- Chimera-users - RBVI Mailing Lists

easy way to make alignments in chimera
by Michał Kadlof 13 Jun '14

13 Jun '14

Hello, I would like to ask if there is any quick way to make aligment (with secondary structure score included) beetwen two homologous protein structures, and save them in Stockholm format (information about missing residues is needed). I have houndreds of such pairs, and it would be very helpfull to do it by script for headless Chimera. -- yours sincerely Michael Kadlof University of Warsaw

2 3

Subclass chimera.Molecule
by Jaime Rodríguez-Guerra 13 Jun '14

13 Jun '14

Hello, I am trying to extend the chimera.Molecule class() to add a few methods and attributes, but the followin error arises: TypeError: Error when calling the metaclass bases type '_molecule.Molecule' is not an acceptable base type File "/home/jr/x/gaudi/gaudi/molecule.py", line 51, in <module> class Compound(chimera.Molecule): Is there any workaround? I want my Compound objects to behave like standard chimera Molecules (with all their attributes and stuff), and also be able to call custom methods on that Molecule. Thanks in advance, Jaime.

3 3

how can i register to use chimera
by carlos martinez 12 Jun '14

12 Jun '14

how can i register to use chimera program

2 1

python printing in x3d2collada.py
by Dougherty, Matthew T 11 Jun '14

11 Jun '14

I was delving into the chimera code and wanted to print some variables to better understand how the code works. When I use a print statement I do not see anything in the reply log or the IDLE window. here is an example for filename in args: print filename print >> sys.stdout, "FN: %s" % filename Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

2 2

Re: [Chimera-users] "ligand" category for selection
by Hurt, Darrell (NIH/NIAID) [E] 10 Jun '14

10 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.

3 7

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 >>>> >>> >> >

1 0

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 >>> >> >

1 0

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.

3 2

CASTp data
by Felipe Vasquez 09 Jun '14

09 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

2 1

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

2 3

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

2 2

Re: [Chimera-users] normalizing attributes through point mutant models
by Elaine Meng 05 Jun '14

05 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

1 0

warning: Ignored bad PDB record found on line
by Xiao-Bo Li 05 Jun '14

05 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

2 2

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

2 3

Setting the vertex density in a script
by Hurt, Darrell (NIH/NIAID) [E] 05 Jun '14

05 Jun '14

Hi Chimera friends, To save memory and reduce exported geometry sizes, I want to use a script to automatically scale the vertex density of generated molecular surfaces by the size of the molecule. Is there a way to grab the size (number of atoms?) of the loaded molecule(s) and use that with some simple math to set the vertex density value? I know this will reduce surface fidelity, but for very large molecules, the mesh size becomes unwieldy. On a separate, but related note, when loading a volumetric file like electron microscopy data, the "step" size in the Volume Viewer automatically adjusts (1, 2, 4, 8, 16) to optimize visual performance and memory. I'm using a script to import volumetric data and then "Export Scene…". For that export, I want to drop down the step to the next lowest step to get a smoother mesh. I can just set the step value to the minimum with something like "volume #0 step 1 limitVoxelCount false", but this risks maxing out the memory and crashing for very large data sets. Is there a way to use a script to get the current step value and then lower by one step for my export? 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.

