- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Just starting out
by burt.goldberg＠gmail.com 03 Jun '13

03 Jun '13

Dear Elaine, it is very hard for Senior faculty to audit a class. As for the Biochemistry well I have been teaching it for several decades. My interest is to learn how to use Chimera better and I will be working with a post doc experienced in using Chimera. I just want to read so I can ask intelligent questions. I am employing this in an on going research project. Thank you again for you help. ------Original Message------ From: Elaine Meng To: burt.goldberg(a)gmail.com Cc: chimera-users(a)cgl.ucsf.edu List ReplyTo: chimera-users(a)cgl.ucsf.edu List Subject: Re: [Chimera-users] Just starting out Sent: Jun 1, 2013 12:53 PM Hi Burt, This forum is meant for questions about the Chimera program. Proteomics and informatics are vastly broader areas. You might want to look for recent textbooks and journal articles on those topics, and/or audit some classes, and/or attend the group meetings and seminars of academic researchers in those areas. It's not clear whether learning Chimera should be one of your goals at this point. Which tools and programs are needed depend on the research problem at hand, and the types of data that are available for tackling that problem. If you do want to learn how to use Chimera, there are indeed several step-by-step tutorials. Before doing any tutorials you can explore the website just to get a better sense of what the program is for: <http://www.cgl.ucsf.edu/chimera/index.html> The "Quick Links" section on that page includes tutorials. Best, 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 Jun 1, 2013, at 9:34 AM, burt.goldberg(a)gmail.com wrote: > Dear all, after 40+ years doing wet work I had to leave the bench, medical reasons, and so although my students continue doing work at the bench I have decide to go the route of proteimics and informatic for myself. The informatics is fine. How do I get started on the proteimics? Does the tutorial help? Any thing some one can suggest I read first? Thank, Burt > Sent via BlackBerry from T-Mobile Sent via BlackBerry from T-Mobile

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How to calculate the deviation of two ligands in the same pocket
by felipe vasquez 03 Jun '13

03 Jun '13

Hi, I am working on the modeling of one ligand in a native and mutant receptor. The ligand occupies different positions in the binding cavity, and I am interested in estimate this difference. However, if RMSD is calculated via MatchMaker, the ligand in mutant receptor (non-reference) is moved from its original position to try to minimize the deviation compared to ligand in native receptor (reference). How can I calculate the difference in the ligand position between the two receptors, in an appropriate manner? Best regards, * * *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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How to force Chimera to properly analyze and visualize in each MD movie frame the ribon representation of the protein structure ?
by Marek Maly 01 Jun '13

01 Jun '13

Dear all, I just found that if one loads several frames from the simulation (Amber prmtop + inpcrd, *.rst files) chimera calculate/set the character of ribons (random colil, beta sheet, alpha helix) just using the first loaded frame and even if structure of the protein is changing in the next frames (e.g. forming beta sheet structure from the originally random coil), the visual ribon representation is not changed. I found this, when I loaded just the isolated frame from the simulation and saw nice forming of the local beta sheet which was nicely highlighted by proper ribon representation (wide arrow) in the palce where was originally (in the initial frame) just random coil. But when I loaded both (initial frame and that after some MD simulation), chimera keep to use random coil representation for both frames. I did also reverse experiment i.e. first loaded later frame from MD simulation and then the initial frame and this time chimera fixed for both frames beta sheet representation in that protein area. Please is there any possibility to prevent such unwanted behavior and to force Chimera that analyses properly protein configuration at each loaded frame and eventually changes properly the ribon representation ? Thank you in advance for any useful advices ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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fetching EDS files from the web (python script)
by Laleh 31 May '13

31 May '13

Hello. I'm wondering how I can fetch a bunch of EDS files (from the EDS server) and save them in my local machine in .mrc format. I don't want to do this manually one by one from the user interface... I tried to use open_volume_file with different settings; but it is not working... I'm surprised because this is very starightforward with pdb files. I appreciate your help. Thanks in Advance, Laleh

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castP, Chimera and atom numbers
by Boaz Shaanan 29 May '13

29 May '13

Hi, Apparently Chimera insists on consecutive serial atom numbers (the first column after ATOM in the pdb file) when it reads in castp files. If that's not the case (as most often happens when hydrogens are attached during the refinement run but are not written out to the final pdb) Chimera complains about incompatibility between the mouth file and coordinates and refuses to read in the castp files. This is my first encounter with a program that cares about the atom number column but I learnt it the hard way. Cheers, 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

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Tube representation picture of the eigenvector
by Prasanna Venkatesh 29 May '13

29 May '13

Dear Chimera users and supporters, I would like to generate a tube representation picture similar to one in the article (Figure 5 in "MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation"). Through Gromacs, I have average.pdb and extreme.pdb of my protein for the MD simulations. Please help me by providing the steps to make the picture. I asked the question earlier but not getting the similar picture with the answer provided. I don't know I asked it right the last time. Thank you in advance. Regards, Prasanna.

