- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] "ligand" category for selection
by Hurt, Darrell (NIH/NIAID) [E] 11 Jun '14

11 Jun '14

I guess one way to do it might be to use a different specifier for ligands, like maybe: :/numAtoms<100 -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: <Hurt>, Darrell Hurt <darrellh(a)niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] "ligand" category for selection Hi Chimera friends, I'm trying to use the attached MOL file (dopamine) in Chimera and I want to run a Python script on it. My script does some things to the molecule using selection categories. I'm trying to select this molecule as "ligand", but I get a "No atoms specified" error. Alternatively, is there a way in Python to ignore the error if I get it and keep processing the rest of the script? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Fwd: STL Output
by Tom Goddard 10 Jun '14

10 Jun '14

Begin forwarded message: > From: Tom Goddard > Subject: Re: [Chimera-users] STL Output > Date: June 10, 2014 at 2:02:27 PM PDT > To: Eric Bell <Eric.Bell(a)oberlin.edu> > > Hi Eric, > > Chimera doesn’t represent molecules as polyhedrons. Are the orange octahedrons each representing one molecule? And what are the red spheres at the corners, with some red spheres out in space? And what are the little attached pink spheres? This kind of display would require a new Chimera plug-in. The graphics would be easy to do in Chimera. I don’t think such a model would hold together very well when printed in 3d. > > The Crystal Contacts tool in Chimera is remotely related, showing contacts between asymmetric units in a crystal > > https://www.cgl.ucsf.edu/chimera/experimental/crystal_contacts/clashes.html > > Tom > > > On Jun 10, 2014, at 1:50 PM, Eric Bell wrote: > >> Dear Tom, >> >> The polyhedral models look something like the attached image. Does chimera do anything like this or would I have to code a separate plugin? >> >> Thanks, >> Eric<polyhedra.jpg> >> On Jun 10, 2014, at 2:15 PM, Tom Goddard wrote: >> >>> Hi Eric, >>> >>> Not sure what kind of CrystalMaker polyhedral models you were thinking about printing. Chimera can show crystal unit cells. Here are 4 unit cells each containing 8 copies of a small protein (1a0m) shown with the Chimera Unit Cell tool (menu Tools / Higher Order Structure / Unit Cell) with the proteins shown as solvent excluded surfaces (menu Actions / Surface) and each unit cell colored differently (selected by hand with a mouse drag, then used menu Actions / Color). >>> >>> Tom >>> >>> <1a0m_2x2_unitcells.jpg> >>> >>> >>> On Jun 8, 2014, at 7:47 PM, Eric Bell wrote: >>> >>>> Dear Chimera Developers, >>>> >>>> My name is Eric Bell, and I am a student at Oberlin College. I have been using Chimera for 3d printing of molecular models because of its ability to handle many of the processes needed for atom editing as well as its ability to export in an .stl format. However, an issue I've run into is that the resolution of those .stl meshes is rather high, and there does not exist an option, to my knowledge, to alter the amount of vertices on the spheres. This causes an issue when we want to print spacefill models of large molecules, because Chimera will output such large files that our software isn't able to properly process the file without serious resource consumption. Is there anything that I as a user can alter to change the resolution of these spheres, or is it a setting that has been compiled so that I can't edit it without recompiling? I am familiar with python so navigating code would not be an issue for me if necessary. Thank you! >>>> >>>> Sincerely, >>>> Eric Bell >>>> >>>> P.S. Another thing we were looking for that has yet to be done is to print polyhedral models like those in programs such as CrystalMaker. As far as I know Chimera doesn't have this functionality but a programming environment called Bsoft is using the native save file format of chimera to do it because of its similarity to XML. >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

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Fwd: STL Output
by Tom Goddard 10 Jun '14