2 5

Re: [Chimera-users] Missing cavities
by Eric Pettersen 05 Jun '14

05 Jun '14

On Jun 5, 2014, at 7:38 AM, sapeptides <sapeptides(a)gmail.com> wrote: > Hi Erik, > > I'm writing because I have noticed that in the new versions of chimera when I create a surface and then try to "cut" it (with the side view tool) to see inside the model I obtain this weird picture (attached), whereas in the old versions (how old I do not remember but I created a stunning images of various active sites) it was possible to check all the cavities inside the molecular structures. > I was wondering if you could suggest how to visualize pockets and clefts when the vdw or solvent accessible surface is present. > > Thanks a lot! > Susanna Hi Susanna, It's best to send questions like this to the chimera-users list rather than me directly so that others can benefit from the answer and since I may not actually be the best person to answer the question. For instance, I have no good ideas about showing cavities effectively with VDW or solvent-accessible surfaces and hope someone else can chime in there. As for the lack of cavities in your image, did Chimera issue a warning when it computed the surface saying that "[c]alculation of some surface components failed" and that "[a] single component of the surface was calculated"? If so, that means that calculation of interior cavities failed and Chimera is showing the exterior surface only (which the error message does say if you read it in its entirety). That would produce the lack of interior cavities you observed. If you didn't get such a message, can you supply the PDB ID for this structure (or PDB file) so I can investigate? Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

3 2

"ligand" category for selection
by Hurt, Darrell (NIH/NIAID) [E] 05 Jun '14

05 Jun '14

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.

2 2

Chimera display problem
by sea 03 Jun '14

03 Jun '14

Hi, I recently changed graphics card. This caused a problem to display image properly in Chimera (see attached screenshot). My new graphics card is MSI RADEON R7 240, chimera version 1.9. Does anyone encounter similar problem, or know how to fix it? Best regards Pu Qian

2 1

Asking Help: Academic User
by Robin Parmar 03 Jun '14

03 Jun '14

Hello, Warm Greetings! Thank you for Allowing me to use Chimera through academic license. Yesterday(June 2nd) I was prompted to update Chimera to 1.9 version. I accepted and installed it successfully on my system (windows7pro). Before that I had removed Chimera 1.8.8. The problem I face is, I can not open certain .pdb/.pdbqt fies saved in my comuter. such files even do not exhibit chimera logo which earlier version did. Even with "choose default program" system can not open these files insted other program (like spdbv) open them. I have not made any change in my system after installing new version. Can I reinstall earlier vrsion(1.8)? Kindly suggest me what best I should do to avail service (Academic Research) of chimera again. Regards. -Robin

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 134, Issue 4
by Boaz Shaanan 03 Jun '14

03 Jun '14

Thanks a lot Tom, This is wonderful. I'll try it as soon as it's on the site. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 Message: 7 Date: Tue, 3 Jun 2014 11:52:46 -0700 From: Tom Goddard <goddard(a)sonic.net> To: Boaz Shaanan <bshaanan(a)bgu.ac.il>, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh(a)niaid.nih.gov> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] About direct fetching biological assemblies into Chimera Message-ID: <2FF03268-945D-4B45-B2BE-1A7B17370069(a)sonic.net> Content-Type: text/plain; charset=windows-1252 Hi Darrell, Boaz, I made a few improvement to the fetching of PDB biological unit files that will be in tonight?s daily build. 1) Made fetching biounit give each assembly a separate top level model id number and separate color. Before all the assemblies were grouped together in Model Panel, and now each assembly is on a separate line in Model Panel. 2) Renamed biounit file type and prefix from pdbbuID to biounitID. So use Chimera command ?open biounitID:1hho?. 3) Allowed specifing a specific biounit by number using pdb id plus "." followed by number, eg. 3fad.2. This works in the Fetch by Id dialog and on the command-line. Also to fetch a few different biounits you can use 3xyz.1.3.8 with each . specifying another assembly number. Used "." instead of comma since commas separate multiple identifiers in the fetch dialog. Tom On Jun 3, 2014, at 5:52 AM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > Hi Tom, > > This is a nice addition but can you ALSO give the option of fetching just one of the biological assemblies? It is my experience that biological assemblies for a particular pdb entry consist of one correct assembly, in the sense of biological function corresponding to the description given by the depositors and other assemblies. I usually flip between the assemblies on the RCSB website before deciding which one to fetch. With your new addition this of course can all be done now in Chimera but if possible, I'd rather not waste time and disk space with meaningless assemblies. What do you think? > > Cheers, > > Boaz ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 134, Issue 4 *********************************************

