydrogens with many positive charges have been deleted, mostly
> negative charges will be left, and you will get an incorrect very red
> surface using the Coulombic Surface Coloring dialog.)
> > >
> > > Normally the protein wouldn't have strange residues that require a
> separate charge calculation, and this circuitous process wouldn't be
> required.
> > > Best,
> > > Elaine
> > > ----------
> > > Elaine C. Meng, Ph.D.
> > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > > Department of Pharmaceutical Chemistry
> > > University of California, San Francisco
> > >
> > > On Jan 27, 2014, at 6:56 PM, Haresh Tukaram More <htm211 at nyu.edu>
> wrote:
> > >
> > > > Thanks a lot Elaine. I will try to work on it now and see if I can
> get any results.
> > > >
> > > > Regards,
> > > > Haresh
> > > >
> > > >
> > > > On Mon, Jan 27, 2014 at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu>
> wrote:
> > > > Hi Haresh,
> > > > The Reply Log message (see the bottom part of what you sent) says
> there was a problem calculating the charges of your mutated residues and
> that you should try running Add Charge first, so that's what I would
> recommend.  Add Charge is in the menu under Tools.. Structure Editing, or
> can be run with command "addcharge".  It has two options for calculating
> the charges of nonstandard residues: AM1-BCC or Gasteiger.  Since the
> message shows there was a problem calculating using the AM1-BCC method on
> your mutated residues, I would try the Gasteiger method instead.
> > > >
> > > > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html
> >
> > > > <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> > > >
> > > > Then, after you run Add Charge successfully, you can run Coulombic
> again.  It will automatically detect that the charges have already been
> calculated, and use those charges for calculating the ESP and coloring the
> surface.
> > > >
> > > > Actually I tried calculating charges for a single
> 5,5,5-trifluoroleucine residue by itself (in Chimera, can use "open
> pubchem:259832" to fetch it by PubChem CID)
> > > > <
> http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs>
> > > > ...and both methods, AM1-BCC and Gasteiger, worked fine; however
> maybe the calculation is more difficult in your structure where it sounds
> like the two mutated residues are treated together.
> > > >
> > > > I hope this helps,
> > > > Elaine
> > > > ----------
> > > > Elaine C. Meng, Ph.D.
> > > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > > > Department of Pharmaceutical Chemistry
> > > > University of California, San Francisco
> > > >
> > > > On Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu>
> wrote:
> > > >
> > > > > Hi,
> > > > > I tried to get the Coulombic surface coloring for one of the
> protein that I modified by removing certain residue at the C-termini and
> then mutated some residues to the non-natural amino acid
> 5,5,5-trifluoroleucine using Swisssidechin option. I am getting this error
> which I am not able to understand.
> > > > >
> > > > > Disabled GPU programs because a graphics driver bug
> > > > >   was encountered while compiling a vertex shader.
> > > > >
> > > > > #0, chain A: COMP
> > > > > #0, chain B: COMP
> > > > > #0, chain C: COMP
> > > > > #0, chain D: COMP
> > > > > #0, chain E: COMP
> > > > > C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
> > > > > MSMSLIB 1.3 started on Local PC
> > > > > Copyright M.F. Sanner (March 2000)
> > > > > Compilation flags
> > > > >
> > > > > Surface CC TFLE.pdb, category main, probe radius 1.4, vertex
> density 2
> > > > >   22 connected surface components
> > > > >   Total solvent excluded surface area = 10393.6
> > > > >     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059,
> 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549,
> 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319,
> 26.9429
> > > > >   Total solvent accessible surface area = 10372
> > > > >     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165,
> 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737,
> 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394,
> 0.0674059, 0.0311705
> > > > > No SEQRES records for combination (#-2147483648.-2147483648) chain
> A; guessing terminii instead
> > > > > No SEQRES records for combination (#-2147483648.-2147483648) chain
> B; guessing terminii instead
> > > > > No SEQRES records for combination (#-2147483648.-2147483648) chain
> C; guessing terminii instead
> > > > > No SEQRES records for combination (#-2147483648.-2147483648) chain
> D; guessing terminii instead
> > > > > No SEQRES records for combination (#-2147483648.-2147483648) chain
> E; guessing terminii instead
> > > > > Chain-initial residues that are actual N terminii:
> #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B,
> #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D,
> #-2147483648.-2147483648 MET 27.E
> > > > > Chain-initial residues that are not actual N terminii:
> > > > > Chain-final residues that are actual C terminii:
> #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B,
> #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D,
> #-2147483648.-2147483648 TFLE 67.E
> > > > > Chain-final residues that are not actual C terminii:
> > > > > 424 hydrogen bonds
> > > > > Hydrogens added
> > > > > Charge model: AMBER ff12SB
> > > > > Assigning partial charges to residue TFLE+TFLE (net charge +0)
> with am1-bcc method
> > > > > Running ANTECHAMBER command: C:/Program Files/Chimera
> 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2
> -c bcc -nc 0 -j 5 -s 2
> > > > > (TFLE+TFLE)
> > > > >
> > > > > Cannot automatically determine charges for residue TFLE+TFLE;
> > > > > Run AddCharge tool manually to add charges and then rerun ESP
> > > > >
> > > > > Can someone please tell me a step by step procedure to make this
> work.
> > > > > Thanks & Regards,
> > > > > Haresh
> > > >
> > > >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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From meng at cgl.ucsf.edu  Tue Jan 28 15:36:54 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 28 Jan 2014 15:36:54 -0800
Subject: [Chimera-users] setting secondary structure of amino acid residues
In-Reply-To: <CACWQECSCFqTaeuCoYNw8w9MFkyA2OLs0Y0MPBwVqSyvA-ZjnYw@mail.gmail.com>
References: <CACWQECRF5+1+ouPjHMNZY7WTWWcj1W67wKJ9D+G4-YWNj_V6vg@mail.gmail.com>
	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
	<CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
	<F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>
	<CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>
	<6A125701-E7A2-451F-A765-CC079D07E12C@cgl.ucsf.edu>
	<CACWQECRSRQOVGtp0jx_74G_Fwoe-wNrZ39XZox5m3A6m2AjHMg@mail.gmail.com>
	<00646B58-7EF6-489E-B4F3-CE36A8491494@cgl.ucsf.edu>
	<CACWQECSCFqTaeuCoYNw8w9MFkyA2OLs0Y0MPBwVqSyvA-ZjnYw@mail.gmail.com>
Message-ID: <0F80B2C8-629B-4BAD-BA6F-3D2431CD9DE3@cgl.ucsf.edu>