10 Jun '14

> From: Eric Bell > Subject: Re: [Chimera-users] STL Output > Date: June 10, 2014 at 1:50:49 PM PDT > To: Tom Goddard > > Dear Tom, > > The polyhedral models look something like the attached image. Does chimera do anything like this or would I have to code a separate plugin? > > Thanks, > Eric > On Jun 10, 2014, at 2:15 PM, Tom Goddard wrote: > >> Hi Eric, >> >> Not sure what kind of CrystalMaker polyhedral models you were thinking about printing. Chimera can show crystal unit cells. Here are 4 unit cells each containing 8 copies of a small protein (1a0m) shown with the Chimera Unit Cell tool (menu Tools / Higher Order Structure / Unit Cell) with the proteins shown as solvent excluded surfaces (menu Actions / Surface) and each unit cell colored differently (selected by hand with a mouse drag, then used menu Actions / Color). >> >> Tom >> >> <1a0m_2x2_unitcells.jpg> >> >> >> On Jun 8, 2014, at 7:47 PM, Eric Bell wrote: >> >>> Dear Chimera Developers, >>> >>> My name is Eric Bell, and I am a student at Oberlin College. I have been using Chimera for 3d printing of molecular models because of its ability to handle many of the processes needed for atom editing as well as its ability to export in an .stl format. However, an issue I've run into is that the resolution of those .stl meshes is rather high, and there does not exist an option, to my knowledge, to alter the amount of vertices on the spheres. This causes an issue when we want to print spacefill models of large molecules, because Chimera will output such large files that our software isn't able to properly process the file without serious resource consumption. Is there anything that I as a user can alter to change the resolution of these spheres, or is it a setting that has been compiled so that I can't edit it without recompiling? I am familiar with python so navigating code would not be an issue for me if necessary. Thank you! >>> >>> Sincerely, >>> Eric Bell >>> >>> P.S. Another thing we were looking for that has yet to be done is to print polyhedral models like those in programs such as CrystalMaker. As far as I know Chimera doesn't have this functionality but a programming environment called Bsoft is using the native save file format of chimera to do it because of its similarity to XML. >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >

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STL Output
by Eric Bell 10 Jun '14

10 Jun '14

Dear Chimera Developers, My name is Eric Bell, and I am a student at Oberlin College. I have been using Chimera for 3d printing of molecular models because of its ability to handle many of the processes needed for atom editing as well as its ability to export in an .stl format. However, an issue I've run into is that the resolution of those .stl meshes is rather high, and there does not exist an option, to my knowledge, to alter the amount of vertices on the spheres. This causes an issue when we want to print spacefill models of large molecules, because Chimera will output such large files that our software isn't able to properly process the file without serious resource consumption. Is there anything that I as a user can alter to change the resolution of these spheres, or is it a setting that has been compiled so that I can't edit it without recompiling? I am familiar with python so navigating code would not be an issue for me if necessary. Thank you! Sincerely, Eric Bell P.S. Another thing we were looking for that has yet to be done is to print polyhedral models like those in programs such as CrystalMaker. As far as I know Chimera doesn't have this functionality but a programming environment called Bsoft is using the native save file format of chimera to do it because of its similarity to XML.

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CASTp data
by Felipe Vasquez 10 Jun '14

10 Jun '14

Hi, I am currently trying to identify certain features from a particular binding cavity, and I decided to use CASTp plugin from Chimera. However, I realized that the data obtained directly from CASTp online server are not the same that those obtained by CASTp from Chimera. Examples include not only the number of pockets, but also the volume and surface area of them. What is the meaning of this confusing results? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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electrostatic potential based on Swiss-Model
by Jingga Inlora 06 Jun '14

