- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [EXT] Re: Problem with electrostatic surface
by Benedikt Moissl 26 Mar '20

26 Mar '20

Hi Elaine, thank you a lot for your fast response! Your suggestion helped and my problem is solved :-) Best regards Benedikt -----Ursprüngliche Nachricht----- Von: Elaine Meng <meng(a)cgl.ucsf.edu> Gesendet: Dienstag, 24. März 2020 18:27 An: Benedikt Moissl <benedikt.moissl(a)biologie.uni-regensburg.de> Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> Betreff: [EXT] Re: [Chimera-users] Problem with electrostatic surface Hi Benedikt, You still need to show the surface of your molecule, e.g. with command "surface #0 & protein" (or "surface #1 & protein" since they are the same atomic coordinates). After you do that, it will be listed in the menu of choices of what surface to color in the Surface Color dialog. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 23, 2020, at 11:35 PM, Benedikt Moissl <benedikt.moissl(a)biologie.uni-regensburg.de> wrote: > > 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

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Re: [Chimera-users] cobalt in Chimera
by Elaine Meng 25 Mar '20

25 Mar '20

On Mar 24, 2020, at 8:02 PM, Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> wrote: > Hi, Elaine, > I am trying to minimize an edited structure, Tools -> Structure Editing -> Minimize Structure --- using all default parameters, however, the cofactor B12 has a cobalt atom and that gives me an error message “Failure running ANTECHAMBER for residue B12[non-Co]. May I ask how to solve this problem? > Thank you. > Best regards, > Sc ke Hi Sc ke, It is not the cobalt ion causing the problem. That message says that ANTECHAMBER charge calculation failed on the non-Co part of residue B12, which means all the rest of the atoms besides Co, which is handled separately. That residue is large and complex and has a phosphate, all factors that are more likely to cause a failure of the AM1-BCC charge calculation method. You may have to use the simpler charge calculation method "Gasteiger" as specified in the Add Charge dialog. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addchar…> (For next time, to ensure you get an answer please send Chimera questions to chimera-users(a)cgl.ucsf.edu, CC-d here, rather than my individual address.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Problem with electrostatic surface
by Benedikt Moissl 24 Mar '20

24 Mar '20

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/i…>) University of Regensburg | Universitätsstraße 31 | D-93053 Regensburg | Room: WN_E3._2.323 | Phone: +49 941 943 3184 | Fax: +49 941 943 2403 | Mail: benedikt.moissl(a)ur.de <mailto:benedikt.moissl@ur.de>

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3. Problem with electrostatic surface (Benedikt Moissl)
by Boaz Shaanan 24 Mar '20

24 Mar '20

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problems in opening PDB file
by Laura Rotilio 24 Mar '20

24 Mar '20

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. +39-0382-985525/985534 Fax +39-0382-528496 Web www.unipv.it/biocry

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automating a task
by Dieter Blaas 24 Mar '20

24 Mar '20

Dear Elaine and all, I need to run the following repeatedly on five loaded volumes (x1.mrc, x2.mrc, x3.mrc, x4.mrc, and x5.mrc) each time with a different x: Tools > Volume Data > Surface Color > Color Surface x1.mrc by volume data gradient norm volume file x1.mrc > options set > color The colors and palette settings remain the same for all runs. Is there a way of automating this with a script? I have tried to save the session, change all occurrences of x for the different x but on evoking the modified python script all volumes are shown in the correct arrangement and level but not coloured and I get the Chimera Warning: Could not restore surface color on surface model with id 0.0 because volume used in colouring was not restored Thank you very much, stay healthy! Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Unstructured residues disappear from sequence after save and reopen
by Rob Blakemore 23 Mar '20

23 Mar '20

Hi, I'm encountering a problem wherein unstructured residues are present in the sequence the first time I fetch it from PDB, but are omitted after I save the file locally and reopen it. Has anyone else encountered this and would you happen to know a workaround? Details I'm running Chimera 1.14 (build 42094) on MacOS Mojave V10.14.6 I'm using 6VXX as the PDB file. When I fetch a structure by ID: (PDB mmCIF) and open a sequence (Tools --> Sequence --> Sequence), it shows me a complete sequence containing both residues present in the structure, as well as unresolved/unstructured residues. The unresolved residues are outlined by a red border. However, if I save this session to a file or save the structure to PDB and then reopen it; if I then open the sequence, it only shows me the sequence of residues present in the structure, and omits all of the unresolved / unstructured residues. (All the red outlined residues are now gone) Is there any way to preserve the unstructured residues when saving these files? Thank you, Rob Blakemore robert.blakemore(a)tufts.edu

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mailing list glitch
by Greg Couch 19 Mar '20

19 Mar '20

FYI, if you tried to send email to chimera-users(a)cgl.ucsf.edu in the last 6 hours and it was rejected, try again. It should be fixed now.