Hi Haresh,
To run ksdssp, just enter command "ksdssp" ? this does not change the coordinates of the structure, it just tries to identify which parts are helix and which are strand based on where it sees backbone H-bonds. If the ribbon is still not like the helix or strand width after you use "ksdssp" it means that the conformation does not look like helix or strand according to ksdssp.  

When you use addaa, make sure to specify the desired conformation.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html>

Another way instead of addaa to build the 14 residues is with Build Structure (in menu under Tools? Structure Editing), section Start Structure, choice "peptide", which will then give a further dialog for setting phi/psi angles with suggestions available for different secondary structures.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>
You would build the peptide as a separate new model, but then use the Join Models section of Build Structure to attach it to the N-term of your protein.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>

HOWEVER, even if you built the conformation correctly, it depends whether you tried to make a strand or a helix.  Even if the peptide is in a beta-strand conformation, ksdssp will not identify a single strand by itself.  It only identifies a beta-strand when the backbone is positioned to H-bond with another beta-strand, as in a hairpin or sheet.

You could just force Chimera to show the residues as helix or strand no matter what the reality is or what ksdssp thinks, for example, selecting all those residues and then if you wanted them to be considered strand, using commands:
setattr r isHelix false sel
setattr r isStrand true sel
(just trade "isHelix" and "isStrand" in those commands if you wanted the residues to be considered helix)

For helix, an additional possibility is to try using ksdssp again but with command-line options to use less strict parameter values.  <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

You can search the manual for strings like "ksdssp" or "building peptides" from the Chimera Help menu.
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 28, 2014, at 2:43 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:

