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Today's Topics:

   1. Re: problems in opening PDB file (Marco Sette)
   2. Re: problems in opening PDB file (Eric Pettersen)
   3. Problem with electrostatic surface (Benedikt Moissl)


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

Message: 1
Date: Tue, 24 Mar 2020 16:34:03 +0100
From: Marco Sette <sette@uniroma2.it>
To: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] problems in opening PDB file
Message-ID: <cf0bb412-cc4f-37f8-6450-bc9281dd7b8a@uniroma2.it>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Dear Laura,

maybe you can have a look at your pdb file by using a text editor to
check if the pdb contains some unusual portion (like missing residues).
As far I know Chimera tries to reconstruct missing residues but
sometimes there could be something wrong.

Best regards

Marco


Il 24/03/2020 10:05, Laura Rotilio ha scritto:
> Goodmorning,
> I'm writing because I'm trying to open my pdb file but this error came
> out "Attempt to form loop bond".
> I tried to have a look at the _init_.py file in the line 1109 and I
> found this message:
> molList = pdbio.readPDBfile(file, errOut=errLog)
>
> I can't understand this message and I don't know how to eventually
> modify my pdb file in order to be able to open it.
>
> Thanks in advance for helping?me,
> Laura Rotilio
>
>
> --
>
> Laura Rotilio, Ph.D. Student
>
> *Structural Biology Lab., Prof. A. Mattevi*
>
> Dept. Biology and Biotechnology "L. Spallanzani"
>
> University of Pavia
>
> Via Ferrata 9, 27100 Pavia
>
> Italy
>
> Tel. +39-0382-985525 <tel:%2B39-0382-985525>/985534
>
> Fax +39-0382-528496 <tel:%2B39-0382-528496>
>
> Web www.unipv.it/biocry <http://www.unipv.it/biocry>


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

--
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette@uniroma2.it
e-mail: m77it@yahoo.it
Tel.: +39-0672594424
Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette

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Message: 2
Date: Tue, 24 Mar 2020 08:47:45 -0700
From: Eric Pettersen <pett@cgl.ucsf.edu>
To: Laura Rotilio <laura.rotilio@iusspavia.it>
Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] problems in opening PDB file
Message-ID: <AAE13D11-5BC1-4836-B845-0FDC745949E7@cgl.ucsf.edu>
Content-Type: text/plain; charset="utf-8"

Hi Laura,
        The ?loop bond? message specifically means that your PDB file has a CONECT or LINK record that says that an atom is bonded to itself!  So my advice would be to edit your PDB file and remove all CONECT and LINK records and let Chimera figure out the bonds on its own.

--Eric

        Eric Pettersen
        UCSF Computer Graphics Lab


> On Mar 24, 2020, at 2:05 AM, Laura Rotilio <laura.rotilio@iusspavia.it> wrote:
>
> Goodmorning,
> I'm writing because I'm trying to open my pdb file but this error came out "Attempt to form loop bond".
> I tried to have a look at the _init_.py file in the line 1109 and I found this message:
> molList = pdbio.readPDBfile(file, errOut=errLog)
>
> I can't understand this message and I don't know how to eventually modify my pdb file in order to be able to open it.
>
> Thanks in advance for helping me,
> Laura Rotilio
>
>
> --
> Laura Rotilio, Ph.D. Student
>
> Structural Biology Lab., Prof. A. Mattevi
>
> Dept. Biology and Biotechnology "L. Spallanzani"
>
> University of Pavia
>
> Via Ferrata 9, 27100 Pavia
>
> Italy
>
> Tel. +39-0382-985525 <tel:%2B39-0382-985525>/985534
>
> Fax +39-0382-528496 <tel:%2B39-0382-528496>
> Web www.unipv.it/biocry <http://www.unipv.it/biocry>_______________________________________________


> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Message: 3
Date: Tue, 24 Mar 2020 07:35:10 +0100
From: "Benedikt Moissl" <benedikt.moissl@biologie.uni-regensburg.de>
To: <chimera-bugs@cgl.ucsf.edu>
Subject: [Chimera-users] Problem with electrostatic surface
Message-ID:
        <000301d601a6$5e2f85e0$1a8e91a0$@biologie.uni-regensburg.de>
Content-Type: text/plain; charset="utf-8"

Dear Chimera team,
 
I am trying to display color the surface of my molecule according with Poisson-Boltzmann electrostatics using Chimera 1.14. I ran the PDB2PQR tool as described in the user guide and obtained a PDB2PQR file. With that, I ran the APBS tool and obtained a .dx file. As described, the Surface Color panel opens automatically, but here I am unable to choose my structure file for "color surface" (s. attachment 1). I can only choose the .dx file, which does not work. All three models obtained during this process are opened in the model panel though (s. attachment 2).
 
Do you have any idea on how to fix this?
 
Thank you very much in advance and keep up the great work!
 
Benedikt Moissl
____________________________________________________________
 
Institute of Biochemistry, Genetics & Microbiology
Department of Microbiology & Archaea Center
Grohmann Lab ? Single-molecule Biochemistry (Homepage <https://www.uni-regensburg.de/biologie-vorklinische-medizin/mikrobiologie/index.html>)
 
University of Regensburg | Universit?tsstra?e 31 | D-93053 Regensburg | Room: WN_E3._2.323 | Phone: +49 941 943 3184 | Fax: +49 941 943 2403 | Mail: benedikt.moissl@ur.de <mailto:benedikt.moissl@ur.de>
 
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