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How to deselect a subset of atoms in a non-standard residue
by felipe vasquez 28 May '13

28 May '13

Hi, I am trying to select all hydrogens atoms in a protein structure to achieve an energy minimization process. However, I would like to discard of the selection the hydrogen atoms of a non-standard residue (in my case a cofactor, NADPH). How can I deselect only this subset of hydrogen atoms of the whole hydrogens selection? Best regards, *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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How to delete range of solvent molecules
by felipe vasquez 22 May '13

22 May '13

Hi, I am trying to prepare a protein structure for docking, and I want to keep just one or a couple of water molecules. How can I do achieve this goal, deleting the rest of solvent molecules? Thanks in advance. Best regards, * * * * *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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Distance measuring
by T-I 22 May '13

22 May '13

Dear Chimera, I want to know something very simple which is making my life very difficult at the moment. I have an EM map of a virus capsid and I would like to make various distance measurements. I simply want to draw a strait line and measure it or place two points on the map and measure the distance between them. I have read all your help files on this matter and I cannot make any sense out of the instructions Can you help me out ? Thankyou Mr A.I

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Fitmap in batch mode
by ingvar 22 May '13

22 May '13

Hello, I am trying to run fitmap on a set of volumes on a server without a display. I would like to collect the results of the top hits to store in a database – correlation coefficients, inclusion scores, and the transforms. The only way I found to collect the fitting results is to save the session after displaying the listFits dialog. The listFits dialog cannot be displayed when running Chimera in –nogui mode, otherwise this would have been a solution. I tried to use a virtual display, with Xvfb. I have used Xvfb with some java applications in the past. When I use Xvfb with Chimera, it appears that Chimera do not want to start up properly, the process just hangs, i.e. no cpu usage. Is there a way around this, or am I asking for an enhancement, e.g. a “writeListFile toFile” option. I am on RHEL 6.2/6.3 if that matter. Noticed that there is a local correlation option in the pipeline for Chimera 1.8, looking forward to try it out. Kind Regards, Ingvar Typical python script: from chimera import runCommand as rc rc("open emd_5500.map") rc("volume #0 level 1.34 transparency 0.5") rc("open emd_2017.map") rc("volume #1 level 0.58 transparency 0.5") rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2 listFits false") #rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2") rc("save session5500_2017") rc("stop now") Setup to run with Xvfb (in bash): i=0 while [ -f /tmp/.X$i-lock ] do i=$[$i+1] done Xvfb :$i & pid=$! export DISPLAY=:$i chimera fit5500_2017.py kill $pid

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Pipes and planks representation
by Ernesto Arias Palomo 21 May '13

21 May '13

Dear chimera developers, I have noticed that in the last Chimera releases you have significantly improved the 'pipes and planks' representation. I find it particularly useful because, in my opinion, it makes the structures look simpler and clearer, especially when you are displaying large PDBs. I would like to suggest an improvement. It would be really useful if you could make that representation an attribute of the structure (like the 'ribbons' one) instead of a separate object. That way one could easily show, hide or color different regions of the structure without having to modify the actual PDB file. Thank you very much for your help, and congratulations for your great work. Cheers, Ernesto.

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Re: [Chimera-users] RMSD i.b and RMSD u.b
by Elaine Meng 20 May '13

20 May '13

Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of just my address. The RMSD lb (lower bound) and RMSD ub (upper bound) of a docked ligand are calculated by AutoDock Vina and are described in the manual for that program: <http://vina.scripps.edu/manual.html> (go to that page and search for "RMSD") I believe they just indicate how similar each position is to the best-scoring position found. I hope this helps, 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 20, 2013, at 6:10 AM, Muhammad ALi <muh.ali741(a)yahoo.com> wrote: > AOA > > sir > when I check my result with ViewDock their are two RMSD values i.e RMSD i.b and RMSD u.b plz tell me about them.....