> Hi Elaine,
> Yes I did exactly the way you explained and it is working now. 
> I have another question. I need to add some 14 residues on N-termius of the protein which I did using the addaa command. However, I am unable to simulate its secondary structure using ksdssp. I am not sure how to run this command in command line. Or am I doing something wrong in terms of predicting the structures.
> Can you please let me know what do I need to do in terms of getting the structure of protein after addsing residues on N-terminus.
> Thanks,
> Haresh
> 




From meyersonj at mail.nih.gov  Tue Jan 28 14:29:25 2014
From: meyersonj at mail.nih.gov (Joel Meyerson)
Date: Tue, 28 Jan 2014 17:29:25 -0500
Subject: [Chimera-users] Coloring map by curvature
Message-ID: <CAMsg=btLG9_JtLryFMEfzK+0Ews3ukc2xrdV7TwuF4hvgEB_Zg@mail.gmail.com>

Hi,
Is it possible to color a map based on surface curvature?
Thanks,
Joel
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From goddard at sonic.net  Tue Jan 28 16:36:48 2014
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 28 Jan 2014 16:36:48 -0800
Subject: [Chimera-users] Coloring map by curvature
In-Reply-To: <CAMsg=btLG9_JtLryFMEfzK+0Ews3ukc2xrdV7TwuF4hvgEB_Zg@mail.gmail.com>
References: <CAMsg=btLG9_JtLryFMEfzK+0Ews3ukc2xrdV7TwuF4hvgEB_Zg@mail.gmail.com>
Message-ID: <59E07705-5258-4AD5-8D67-A3E5DF99DC9B@sonic.net>

Hi Joel,

  No, Chimera does not compute surface curvature.  It would not be too hard to make a Python script that computed it and used it to color a surface.  The main trouble is defining numerically the curvature for a triangulated surface at each vertex.  Why are you interested in this?  Is the idea to simulate ambient occlusion lighting where surface cavities are dark and projections are brighter?  Is the idea to try it on EM maps or molecular surfaces?

	Tom


On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote:

> Hi,
> Is it possible to color a map based on surface curvature?
> Thanks,
> Joel
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From meyersonj at mail.nih.gov  Tue Jan 28 18:08:56 2014
From: meyersonj at mail.nih.gov (Joel Meyerson)
Date: Tue, 28 Jan 2014 21:08:56 -0500
Subject: [Chimera-users] Coloring map by curvature
In-Reply-To: <59E07705-5258-4AD5-8D67-A3E5DF99DC9B@sonic.net>
References: <CAMsg=btLG9_JtLryFMEfzK+0Ews3ukc2xrdV7TwuF4hvgEB_Zg@mail.gmail.com>
	<59E07705-5258-4AD5-8D67-A3E5DF99DC9B@sonic.net>
Message-ID: <CAMsg=bskxpuqmbBHTOQmk7gBnm9oG+iDR91GACBZ_7=n2G5z7g@mail.gmail.com>

Hi Tom,
I have cryo-EM maps for two conformations of a protein, both in the 15
Angstrom resolution range. The conformations are visibly different, but I
am also interested in seeing where they differ in terms of their surface
curvature, as it could have bearing on how I interpret the conformations.
If there's any other info I can provide just let me know.
Thanks!
Joel


On Tue, Jan 28, 2014 at 7:36 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Joel,
>
>   No, Chimera does not compute surface curvature.  It would not be too
> hard to make a Python script that computed it and used it to color a
> surface.  The main trouble is defining numerically the curvature for a
> triangulated surface at each vertex.  Why are you interested in this?  Is
> the idea to simulate ambient occlusion lighting where surface cavities are
> dark and projections are brighter?  Is the idea to try it on EM maps or
> molecular surfaces?
>
>         Tom
>
>
> On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote:
>
> > Hi,
> > Is it possible to color a map based on surface curvature?
> > Thanks,
> > Joel
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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From pollack.1 at osu.edu  Wed Jan 29 04:41:19 2014
From: pollack.1 at osu.edu (Pollack, J)
Date: Wed, 29 Jan 2014 12:41:19 +0000
Subject: [Chimera-users] Coloring map by curvature
In-Reply-To: <59E07705-5258-4AD5-8D67-A3E5DF99DC9B@sonic.net>
References: <CAMsg=btLG9_JtLryFMEfzK+0Ews3ukc2xrdV7TwuF4hvgEB_Zg@mail.gmail.com>
	<59E07705-5258-4AD5-8D67-A3E5DF99DC9B@sonic.net>
Message-ID: <24E32E0182934B4BBFD71A8018107736900D0BEE@CIO-KRC-D1MBX03.osuad.osu.edu>

