Andrew=2C=

Protein depiction is a pretty vague term. Same as best.= So instead of giving you my biased answer (the software I use the most or = my favorite) I'll give you a list of the software I use to visualize protei= ns in one way or another:

PyMol

VMD

Yasara

Rasmol =3B

SPDVB viewer

UCSF= Chimera

Each one in the list has features shared = with the others and quite a few that are unique. So=2C since they are all f= ree=2C try them and find the best for you.

Best re= gards

From: owner-chemistry(~)ccl.net
= To: acheron24(~)hotmail.com
Subject: CCL: best software for protein struct= ures depiction
Date: Sun=2C 2 Feb 2014 11:00:52 +0400

Hi Andrey=2C

in my opinion PyMOL is best for many = cases. But if you want something outstanding you may look at hybrid techini= ques when you use combination

of PyMOL and professional 3D softwa= re (like Blender=2C 3ds Max and so on). As an exampe you may have a look at= our tutorial =3B

=0A=

http://kodomo.fbb.msu.ru/wiki/Main/Modelling/Blender

Or may try EPMV which allows import PDB files direc= tly into professional 3D packages.

=0A=

http://epmv.scr= ipps.edu/

Hope this will of use for you.

Regards=2C

Arthur

=0A=

2014-01-31 Andrew Voronkov drugdesign[*]yandex.ru &= lt=3Bowner= -chemistry-=2C-ccl.net>=3B:
=0A=

=0A= Sent to CCL by: Andrew Voronkov [drugdesign=2C=2Cyandex.ru]
=0A= Dear CCL users=2C
=0A= what is on your oinion the best software for protein structure depictions?<= br>=0A=
=0A= Sincerely yours=2C
=0A= Andrey
=0A=
=0A=
=0A=
=0A= -=3D This is automatically added to each message by the mailing script =3D-= <=3Bbr

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= --_c69ab617-cbce-485a-ab7a-f2978afd74c2_-- From owner-chemistry@ccl.net Mon Feb 3 05:42:01 2014 From: "Mohan maruthi sena maruthi.sena..gmail.com" To: CCL Subject: CCL:G: Scan the distance between dummy atom and methane Message-Id: <-49630-140203053919-12079-aBQdCsXLxfYbbUO7dtoXLQ,,server.ccl.net> X-Original-From: Mohan maruthi sena Content-Type: multipart/alternative; boundary=f46d04446a4988c31804f17e224a Date: Mon, 3 Feb 2014 16:09:14 +0530 MIME-Version: 1.0 Sent to CCL by: Mohan maruthi sena [maruthi.sena=-=gmail.com] --f46d04446a4988c31804f17e224a Content-Type: text/plain; charset=ISO-8859-1 Hi all, My system of interest consists of benzene+ methane, The methane(carbon) is exactly 3.8 angstroms distance from the center of benzene. I want to calculate energy as function of varying distance between methane(carbon) and benzene center. I defined a dummy atom at the center of benzene and performed scan as available in gaussian09. After completion of the run, I saw that dummy atom moves away from the ring instead of methane carbon. How can i fix this? Thanks, Mohan --f46d04446a4988c31804f17e224a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi all,

=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 My system of interest consists of benzene+ methane, The methane(carb= on) is exactly 3.8 angstroms distance from the center of benzene. I want to= calculate energy as function of varying distance between methane(carbon) a= nd benzene center. I defined a dummy atom at the center of benzene=A0 and p= erformed scan as available in gaussian09. After completion of the run, I sa= w that dummy atom moves away from the ring instead of methane carbon. How c= an i fix this?

Thanks,

Mohan

--f46d04446a4988c31804f17e224a-- From owner-chemistry@ccl.net Mon Feb 3 07:14:00 2014 From: "S.Chandra Shekar chandrashekar[A]iisertvm.ac.in" To: CCL Subject: CCL:G: Scan the distance between dummy atom and methane Message-Id: <-49631-140203071038-2301-qfUGCOLI1iHSLV2QOPitVw[-]server.ccl.net> X-Original-From: "S.Chandra Shekar" Content-Type: multipart/alternative; boundary=001a1133eac802ecb304f17f6921 Date: Mon, 3 Feb 2014 17:40:31 +0530 MIME-Version: 1.0 Sent to CCL by: "S.Chandra Shekar" [chandrashekar.]^[.iisertvm.ac.in] --001a1133eac802ecb304f17f6921 Content-Type: text/plain; charset=ISO-8859-1 hi mohan, make a bond between the dummy atom and carbon atoms in benzene. On Mon, Feb 3, 2014 at 4:09 PM, Mohan maruthi sena maruthi.sena..gmail.com < owner-chemistry]^[ccl.net> wrote: > Hi all, > My system of interest consists of benzene+ methane, The > methane(carbon) is exactly 3.8 angstroms distance from the center of > benzene. I want to calculate energy as function of varying distance between > methane(carbon) and benzene center. I defined a dummy atom at the center of > benzene and performed scan as available in gaussian09. After completion of > the run, I saw that dummy atom moves away from the ring instead of methane > carbon. How can i fix this? > > > Thanks, > Mohan > --001a1133eac802ecb304f17f6921 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

hi mohan,

make a bond between the dummy atom and= carbon atoms in benzene.

