Dear all, what is the way to add pseubond between metal and chelating atoms? if you could tell me what are the "mouse driven" and "script driven" manner I'll be very pleased.... all the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Diumenge, Maig 10, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 11
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Today's Topics:
1. Protonate heteroatoms only (Francesco Pietra) 2. Re: Protonate heteroatoms only (Eric Pettersen)
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Message: 1 Date: Sat, 9 May 2009 23:35:37 +0200 From: Francesco Pietra <chiendarret@gmail.com> Subject: [Chimera-users] Protonate heteroatoms only To: chimera <chimera-users@cgl.ucsf.edu> Message-ID: <b87c422a0905091435q4a1671e2td61284cf092e7fb6@mail.gmail.com> Content-Type: text/plain; charset=UTF-8
Hi: Is there a command in Chimera to protonate (Sybyl-type) the heteroatoms only (or deprotonate the other elements from a fully protonated protein)? thanks francesco pietra
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Message: 2 Date: Sat, 9 May 2009 15:27:55 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [Chimera-users] Protonate heteroatoms only To: Francesco Pietra <chiendarret@gmail.com> Cc: chimera <chimera-users@cgl.ucsf.edu> Message-ID: <67264749-1F9E-4B02-9B42-FF0A1DD99C30@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed
del HC
will delete all hydrogens bonded to carbons (their IDATM types are HC). --Eric
Eric Pettersen USCF Computer Graphics Lab
On May 9, 2009, at 2:35 PM, Francesco Pietra wrote:
Hi: Is there a command in Chimera to protonate (Sybyl-type) the heteroatoms only (or deprotonate the other elements from a fully protonated protein)? thanks francesco pietra _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Hi JD, The "user interface" (i.e. no programming) way is to create a text file listing the desired pseudobonds and their colors and read it in with PseudoBond Reader. The tool and file format are described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...
I don't know the python way, but perhaps looking in the code for PseudoBond Reader will help ( share/PBReader/ within your Chimera installation). Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 12, 2009, at 8:19 AM, Jean Didier Pie Marechal wrote:
Dear all,
what is the way to add pseubond between metal and chelating atoms? if you could tell me what are the "mouse driven" and "script driven" manner I'll be very pleased.... all the best, JD
On May 12, 2009, at 8:39 AM, Elaine Meng wrote:
Hi JD, The "user interface" (i.e. no programming) way is to create a text file listing the desired pseudobonds and their colors and read it in with PseudoBond Reader. The tool and file format are described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...
I don't know the python way, but perhaps looking in the code for PseudoBond Reader will help ( share/PBReader/ within your Chimera installation).
The "programming way" is ('metal' and 'chel' are the two atoms): mol = metal.molecule from chimera.misc import getPseudoBondGroup group = getPseudoBondGroup("coordination complexes of %s (%s)" % (mol.name, mol), associateWith=[mol]) group.newPseudoBond(metal, chel) --Eric
participants (3)
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Elaine Meng -
Eric Pettersen -
Jean Didier Pie Marechal