Hey folks!!! You have got my email address mixed up with others...this is the second mysterious incomprehensible message meant for somebody else sent by a different advisor...fix it.....this one by Tom the other by a woman (I deleted the message - it was  long one.........) Stay well......regards, Dennis



-----Original Message-----
From: chimera-users-bounces at cgl.ucsf.edu [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Tom Goddard
Sent: Tuesday, January 28, 2014 7:37 PM
To: Joel Meyerson
Cc: chimera-users at cgl.ucsf.edu List
Subject: Re: [Chimera-users] Coloring map by curvature

Hi Joel,

  No, Chimera does not compute surface curvature.  It would not be too hard to make a Python script that computed it and used it to color a surface.  The main trouble is defining numerically the curvature for a triangulated surface at each vertex.  Why are you interested in this?  Is the idea to simulate ambient occlusion lighting where surface cavities are dark and projections are brighter?  Is the idea to try it on EM maps or molecular surfaces?

	Tom


On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote:

> Hi,
> Is it possible to color a map based on surface curvature?
> Thanks,
> Joel
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


_______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users





From darrellh at niaid.nih.gov  Wed Jan 29 08:44:17 2014
From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E])
Date: Wed, 29 Jan 2014 16:44:17 +0000
Subject: [Chimera-users] Coloring map by curvature
In-Reply-To: <CAMsg=bskxpuqmbBHTOQmk7gBnm9oG+iDR91GACBZ_7=n2G5z7g@mail.gmail.com>
References: <CAMsg=btLG9_JtLryFMEfzK+0Ews3ukc2xrdV7TwuF4hvgEB_Zg@mail.gmail.com>
	<59E07705-5258-4AD5-8D67-A3E5DF99DC9B@sonic.net>
	<CAMsg=bskxpuqmbBHTOQmk7gBnm9oG+iDR91GACBZ_7=n2G5z7g@mail.gmail.com>
Message-ID: <CF0E951E.C16B%darrellh@niaid.nih.gov>

Hi Joel,

I love Chimera and use it all the time. However, a quick-and-dirty solution to your problem might be to try Meshlab. It is kind of buggy software, but can be very useful. Here's a tutorial/blog entry that I found in a quick search. At the very least, it describes what I think Tom was communicating about enhancing surface shading:
http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-and.html

FWIW,
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559
Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<https://twitter.com/niaidbioit>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

From: <Meyerson>, "Joel [F] (NIH/NCI)" <meyersonj at mail.nih.gov<mailto:meyersonj at mail.nih.gov>>
Date: Tuesday, January 28, 2014 9:08 PM
To: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> List" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] Coloring map by curvature

Hi Tom,
I have cryo-EM maps for two conformations of a protein, both in the 15 Angstrom resolution range. The conformations are visibly different, but I am also interested in seeing where they differ in terms of their surface curvature, as it could have bearing on how I interpret the conformations. If there's any other info I can provide just let me know.
Thanks!
Joel


On Tue, Jan 28, 2014 at 7:36 PM, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:
Hi Joel,

  No, Chimera does not compute surface curvature.  It would not be too hard to make a Python script that computed it and used it to color a surface.  The main trouble is defining numerically the curvature for a triangulated surface at each vertex.  Why are you interested in this?  Is the idea to simulate ambient occlusion lighting where surface cavities are dark and projections are brighter?  Is the idea to try it on EM maps or molecular surfaces?