On Mon, Feb 3, 2014 at 4:09 PM, Mohan maruthi sena = maruthi.sena..gmail.com = <owner-chem= istry]^[ccl.net> wrote:

Hi all,
<= /div>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 My system of interest consists of benze= ne+ methane, The methane(carbon) is exactly 3.8 angstroms distance from the= center of benzene. I want to calculate energy as function of varying dista= nce between methane(carbon) and benzene center. I defined a dummy atom at t= he center of benzene=A0 and performed scan as available in gaussian09. Afte= r completion of the run, I saw that dummy atom moves away from the ring ins= tead of methane carbon. How can i fix this?

Thanks,
Mohan

--001a1133eac802ecb304f17f6921-- From owner-chemistry@ccl.net Mon Feb 3 10:44:00 2014 From: "Tymofii Nikolaienko tim_mail() ukr.net" To: CCL Subject: CCL:G: Scan the distance between dummy atom and methane Message-Id: <-49632-140203103845-32590-kU7JQLr5FgMVa4vuafCIcA _ server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 03 Feb 2014 17:38:29 +0200 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail[A]ukr.net] Dear Mohan, have you used a constraints to fix the position of the dummy atom with respect to the benzene ring? Best regards, Tymofii 03.02.2014 12:39, Mohan maruthi sena maruthi.sena..gmail.com wrote: > Hi all, > My system of interest consists of benzene+ methane, The > methane(carbon) is exactly 3.8 angstroms distance from the center of > benzene. I want to calculate energy as function of varying distance > between methane(carbon) and benzene center. I defined a dummy atom at > the center of benzene and performed scan as available in gaussian09. > After completion of the run, I saw that dummy atom moves away from the > ring instead of methane carbon. How can i fix this? > > > Thanks, > Mohan From owner-chemistry@ccl.net Mon Feb 3 12:29:00 2014 From: "Stephen.Garrison _ srnl.doe.gov" To: CCL Subject: CCL:G: Scan the distance between dummy atom and methane Message-Id: <-49633-140203122703-25570-pO9F6Lq7aPrkLhLhY2LoDg|*|server.ccl.net> X-Original-From: Stephen.Garrison[-]srnl.doe.gov Content-Type: multipart/alternative; boundary="=_alternative 005FD28A85257C74_=" Date: Mon, 3 Feb 2014 12:26:37 -0500 MIME-Version: 1.0 Sent to CCL by: Stephen.Garrison-,-srnl.doe.gov This is a multipart message in MIME format. --=_alternative 005FD28A85257C74_= Content-Type: text/plain; charset="US-ASCII" First, are you doing a rigid (g09 keyword "scan") or relaxed (g09 keyword "opt") scan? Second, are you constraining the benzene to retain D6h symmetry? I am going to assume you are constraining benzene to retain D6h symmetry at all steps, otherwise you need to think very carefully as to what you mean by "the center of the benzene" when you specify your system (distances, angles, and dihedrals). If you are doing a rigid scan, I believe g09 leaves the z-matrix you defined in the input alone. Therefore, the angle and dihedral that specify the location of the dummy atom need to be defined relative to the benzene ring in a such a fashion as to always lie in the plane of the benzene molecule. If you are doing a relaxed scan, g09 does the optimization in redundant coordinates. You need to include a ModRedundant section in your input to fix the location of dummy atom relative to multiple carbon atoms within the ring. (If I remember my g09 input syntax correctly,) What is below should help you specify the carbon atoms of the benzene ring with a dummy center (and a dummy 1 Ang. below) that is constrained to D6h symmetry such that you can add what else you need: X X 1 rXX C 1 rCX 2 aCXX C 1 rCX 2 aCXX 3 d180 C 1 rCX 2 aCXX 3 d60 C 1 rCX 2 aCXX 5 d180 C 1 rCX 2 aCXX 3 -d60 C 1 rCX 2 aCXX 7 d180 Variables: rCX=1.4 Constants: rXX=1.0 aCXX=90.0 d180=180.0 d60=60.0 Stephen -- Stephen L. Garrison, Ph.D. - H-Canyon Technical Support Engineering - Assistant Editor, Int'l. Journal of Hydrogen Energy Savannah River Site 704-2H, Room 190 Aiken, SC 29808 803-208-8523 Stephen.Garrison#,#SRNL.doe.gov > From: "Mohan maruthi sena maruthi.sena..gmail.com" To: "Garrison, Stephen " , Date: 02/03/2014 06:00 AM Subject: CCL:G: Scan the distance between dummy atom and methane Sent by: owner-chemistry+stephen.garrison==srnl.doe.gov#,#ccl.net Hi all, My system of interest consists of benzene+ methane, The methane(carbon) is exactly 3.8 angstroms distance from the center of benzene. I want to calculate energy as function of varying distance between methane(carbon) and benzene center. I defined a dummy atom at the center of benzene and performed scan as available in gaussian09. After completion of the run, I saw that dummy atom moves away from the ring instead of methane carbon. How can i fix this? Thanks, Mohan --=_alternative 005FD28A85257C74_= Content-Type: text/html; charset="US-ASCII" First, are you doing a rigid (g09 keyword "scan") or relaxed (g09 keyword "opt") scan? Second, are you constraining the benzene to retain D6h symmetry? I am going to assume you are constraining benzene to retain D6h symmetry at all steps, otherwise you need to think very carefully as to what you mean by "the center of the benzene" when you specify your system (distances, angles, and dihedrals).