1 0

<< creating MOL2 files with different SET records >>
by Hatuey Hack 03 Jun '14

03 Jun '14

Hello, I will like to know if it is possible with Chimera to create MOL2 files that include other MOL2 records like these: @<TRIPOS>SET ATOM$BY_TYPE STATIC ATOMS COLORGROUP SYSTEM 5 1 2 3 4 5 LINK_HS STATIC ATOMS <user> **** 4 2 3 4 5 @<TRIPOS>NORMAL @<TRIPOS>FF_PBC FORCE_FIELD_SETUP_FEATURE Force Field Setup information v1.0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 NONE 2 0 0 0 0 0 0 0 0 0 0 0 0 Best regards, Hatuey

2 1

Saving Sessions with surface data
by Arjun Dayal 03 Jun '14

03 Jun '14

Hi, I imported several .STL files into Chimera that I generated using TrakEM2. These import as individual surface objects in Chimera. I am then able to color the objects differently and generate some publication-quality screenshots. However, I am unable to save and restore the Chimera session. Upon trying to restore the session, I am presented with a blank screen. The program does not report any errors and even says "Done opening SESSION.py". It seems that the program never loaded the surface files. How does Chimera know where the surface files are located? I saw no mention of their location inside the session PY file. How can I save my session so that next time I open Chimera, all of my surfaces load with the colors, transparency, etc. that I assigned them in Chimera? -- Arjun Dayal Pritzker School of Medicine | Class of 2016 University of Chicago

2 1

rotamers, contacts, H-bonds
by Elaine Meng 03 Jun '14

03 Jun '14

Hello Maryam, This sounds like a chimera-users question (chimera-dev is more about programming), so I CC'd that address. You can use Distance measurements, Find Contacts/Clashes and/or FindHBond to look at the interactions of the residue. See menu under Tools.. Structure Analysis, and instructions: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findcla…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo…> For looking at rotamers of amino acids, both same type as native (no mutation) or different type (mutation) you could use the Rotamers tool (in menu under Tools… Structure Editing). The rotamers list also connects to finding contacts and Hbonds through its Columns menu, see "evaluation" in the Rotamers manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot…> For examples of measuring distances, identifying contacts and H-bonds, and using Rotamers, I recommend you try the "Structure Analysis and Comparison" tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 28, 2014, at 2:05 AM, "maryam.khoshnejat" <maryam.khoshnejat(a)modares.ac.ir> wrote: > hello > could you help me? > i should model specific mutant residue of protein . i have PDB file and rotamer of mutant residue > how can i find coordination of mutant residue based on backbone and CB coordination of native residue , rotamer and atom bonding distance > i need a code for finding coordination of mutant residue > regards

1 0

Fetch biological unit?
by Hurt, Darrell (NIH/NIAID) [E] 02 Jun '14

02 Jun '14

Hi Chimera friends, The PQS server still works well for downloading the biological unit, but (as noted) it doesn't have every structure in it. The PDB itself provides the biological unit(s) for download in their weird ".pdb1", ".pdb2", etc. format for every entry in the database (even if it is redundant). Is there a way to grab those files from the PDB itself using the Chimera interface? The repository is in: ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates 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.

3 4

Issue with Comparative Modeling Tutorial
by Janan Zhu 31 May '14

31 May '14

Hi, I'm new to Chimera and I've been trying to learn about the various features of the program through the tutorials. I've been having issues with the Comparative Modeling Tutorial from the User Guide (link here <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html>) - for some reason, when I try to get updated zDOPE scores after deleting the unaligned termini of the target sequence, the zDOPE scores fail to update, and I only get new RMSD and overlap values. If I try calculating the scores again, I get a message that all models already have scores assigned. I've tried this both with the tutorial structure and some of my own structures and I get the same result. Could anyone possibly provide any assistance with this? Thank you, Janan Zhu -- Janan Zhu Duke University '16

2 1