        Tom


On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote:

> Hi,
> Is it possible to color a map based on surface curvature?
> Thanks,
> Joel
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users





From goddard at sonic.net  Wed Jan 29 12:31:32 2014
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 29 Jan 2014 12:31:32 -0800
Subject: [Chimera-users] Coloring map by curvature
In-Reply-To: <CAMsg=btvGehr7HbxuehacQ7nCwZOzCK91fqA9m9gfV3j7q05qw@mail.gmail.com>
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	<59E07705-5258-4AD5-8D67-A3E5DF99DC9B@sonic.net>
	<CAMsg=bskxpuqmbBHTOQmk7gBnm9oG+iDR91GACBZ_7=n2G5z7g@mail.gmail.com>
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	<CAMsg=btvGehr7HbxuehacQ7nCwZOzCK91fqA9m9gfV3j7q05qw@mail.gmail.com>
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Hi Joel,

  I don't think surface curvature will be helpful understand the differences between two EM maps.  But I was curious what it would look like.  So here's a Python script and an image on a simulated map at 15 Angstroms.  You use the script by opening your map, selecting the surface (ctrl-click on it), then open the curvature.py script (menu File / Open?).  Here's a description of the method it uses from the comments at the top of the curvature.py file.

# Color selected surface pieces by mean curvature.
#
# Gray at the average curvature value over the surface, and blue and red
# at +/- 3 standard deviations of curvature values across the surface.
#
# The curvature is estimated from the vertices and normals of the triangulated
# surface in simple way which will show artifacts from non-isotropic meshes.
# For each triangle edge it computes the normal vector rotation from one vertex
# to the other divided by the edge length.  The vertex mean curvature is the
# mean of the curvatures computed for each edge.
#

And the steps to make the example image

	open 1grl
	molmap #0 15 grid 2 model #1
	select #1
	open ~/Desktop/curvature.py

  Tom




On Jan 29, 2014, at 9:40 AM, Joel Meyerson  wrote:

> Hi Darrell,
> Thanks for the tip! I hadn't considered mesh lab but that link you sent looks promising. I'll also wait to see if Tom has any further suggestions.
> Joel
> 
> 
> On Wed, Jan 29, 2014 at 11:44 AM, Hurt, Darrell (NIH/NIAID) [E]  wrote:
> Hi Joel,
> 
> I love Chimera and use it all the time. However, a quick-and-dirty solution to your problem might be to try Meshlab. It is kind of buggy software, but can be very useful. Here's a tutorial/blog entry that I found in a quick search. At the very least, it describes what I think Tom was communicating about enhancing surface shading:
> http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-and.html
> 
> FWIW,
> Darrell
> 
> -- 
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
>  
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> 
> 
> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
> From: <Meyerson>, "Joel [F] (NIH/NCI)" 
> Date: Tuesday, January 28, 2014 9:08 PM
> To: Tom Goddard 
> Cc: "chimera-users at cgl.ucsf.edu List" <chimera-users at cgl.ucsf.edu>
> 
> Subject: Re: [Chimera-users] Coloring map by curvature
> 
> Hi Tom,
> I have cryo-EM maps for two conformations of a protein, both in the 15 Angstrom resolution range. The conformations are visibly different, but I am also interested in seeing where they differ in terms of their surface curvature, as it could have bearing on how I interpret the conformations. If there's any other info I can provide just let me know.
> Thanks!
> Joel
> 
> 
> On Tue, Jan 28, 2014 at 7:36 PM, Tom Goddard wrote:
> Hi Joel,
> 
>   No, Chimera does not compute surface curvature.  It would not be too hard to make a Python script that computed it and used it to color a surface.  The main trouble is defining numerically the curvature for a triangulated surface at each vertex.  Why are you interested in this?  Is the idea to simulate ambient occlusion lighting where surface cavities are dark and projections are brighter?  Is the idea to try it on EM maps or molecular surfaces?
> 
>         Tom
> 
> 
> On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote:
> 
> > Hi,
> > Is it possible to color a map based on surface curvature?
> > Thanks,
> > Joel
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> 