If you are doing a rigid scan, I believe g09 leaves the z-matrix you defined in the input alone. Therefore, the angle and dihedral that specify the location of the dummy atom need to be defined relative to the benzene ring in a such a fashion as to always lie in the plane of the benzene molecule.

If you are doing a relaxed scan, g09 does the optimization in redundant coordinates. You need to include a ModRedundant section in your input to fix the location of dummy atom relative to multiple carbon atoms within the ring.

(If I remember my g09 input syntax correctly,) What is below should help you specify the carbon atoms of the benzene ring with a dummy center (and a dummy 1 Ang. below) that is constrained to D6h symmetry such that you can add what else you need:

X
X 1 rXX
C 1 rCX 2 aCXX
C 1 rCX 2 aCXX 3 d180
C 1 rCX 2 aCXX 3 d60
C 1 rCX 2 aCXX 5 d180
C 1 rCX 2 aCXX 3 -d60
C 1 rCX 2 aCXX 7 d180
Variables:
rCX=1.4
Constants:
rXX=1.0
aCXX=90.0
d180=180.0
d60=60.0

Stephen

--
Stephen L. Garrison, Ph.D.
- H-Canyon Technical Support Engineering
- Assistant Editor, Int'l. Journal of Hydrogen Energy

Savannah River Site
704-2H, Room 190
Aiken, SC 29808
803-208-8523
Stephen.Garrison#,#SRNL.doe.gov

From: "Mohan maruthi sena maruthi.sena..gmail.com" <owner-chemistry#,#ccl.net>
To: "Garrison, Stephen " <stephen.garrison#,#srnl.doe.gov>,
Date: 02/03/2014 06:00 AM
Subject: CCL:G: Scan the distance between dummy atom and methane
Sent by: owner-chemistry+stephen.garrison==srnl.doe.gov#,#ccl.net

Hi all,
My system of interest consists of benzene+ methane, The methane(carbon) is exactly 3.8 angstroms distance from the center of benzene. I want to calculate energy as function of varying distance between methane(carbon) and benzene center. I defined a dummy atom at the center of benzene and performed scan as available in gaussian09. After completion of the run, I saw that dummy atom moves away from the ring instead of methane carbon. How can i fix this?

Thanks,
Mohan
--=_alternative 005FD28A85257C74_=-- From owner-chemistry@ccl.net Mon Feb 3 15:13:00 2014 From: "Andrew Orry andy~~molsoft.com" To: CCL Subject: CCL: best software for protein structures depiction Message-Id: <-49634-140203151143-8976-ePFBa1PPFjdrDf5ZEy1/lA,+,server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 03 Feb 2014 12:10:40 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy,molsoft.com] Andrey, You can try MolSoft's free ICM-Browser (http://www.molsoft.com/icm_browser.html) for Win/Linux/Mac or iMolview (http://www.molsoft.com/iMolview.html) for iPad/Android devices. It includes anaglyph stereo (http://www.molsoft.com/news.html#anaglyph3D) so no expensive monitors, glasses, or hardware is needed. There is a free webinar tomorrow (Feb 4th) on how to use the software please see http://www.molsoft.com/training.html for more information. Thanks, Andy On 1/31/2014 9:35 AM, Andrew Voronkov drugdesign[*]yandex.ru wrote: > Sent to CCL by: Andrew Voronkov [drugdesign,,yandex.ru] > Dear CCL users, > what is on your oinion the best software for protein structure depictions? > > Sincerely yours, > Andrey> -- Andrew Orry Ph.D. Senior Research Scientist MolSoft LLC 11199 Sorrento Valley Road, S209 San Diego CA 92121 USA Tel: 858-625-2000 x108 Fax: 858-625-2888 -- www.molsoft.com www.twitter.com/molsoft