- Chimera-users - RBVI Mailing Lists

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

surface ESP in chimera
by sbasu＠ffame.org 30 May '14

30 May '14

Dear Chimera group, Could you please help us resolving the following issues ? 1. Is there a way to load a pre-computed solvent accessible surface (i.e., coordinates of dot surface points stored in a PDB format against source atom types) on top of a protein molecule ? [kindly see the attached example file] 2. Is there a way to print / write the actual dot surface points generated by Chimera into a file (preferably in a PDB format with the source atom records) ? 3. Is there a way to actually compute the electrostatic potentials (ESP) on the solvent accessible surface by chimera using a Delphi interface ? In that case, how can one set the delphi parameters (e.g., partial charges / atomic radii / percentage grid fills / boundary conditions) according to his likings ? 4. We have computed ESP on solvent accessible surface (MS - connolly) using a standalone version of delphi. When we load the phimap.phi onto the chimera-generated surface to obtain the ESP-colored surface map, we find ambiguities between the surface coloring and the actual values of the potentials (almost the entire surface is showing red / white whereas there are obviously positive patches from the actual numbers) ! We suspect that it is due to the inconsistency between two surfaces. Lastly, 5. A trivial question is how to select residue(s) by residue sequence number (e.g., 108 or 108-VAL) from the select drop-down list ? We do not seem to find that option. thanks and regards, Sankar Basu Post Doctoral Fellow Foundation for Applied Molecular Evolution Gainesville, FL 32601

2 2

Saving an EM map to open at a specific Threshold
by Kevin Huynh 30 May '14

30 May '14

Hello, I have finished processing my cryo-EM map and have set the desired volume to threshold=1 with EMAN2; however, I cannot seem to figure out how to save the map in mrc format so that I can open the map at threshold 1. I am wondering if Chimera can save the map in mrc format so that I can open it at threshold 1? If yes, how can this be done? Thanks, Kevin

2 1

merging 2 pdb files
by Adrian Javaherian 30 May '14

30 May '14

Hi, My name is Adrian. I am a graduate student at Bar Ilan University in Israel. I have 2 pdb files, each containing rRNA sequences and I would like to combine the 2 to make 1 pdb file displaying all of the rRNA subunits. I download the Chimera program. Is it possible to do this on your program and if so, can you please tell me how? Thank you so much, Adrian

2 1

Electron density maps
by lecan 30 May '14

30 May '14

Hello Chimera's users, I would like to know if there are a way to see density maps from .mtz files with chimera. I have tried opening a .mtz file after opening a .pdb file, but I got the next error message after choose CCP4 density map in the Type Selection window: Error reading file abc.mtz format ccp4 File size 631624 too small for grid size (1297373728,929300992,1145110528) and 64 bytes of symmetry operators Does anyone could telling me if what I'm trying to do is possible and what is the way to do it? Thank you for your help, Luis L.

3 2

part-time job for Chimera professionals
by Andrew Voronkov 30 May '14

30 May '14

Dear Chimera users, if anyone may be interested in part-time job and additional income through Chimera usage, please let me know. I am looking for someone, who can regularly make nice-looking Chimera pictures. It can be 2-3 hours per week for example. Best regards, Andrew

1 0

Save to a file
by sette＠uniroma2.it 29 May '14

29 May '14

Dear all, I created a simple text file with a list of distances to be measured How to save in a file the measured distances? The saveFile options does not seems to be the solution. I use 1.7 version of Chimera on Windows 7. Thanks, Marco ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

2 5

merging 2 pdb files
by Adrian Javaherian 28 May '14

28 May '14

Hi, My name is Adrian. I am a graduate student at Bar Ilan University in Israel. I have 2 pdb files, each containing rRNA sequences and I would like to combine the 2 to make 1 pdb file displaying all of the rRNA subunits. I download the Chimera program. Is it possible to do this on your program and if so, can you please tell me how? Thank you so much, Adrian

3 3

mmCIF support
by Greg Couch 28 May '14

28 May '14

Hello, I'm working on improving Chimera's mmCIF support. So if anyone has a mmCIF file that is not from the PDB and that they are willing to share, please send it to me. Many thanks, Greg

2 1

domain colouring
by ce 28 May '14

28 May '14

Hi, Could You send me instruction about domain colouring (the quickest way if possible) ? Cheers, J.

2 5

After fitting a PDB into a cryo-EM density, is it possible to color the PDB atoms by the local EM density in the cryo-EM map?
by Lai, Jonathan 27 May '14

27 May '14

Dear Chimera-users, I have several cryo-EM maps of an assembly process and a PDB of the final product; what I want to do is to have a visual depiction of how the local EM density around structural elements in the final product changes over time. After fitting the PDB into the cryo-EM density, I am wondering if it is possible to color the PDB atoms by a reference EM density at each point. For example, I want to color every residue that intersects isosurface == 0 blue, every residue that intersects isosurface == 1 red, and have a continuous color scheme for all intermediate values from (0 to 1). I already have fitted the PDBs into the cryo-EM maps. Is there any easy way to do this? Cheers, Jonathan Lai University of Illinois at Urbana-Champaign

3 2

problem in picking
by Uzma Saqib 27 May '14

27 May '14

Hi , I am not able to pick atoms in Chimera from the graphics window (*picking*). pls help. FYI, snapshot attached. thanks

2 1