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Re: [Chimera-users] [EXT] Re: spheres chimera
by Elaine Meng 19 Mar '20

19 Mar '20

> On Mar 19, 2020, at 8:46 AM, Galotto, Giulia <ggalotto(a)wpi.edu> wrote: > > Elaine, > I tried emailing the address you gave me and it gives me an error, it says that email does not exists. > I am sorry to bother you again, I would be happy to email the right address next time 🙂 > > In the mean time I will write here the problem I was having, feel free to forward it to the chimera address: > > I clip the protein I am trying to visualize and I can actually see it sliced. > When I write conic in the command line it creates a file not clipped of my protein, it basically recreates the original image unclipped. > I tried from both mac and pc. Do you have any idea why that might be? > > Thank you so much for being so responsive to these emails! This is very helpful. The email address chimera-users(a)cgl.ucsf.edu definitely exists. I cc'd it on this message and on the previous message. It may say that you have to wait for the moderator to approve your message, but that usually happens in a day or two. This is the best way to ensure you get an answer. I cannot reproduce this problem. When I clip the protein shown as spheres, for example using the Side View tool, the conic result shows the same clipping except with solid spheres. See attached screenshot. Elaine > > > From: Galotto, Giulia <ggalotto(a)wpi.edu> > Sent: Thursday, March 19, 2020 11:41 AM > To: Chimera <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [EXT] Re: spheres chimera > > Hi all, > I have a question about the conic function. > I clip the protein I am trying to visualize and I can actually see it sliced. > When I write conic in the command line it creates a file not clipped of my protein, it basically recreates the original image unclipped. > I tried from both mac and pc. Do you have any idea why that might be? > > Thank you so much for being so responsive to these emails! This is very helpful. > > Best, > Giulia > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Wednesday, March 18, 2020 6:39 PM > To: Galotto, Giulia <ggalotto(a)wpi.edu> > Cc: Chimera <chimera-users(a)cgl.ucsf.edu> > Subject: [EXT] Re: spheres chimera > > Hi Giulia, > (For next time), please send questions to chimera-users(a)cgl.ucsf.edu instead of me individually. I CC'd that address here. > > There is no option like that for the interactive spheres display, sorry. It is only available for molecular surfaces. > > However, for a non-movable display that is like that, you can try using the "conic" command for rendering to show spheres as solid when they are clipped. You have to first move the structure, then use conic; for example, a Chimera command that works for me on a Mac is: > > conic -o ~/Desktop/myfile.png -s > > ... which will then draw a non-movable image of the current position and create the specified output file. There are other options to this command, see these pages for details: > <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> > <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Mar 18, 2020, at 3:03 PM, Galotto, Giulia <ggalotto(a)wpi.edu> wrote: > > > > Hi, > > I am writing to ask a question about a chimera representation. I am representing the protein as VDW spheres, but I would like the spheres to be filled, not hollow. This is because I am going to do per model clipping and slice the protein in two. When I slice it I see the empty spheres, and I would like the see them filled instead. > > Is there a way to do this? > > Thank you so much! > > Best, > > Giulia Galotto > > Worcester Polytechnic Institute

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Re: [Chimera-users] spheres chimera
by Elaine Meng 18 Mar '20

18 Mar '20

Hi Giulia, (For next time), please send questions to chimera-users(a)cgl.ucsf.edu instead of me individually. I CC'd that address here. There is no option like that for the interactive spheres display, sorry. It is only available for molecular surfaces. However, for a non-movable display that is like that, you can try using the "conic" command for rendering to show spheres as solid when they are clipped. You have to first move the structure, then use conic; for example, a Chimera command that works for me on a Mac is: conic -o ~/Desktop/myfile.png -s ... which will then draw a non-movable image of the current position and create the specified output file. There are other options to this command, see these pages for details: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/conic.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/conic1.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 18, 2020, at 3:03 PM, Galotto, Giulia <ggalotto(a)wpi.edu> wrote: > > Hi, > I am writing to ask a question about a chimera representation. I am representing the protein as VDW spheres, but I would like the spheres to be filled, not hollow. This is because I am going to do per model clipping and slice the protein in two. When I slice it I see the empty spheres, and I would like the see them filled instead. > Is there a way to do this? > Thank you so much! > Best, > Giulia Galotto > Worcester Polytechnic Institute

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