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<p>Hi,</p>
<p><br>
</p>
<p>It seems to me that you didn't generate the surface of the model (I don't see it in your model panel). So, first press 'actions show surface' then go to 'colour surface by electrostatic potential'.</p>
<p><br>
</p>
<p>Stay healthy,</p>
<p><br>
</p>
<p>Boaz</p>
<p><br>
</p>
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<div><font color="#000080" face="Times New Roman" size="3"><em>Boaz Shaanan, Ph.D.
<br>
Dept. of Life Sciences <br>
Ben-Gurion University of the Negev <br>
Beer-Sheva 84105 <br>
Israel <br>
<br>
E-mail: bshaanan@bgu.ac.il<br>
Phone: 972-8-647-2220 <br>
Fax: 972-8-647-2992 or 972-8-646-1710 </em></font></div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of chimera-users-request@cgl.ucsf.edu <chimera-users-request@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, March 24, 2020 6:09 PM<br>
<b>To:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Chimera-users Digest, Vol 203, Issue 18</font>
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Today's Topics:<br>
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1. Re: problems in opening PDB file (Marco Sette)<br>
2. Re: problems in opening PDB file (Eric Pettersen)<br>
3. Problem with electrostatic surface (Benedikt Moissl)<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 24 Mar 2020 16:34:03 +0100<br>
From: Marco Sette <sette@uniroma2.it><br>
To: chimera-users@cgl.ucsf.edu<br>
Subject: Re: [Chimera-users] problems in opening PDB file<br>
Message-ID: <cf0bb412-cc4f-37f8-6450-bc9281dd7b8a@uniroma2.it><br>
Content-Type: text/plain; charset="utf-8"; Format="flowed"<br>
<br>
Dear Laura,<br>
<br>
maybe you can have a look at your pdb file by using a text editor to <br>
check if the pdb contains some unusual portion (like missing residues). <br>
As far I know Chimera tries to reconstruct missing residues but <br>
sometimes there could be something wrong.<br>
<br>
Best regards<br>
<br>
Marco<br>
<br>
<br>
Il 24/03/2020 10:05, Laura Rotilio ha scritto:<br>
> Goodmorning,<br>
> I'm writing because I'm trying to open my pdb file but this error came <br>
> out "Attempt to form loop bond".<br>
> I tried to have a look at the _init_.py file in the line 1109 and I <br>
> found this message:<br>
> molList = pdbio.readPDBfile(file, errOut=errLog)<br>
><br>
> I can't understand this message and I don't know how to eventually <br>
> modify my pdb file in order to be able to open it.<br>
><br>
> Thanks in advance for helping?me,<br>
> Laura Rotilio<br>
><br>
><br>
> -- <br>
><br>
> Laura Rotilio, Ph.D. Student<br>
><br>
> *Structural Biology Lab., Prof. A. Mattevi*<br>
><br>
> Dept. Biology and Biotechnology "L. Spallanzani"<br>
><br>
> University of Pavia<br>
><br>
> Via Ferrata 9, 27100 Pavia<br>
><br>
> Italy<br>
><br>
> Tel. +39-0382-985525 <tel:%2B39-0382-985525>/985534<br>
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<br>
-- <br>
Dr.Marco Sette, Ph.D.<br>
Department of Chemical Sciences and Technology<br>
University of Rome, "Tor Vergata"<br>
via della Ricerca Scientifica, 00133, Rome, Italy<br>
e-mail: sette@uniroma2.it<br>
e-mail: m77it@yahoo.it<br>
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<br>
Message: 2<br>
Date: Tue, 24 Mar 2020 08:47:45 -0700<br>
From: Eric Pettersen <pett@cgl.ucsf.edu><br>
To: Laura Rotilio <laura.rotilio@iusspavia.it><br>
Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu><br>
Subject: Re: [Chimera-users] problems in opening PDB file<br>
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<br>
Hi Laura,<br>
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.<br>
<br>
--Eric<br>
<br>
Eric Pettersen<br>
UCSF Computer Graphics Lab<br>
<br>
<br>
> On Mar 24, 2020, at 2:05 AM, Laura Rotilio <laura.rotilio@iusspavia.it> wrote:<br>
> <br>
> Goodmorning, <br>
> I'm writing because I'm trying to open my pdb file but this error came out "Attempt to form loop bond".
<br>
> I tried to have a look at the _init_.py file in the line 1109 and I found this message:
<br>
> molList = pdbio.readPDBfile(file, errOut=errLog)<br>
> <br>
> 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.
<br>
> <br>
> Thanks in advance for helping me, <br>
> Laura Rotilio<br>
> <br>
> <br>
> -- <br>
> Laura Rotilio, Ph.D. Student<br>
> <br>
> Structural Biology Lab., Prof. A. Mattevi<br>
> <br>
> Dept. Biology and Biotechnology "L. Spallanzani"<br>
> <br>
> University of Pavia<br>
> <br>
> Via Ferrata 9, 27100 Pavia<br>
> <br>
> Italy<br>
> <br>
> Tel. +39-0382-985525 <tel:%2B39-0382-985525>/985534<br>
> <br>
> Fax +39-0382-528496 <tel:%2B39-0382-528496><br>
> Web <a href="http://www.unipv.it/biocry" id="LPlnk374344" previewremoved="true">
www.unipv.it/biocry</a> <<a href="http://www.unipv.it/biocry" id="LPlnk456343" previewremoved="true">http://www.unipv.it/biocry</a>>_______________________________________________
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Website of the Structural Biology Groups at the University of Pavia. Research Investigators are Prof. Andrea Mattevi, Dr. Claudia Binda, and Dr. Federico Forneris</div>
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<a id="LPUrlAnchor_15850686020280.4437694676156676" href="http://www.unipv.it/biocry" target="_blank" style="text-decoration: none;">Structural Biology @ UniPV - index</a></div>
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Message: 3<br>
Date: Tue, 24 Mar 2020 07:35:10 +0100<br>
From: "Benedikt Moissl" <benedikt.moissl@biologie.uni-regensburg.de><br>
To: <chimera-bugs@cgl.ucsf.edu><br>
Subject: [Chimera-users] Problem with electrostatic surface<br>
Message-ID:<br>
<000301d601a6$5e2f85e0$1a8e91a0$@biologie.uni-regensburg.de><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Chimera team,<br>
<br>
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).<br>
<br>
Do you have any idea on how to fix this?<br>
<br>
Thank you very much in advance and keep up the great work!<br>
<br>
Benedikt Moissl<br>
____________________________________________________________<br>
<br>
Institute of Biochemistry, Genetics & Microbiology<br>
Department of Microbiology & Archaea Center<br>
Grohmann Lab ? Single-molecule Biochemistry (Homepage <<a href="https://www.uni-regensburg.de/biologie-vorklinische-medizin/mikrobiologie/index.html" id="LPlnk855170" previewremoved="true">https://www.uni-regensburg.de/biologie-vorklinische-medizin/mikrobiologie/index.html</a>>)<br>
<br>
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 <<a href="mailto:benedikt.moissl@ur.de">mailto:benedikt.moissl@ur.de</a>><br>
<br>
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