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3D Printing our protein
by Bart Janssen 19 May '13

19 May '13

Hi My apologies for what are likely to be stupid questions. We are plant developmental biologists and we just obtained our first X-ray crystal structure for a new hormone receptor in plants. We'd really like to make a 3D model of the protein using one of the 3D printers at our institute. I've been trying to use and understand Chimera for the last week and I'm a bit out of my depth :). I can import our protein 4DNP.pdb and display it using solid surface or using the sphere representations of atoms. I can also display it with the "lid" domain hidden and vice versa. My problem has been getting files that our 3D printer can read. The solid surface model of the whole protein can be exported as a scene in .stl format and that can be printed just fine. Although I can't figure out how to adjust resolution or the smoothness of the exported file. But I'd really like to print the two domains of the protein separately. If I use Solid surface model with the lid hidden what I get is an eggshell like model which has no internal detail. If I use atoms shown as spheres instead I get the internal detail I want BUT when I try and export the scene I get a 2 Gb+ file that is unreadable by the printer. If I export .obj format instead the colleague who runs the printer says the file won't load and appears to have errors. I have a horrible feeling I am going about this entirely the wrong way but I can't find a tutorial that describes what I'm trying to achieve. I do realise chimera is not really written for the somewhat trivial use that I am attempting but it really would be helpful if we had a physical model of the protein to look at. Is there a tutorial I should follow or another part of Chimera (or another program) that I should be using instead? Any advice would be much appreciated. Cheers Bart Bart Janssen Scientist Plant Development team Breeding and genomics Plant and Food Research Private Bag 92169 Auckland 1142 New Zealand Ph +64 09 9257179 bart.janssen(a)plantandfood.co.nz The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.

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showing salt bridges in pdb trajectory movie
by Albert Lyons 18 May '13

18 May '13

Hi all, I am having a problem trying to show salt bridges between selected atoms in a movie of my pdb format trajectory. I am using the following commands in the Per-Frame script, to display H-bonds between the residues but with a less strong distance criterion (to bring the distance of interaction to 6 A) and angle criterion (to make the angle 0deg and so make all angles available): select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 When I apply this script I get a Chimera error saying: Error while sourcing select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 ,line 1: "findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145" Non-alphanumeric character in keyword ':6@2HH2,2HH1,HE,2HH1,1HH1' I have tried tweaking it different ways but just get other error messages, I can't seem to write it in the correct format. Can anyone see a problem with this script and how I might fix it? Cheers Albie

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showing salt bridges in pdb trajectory movie
by Albert Lyons 18 May '13

18 May '13

Hi all, I am having a problem trying to show salt bridges between selected atoms in a movie of my pdb format trajectory. I am using the following commands in the Per-Frame script, to display H-bonds between the residues but with a less strong distance criterion (to bring the distance of interaction to 6 A) and angle criterion (to make the angle 0deg and so make all angles available): select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 When I apply this script I get a Chimera error saying: Error while sourcing select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 ,line 1: "findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145" Non-alphanumeric character in keyword ':6@2HH2,2HH1,HE,2HH1,1HH1' I have tried tweaking it different ways but just get other error messages, I can't seem to write it in the correct format. Can anyone see a problem with this script and how I might fix it? Cheers Albie

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Re: [Chimera-users] Conserved amino acids
by Rebecca Swett 17 May '13

17 May '13

Use match-> align to get a structural superposition and sequence alignment, then set your alignment type to AL2CO. Go to render by attribute and then hit the select by attribute tab. Select the range from 0-whatever your maximum is. Should be around 4 if you've got any conserved tryptophans. That will select all invariant residues. Jean-Paul Boissel <boissel(a)uni-mainz.de> wrote: >Hi, > >By homology modelling, I got putative structures for five closely related >amino acid transporters. Is there any script that will allow the quick >selection and visualisation of the invariant residues on the structures? >Thanks, > >Jean-Paul > > > > > >_______________________________________________ >Chimera-users mailing list >Chimera-users(a)cgl.ucsf.edu >http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Conserved amino acids
by Jean-Paul Boissel 17 May '13

17 May '13

Hi, By homology modelling, I got putative structures for five closely related amino acid transporters. Is there any script that will allow the quick selection and visualisation of the invariant residues on the structures? Thanks, Jean-Paul

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Carbon color of 1 chain
by Markus Heller 16 May '13