06 Jun '14

Hello, I am a graduate student at the University of Michigan and I am currently trying to obtain images of my proteins with electrostatic potentials for my manuscript. For one of my proteins, there is no solved protein structure (by X-ray crystallography or NMR) and I had to use SWISS-MODEL to predict the structure. I did electrostatic potential calculation using DelPhi but when I visualized it using Chimera, the electrostatic distribution is not what I expected. I did notice the electrostatic potential calculations for other previously solved protein structures took much longer and resulted in bigger files, whereas the SWISS-MODEL-predicted protein contains much smaller .phi file size. I was wondering if you have any idea how accurate it is to calculate the electrostatic potential based on a SWISS-MODEL predicted protein structure, and if there are ways to improve the reliability of the calculated electrostatic potentials for that protein? Thank you very much for your help! Sincerely, Jingga Inlora

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undo
by Antón Vila Sanjurjo 06 Jun '14

06 Jun '14

Hello, I am working with chimera sessions involving a large numer of 70S ribosomes. I keep modifying the sessions over and over, so I save new sessions every day. Much of what I do is labeling interesting residues, measuring distances, coloring these residues, etc. Sometimes I make a mistake, like accidentally selecting and modifying a large portion of the model, and I loose an important amount of information. In these cases, I find that there is no way to go back to the previous state of the system, other than clossing the session and re-opening the latest saved one. Unfortunately, this means loosing a lot of unsaved work. While there is an "undo" option under the "select" tab, it does not really allow one to return to the previous state of the system. In fact, I'm not even sure of what it does. My question is, is there a way to return Chimera to the state ocurring immediately before the last action? In case this does not exist, can it be implemented? best, Antón -- Antón Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Química Fundamental Facultade de Ciencias Universidade de A Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s(a)gmail.com

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Re: [Chimera-users] normalizing attributes through point mutant models
by Elaine Meng 06 Jun '14

06 Jun '14

Hello Ruben, If you were asking how to get consistent coloring for the atomic "overlap" attribute for the different complexes: Just make sure to use the same color for the same overlap value. For example, if you color the first complex with yellow for 0.5 overlap and red for 1.0 overlap, make sure to color the other complexes with yellow for 0.5 overlap and red for 1.0 overlap. You can control which color goes with which value in the Render by Attribute tool, as mentioned in the earlier reply: > in the Render by Attribute tool: you can move the colored bars on the histogram directly with the mouse or by typing in values, change the colors of the bars, etc. as explained here: > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm…> ... or if you use the "rangecolor" command, you specify which color goes with which value directly in the command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> Otherwise, I don't know what you are asking. If I haven't already answered your question, you would need to say more about which Chimera tool you are using to study these interfaces, what values you are trying to display (number of clashes? atomic overlap values?), how you are displaying them (with color? with lines?) and exactly what you mean by weighting or normalizing (are you trying to divide the values by some other values?). Since I already described all the related features I can think of, however, there probably isn't a Chimera tool that does exactly what you wanted. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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warning: Ignored bad PDB record found on line
by Xiao-Bo Li 06 Jun '14

06 Jun '14

Hello, This morning I kept getting this error "warning: Ignored bad PDB record found on line nnn" whenever I use the python script to try to open a pdb file. The python script I'm using is the usual "chimera.openModels.open(pdbID, type='PDB')[0]". This function call is how I've always been using Chimera, and this morning is the first time I'm getting this issue. I dont see a problem with my internet connection, and I can open the PDB file using File->Fetch by ID, so it doesn't seem like the pdb file has any problems. Only the python script gives me problems. Is anyone else experiencing this problem? Best, XBL

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normalizing attributes through point mutant models
by Rubén Marrero Diaz De Villegas 05 Jun '14

05 Jun '14

Hello I´m working with one antigen/antibody complexes and different point mutations at the interface. I can calculate and draw at the surface attributes like atomic clashes "overlap", but what I don´t know, is how to normalize the calculation output for 2 complexes, neither render such "normalized" attributes in the models. I have tried at Render attribute tool, the option "create corresponding color key", introducing specific clashes boundaries and their coloring values but there is no "apply" button, such the changes doesn't goes to the model. Any help or tip? Thanks in advance Ruben

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