[Chimera-users] How to measure the radius of density map

Jian Guan jug25 at psu.edu
Fri Jan 3 11:08:41 PST 2014


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

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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)


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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




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