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From meyersonj at mail.nih.gov  Wed Jan 29 13:38:06 2014
From: meyersonj at mail.nih.gov (Joel Meyerson)
Date: Wed, 29 Jan 2014 16:38:06 -0500
Subject: [Chimera-users] Coloring map by curvature
In-Reply-To: <C8DED705-CBB2-44BD-9816-0A246D8562E9@sonic.net>
References: <CAMsg=btLG9_JtLryFMEfzK+0Ews3ukc2xrdV7TwuF4hvgEB_Zg@mail.gmail.com>
	<59E07705-5258-4AD5-8D67-A3E5DF99DC9B@sonic.net>
	<CAMsg=bskxpuqmbBHTOQmk7gBnm9oG+iDR91GACBZ_7=n2G5z7g@mail.gmail.com>
	<CF0E951E.C16B%darrellh@niaid.nih.gov>
	<CAMsg=btvGehr7HbxuehacQ7nCwZOzCK91fqA9m9gfV3j7q05qw@mail.gmail.com>
	<C8DED705-CBB2-44BD-9816-0A246D8562E9@sonic.net>
Message-ID: <CAMsg=bvh5wgrxtE7Te-Ri2+FvyeXyMiUCxWiWhuUXsrquYZp6Q@mail.gmail.com>

Tom,
This works beautifully! In the case of the two conformations I'm viewing,
it provides very useful information. Thanks again.
Joel


On Wed, Jan 29, 2014 at 3:31 PM, Tom Goddard <goddard at sonic.net> wrote:

>  Hi Joel,
>
>    I don't think surface curvature will be helpful understand the
> differences between two EM maps.  But I was curious what it would look
> like.  So here's a Python script and an image on a simulated map at 15
> Angstroms.  You use the script by opening your map, selecting the surface
> (ctrl-click on it), then open the curvature.py script (menu File / Open...).
>  Here's a description of the method it uses from the comments at the top of
> the curvature.py file.
>
>  # Color selected surface pieces by mean curvature.
> #
> # Gray at the average curvature value over the surface, and blue and red
> # at +/- 3 standard deviations of curvature values across the surface.
> #
> # The curvature is estimated from the vertices and normals of the
> triangulated
> # surface in simple way which will show artifacts from non-isotropic
> meshes.
> # For each triangle edge it computes the normal vector rotation from one
> vertex
> # to the other divided by the edge length.  The vertex mean curvature is
> the
> # mean of the curvatures computed for each edge.
> #
>
>  And the steps to make the example image
>
>  open 1grl
> molmap #0 15 grid 2 model #1
> select #1
> open ~/Desktop/curvature.py
>
>    Tom
>
>
>
>  On Jan 29, 2014, at 9:40 AM, Joel Meyerson  wrote:
>
>  Hi Darrell,
> Thanks for the tip! I hadn't considered mesh lab but that link you sent
> looks promising. I'll also wait to see if Tom has any further suggestions.
>  Joel
>
>
> On Wed, Jan 29, 2014 at 11:44 AM, Hurt, Darrell (NIH/NIAID) [E]  wrote:
>
>  Hi Joel,
>
>  I love Chimera and use it all the time. However, a quick-and-dirty
> solution to your problem might be to try Meshlab. It is kind of buggy
> software, but can be very useful. Here's a tutorial/blog entry that I found
> in a quick search. At the very least, it describes what I think Tom was
> communicating about enhancing surface shading:
>
> http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-and.html
>
>  FWIW,
> Darrell
>
>  --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
>
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
>
>
>  Disclaimer: The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be used
> by anyone who is not the original intended recipient. If you have received
> this e-mail in error please inform the sender and delete it from your
> mailbox or any other storage devices. National Institute of Allergy and
> Infectious Diseases shall not accept liability for any statements made that
> are sender's own and not expressly made on behalf of the NIAID by one of
> its representatives.
>
>   From: <Meyerson>, "Joel [F] (NIH/NCI)"
> Date: Tuesday, January 28, 2014 9:08 PM
> To: Tom Goddard
> Cc: "chimera-users at cgl.ucsf.edu List" <chimera-users at cgl.ucsf.edu>
>
> Subject: Re: [Chimera-users] Coloring map by curvature
>
>    Hi Tom,
>  I have cryo-EM maps for two conformations of a protein, both in the 15
> Angstrom resolution range. The conformations are visibly different, but I
> am also interested in seeing where they differ in terms of their surface
> curvature, as it could have bearing on how I interpret the conformations.
> If there's any other info I can provide just let me know.
>  Thanks!
> Joel
>
>
> On Tue, Jan 28, 2014 at 7:36 PM, Tom Goddard wrote:
>
> Hi Joel,
>
>   No, Chimera does not compute surface curvature.  It would not be too
> hard to make a Python script that computed it and used it to color a
> surface.  The main trouble is defining numerically the curvature for a
> triangulated surface at each vertex.  Why are you interested in this?  Is
> the idea to simulate ambient occlusion lighting where surface cavities are
> dark and projections are brighter?  Is the idea to try it on EM maps or
> molecular surfaces?
>
>         Tom
>
>
> On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote:
>
> > Hi,
> > Is it possible to color a map based on surface curvature?
> > Thanks,
> > Joel
>  > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>
>
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From htm211 at nyu.edu  Thu Jan 30 10:53:04 2014
From: htm211 at nyu.edu (Haresh Tukaram More)
Date: Thu, 30 Jan 2014 13:53:04 -0500
Subject: [Chimera-users] setting secondary structure of amino acid
	residues
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	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
	<CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
	<F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>
	<CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>
	<6A125701-E7A2-451F-A765-CC079D07E12C@cgl.ucsf.edu>
	<CACWQECRSRQOVGtp0jx_74G_Fwoe-wNrZ39XZox5m3A6m2AjHMg@mail.gmail.com>
	<00646B58-7EF6-489E-B4F3-CE36A8491494@cgl.ucsf.edu>
	<CACWQECSCFqTaeuCoYNw8w9MFkyA2OLs0Y0MPBwVqSyvA-ZjnYw@mail.gmail.com>
	<0F80B2C8-629B-4BAD-BA6F-3D2431CD9DE3@cgl.ucsf.edu>
Message-ID: <CACWQECQ_Nk-uUDC2SmoRNJxqX02VxtRLXqAuFxEXAFqJ+qj3gA@mail.gmail.com>

Hi Elaine,

I made two different models in a single Chimera window and selected the
N-terminal amino acid of one peptide and C-terminal amino acid of another.
Then I ran the command Join mdoels, but it gives me the error. Can you
please tell me what I am doing wrong here.

I have attached screen shot of the window.

Thanks,
Haresh


On Tue, Jan 28, 2014 at 6:36 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Haresh,
> To run ksdssp, just enter command "ksdssp" ... this does not change the
> coordinates of the structure, it just tries to identify which parts are
> helix and which are strand based on where it sees backbone H-bonds. If the
> ribbon is still not like the helix or strand width after you use "ksdssp"
> it means that the conformation does not look like helix or strand according
> to ksdssp.
>
> When you use addaa, make sure to specify the desired conformation.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html>
>
> Another way instead of addaa to build the 14 residues is with Build
> Structure (in menu under Tools... Structure Editing), section Start
> Structure, choice "peptide", which will then give a further dialog for
> setting phi/psi angles with suggestions available for different secondary
> structures.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start
> >
> You would build the peptide as a separate new model, but then use the Join
> Models section of Build Structure to attach it to the N-term of your
> protein.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
> >
>
> HOWEVER, even if you built the conformation correctly, it depends whether
> you tried to make a strand or a helix.  Even if the peptide is in a
> beta-strand conformation, ksdssp will not identify a single strand by
> itself.  It only identifies a beta-strand when the backbone is positioned
> to H-bond with another beta-strand, as in a hairpin or sheet.
>
> You could just force Chimera to show the residues as helix or strand no
> matter what the reality is or what ksdssp thinks, for example, selecting
> all those residues and then if you wanted them to be considered strand,
> using commands:
> setattr r isHelix false sel
> setattr r isStrand true sel
> (just trade "isHelix" and "isStrand" in those commands if you wanted the
> residues to be considered helix)
>
> For helix, an additional possibility is to try using ksdssp again but with
> command-line options to use less strict parameter values.  <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
>
> You can search the manual for strings like "ksdssp" or "building peptides"
> from the Chimera Help menu.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Jan 28, 2014, at 2:43 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
>
> > Hi Elaine,
> > Yes I did exactly the way you explained and it is working now.
> > I have another question. I need to add some 14 residues on N-termius of
> the protein which I did using the addaa command. However, I am unable to
> simulate its secondary structure using ksdssp. I am not sure how to run
> this command in command line. Or am I doing something wrong in terms of
> predicting the structures.
> > Can you please let me know what do I need to do in terms of getting the
> structure of protein after addsing residues on N-terminus.
> > Thanks,
> > Haresh
> >
>
>
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From meng at cgl.ucsf.edu  Thu Jan 30 11:10:03 2014
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 30 Jan 2014 11:10:03 -0800
Subject: [Chimera-users] joining peptides
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	<7F049E4C-0EB4-4931-AE85-FD9C19A876BC@cgl.ucsf.edu>
	<CACWQECSkgO0tu_NztcunAcTzwx6WSOqq9Fm7=Tczc6jA=EVnTw@mail.gmail.com>
	<F09F6ACD-E3B9-4C2D-A933-2D086B7CEF55@cgl.ucsf.edu>
	<CACWQECQuMvAL5X5iLOz3SLd7BL4RyBgAGM8qxg_xPLaUZukUTw@mail.gmail.com>
	<6A125701-E7A2-451F-A765-CC079D07E12C@cgl.ucsf.edu>
	<CACWQECRSRQOVGtp0jx_74G_Fwoe-wNrZ39XZox5m3A6m2AjHMg@mail.gmail.com>
	<00646B58-7EF6-489E-B4F3-CE36A8491494@cgl.ucsf.edu>
	<CACWQECSCFqTaeuCoYNw8w9MFkyA2OLs0Y0MPBwVqSyvA-ZjnYw@mail.gmail.com>
	<0F80B2C8-629B-4BAD-BA6F-3D2431CD9DE3@cgl.ucsf.edu>
	<CACWQECQ_Nk-uUDC2SmoRNJxqX02VxtRLXqAuFxEXAFqJ+qj3gA@mail.gmail.com>
Message-ID: <E32FC8F2-B1ED-4CC3-B0DA-AAD10B8DA507@cgl.ucsf.edu>

Hi Haresh,
As the message on the dialog says, the two parts must be in two different models, and only the C-term carbon of one and the N-term nitrogen of the other (exactly two atoms) should be selected.  I can't tell if any of those are true from your screen shot.   Make sure they are two different models and hide ribbon (e.g. Actions? Ribbon? hide) so you can see the backbone atoms and make sure only those two atoms are selected.  Possible problems may be you have >2 atoms selected or the wrong atoms, for example, both are at the C-term.
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 30, 2014, at 10:53 AM, Haresh Tukaram More <htm211 at nyu.edu> wrote:

> Hi Elaine,
> 
> I made two different models in a single Chimera window and selected the N-terminal amino acid of one peptide and C-terminal amino acid of another. Then I ran the command Join mdoels, but it gives me the error. Can you please tell me what I am doing wrong here.
> 
> I have attached screen shot of the window.
> 
> Thanks,
> Haresh




From nirodion at syr.edu  Fri Jan 31 12:49:16 2014
From: nirodion at syr.edu (Nikolay Igorovich Rodionov)
Date: Fri, 31 Jan 2014 20:49:16 +0000
Subject: [Chimera-users] Creating output with IDATM naming
Message-ID: <DF38AA25-2547-4BF6-9E20-9E168AB6D568@syr.edu>

Hi,

Does anyone know a way to rename all of the atom names in a PDB file to their IDATM types, so that a new PDB file can be generated with the IDATM naming scheme? 

Best,
Nikolay Rodionov 


From alice777sm at gmail.com  Fri Jan 31 14:18:14 2014
From: alice777sm at gmail.com (Min Woo Sung)
Date: Fri, 31 Jan 2014 16:18:14 -0600
Subject: [Chimera-users] Question about opening mrc and PDB files
Message-ID: <CAB=O3JxrOtuMESciqCqhw5k1pALFFLAmNBh5yBhDn-97nrC_Ew@mail.gmail.com>

Hi,

This is Min Woo Sung from Texas A&M University.
I was using Chimera to see EM structure(.mrc file) and wanted to put a PDB
file to fit that in EM map.

I'm wondering if I can use Chimera to analyze the volume, size or domains
of these two files for the purpose of analysis.

I saw one PDB file seemed much bigger that EM map when I opened it in
Chimera. Do I have to normalize the size of any files? If so, how can I do
that?

Any suggests would greatly appreciated.

Best regard,
Min Woo Sung
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