16 May '13

Hello, I don't seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains. I can't figure out how to get an expression like "color green, chain C C" Or something like that ... How to go about this? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:kessabar@cdrd.ca> | www.cdrd.ca

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Re: [Chimera-users] energy optimization of the modle from homology modeling
by Elaine Meng 16 May '13

16 May '13

Hello, I agree with what Tom Goddard said: "How to make a suitable homology model for docking and what force fields to use are not questions specific to Chimera, they are questions about how to do good quality science, and they depend a great deal on the details of your system. So you aren't likely to get the answers you want on this list." Instead, you have to use your scientific judgement and your knowledge of this protein, how similar it is to the template protein, etc. The procheck statistics are only one thing to consider. One reason is that they are for the whole protein, whereas you mostly care about the binding site. Another is that they focus on stereochemical quality, mainly torsion angles, but not other descriptors such as whether the protein is well packed. You could see what others have done in published papers, and/or ask on the Computational Chemistry List (see <http://ccl.net/cgi-bin/ccl/send_ccl_message>) and the Modeller discussion forum (see <http://salilab.org/modeller/discussion_forum.html>) if it is recommended to minimize homology-modeled structures before docking. In complicated structures like proteins, atoms may "feel" multiple conflicting forces, and minimization will usually relieve some strains (for example, move atoms apart if they are too close together) but increase others (for example, distort the angles of the sidechains containing those atoms). That is why the statistics from procheck got worse. It is important to realize that minimization has very little ability to fix a complicated structure with a rugged energy landscape. It is good for cleaning up small molecules, and sometimes for cleaning up a localized area (leaving the rest of the protein unchanged) where you have made some change such as manually rotating some bonds or mutating a residue. It will not predict any significant conformational change to find the global optimum. If you don't have any specific reason to minimize the structure, it might be better not to minimize it. That is only my guess, and you could probably get more expert opinions by asking your question on the other discussion lists mentioned above. If your docking doesn't take too long, you could try docking to more than conformation of the protein (more than one model). Chimera does not do molecular dynamics, although it can show MD results from other programs. However, Modeller itself does sampling to generate multiple models. Also, you could consider using Modeller to further refine parts of the model(s) from the first Modeller calculation. The Modeller scores should provide some indication of which models and refinements are better. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> I hope this helps, 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 14, 2013, at 9:39 AM, Conrad Huang wrote: > Unfortunately, that is getting well beyond my understanding of molecular mechanics. I will have to defer this to our expert when she returns. > > Conrad > > On 5/13/2013 7:56 PM, aixintiankong wrote: >> Dear, >> Thank you for your patience to answer my questions in detail. >> Before /minimizating/ the model, i use the procheck to check the >> quality of the model. the residues in most favoured regions is 95.6% and >> the disallowed regions is 0.0%, the the residues had an averaged 3D-1D >> score>0.2 is 92.02% and the errat is 90.55. >> if i use the chimera to minimizate the model after 200 steps, the >> most favoured regions is 85.5% and the disallowed regions is 0.4%, the >> the residues had an averaged 3D-1D score>0.2 is 99.2% and the errat is >> 95.968. >> if i use the chimera to minimizate the model after 250 using the >> ff99sb! force filed, the most favoured regions is 92.1% and the >> disallowed regions is 0.4%, the the residues had an averaged 3D-1D >> score>0.2 is 96.96% and the errat is 98.000. >> if i use the chimera to minimizate the model after 500ns the most >> favoured regions is 90.8% and the disallowed regions is 0.4%, the the >> residues had an averaged 3D-1D score>0.2 is 96.58% and the errat is 96.047. >> which one model should i select to make docking . >> thank you very much! >> >> At 2013-05-14 00:24:03,"Conrad Huang" <conrad(a)cgl.ucsf.edu> wrote: >>> Unfortunately, our local expert on this is on vacation and will be back >>> at the end of the week, so a more definitive answer should come then. >>> In the mean time, I'll try to answer as best as I can. >>> >>> First, Homology Modeling uses Modeller and that does a bit of >>> optimization already. If the model structure looks reasonable, further >>> energy optimization might be helpful. On the other hand, if the model >>> has extended chains because Modeller does not have appropriate templates >>> or just looks unreasonable because the model is not well packed or has >>> large dangling loops, then energy minimization probably will not help. >>> >>> Second, I do not know the answer, but have you tried using the default >>> paramters? >>> >>> Third, conjugate gradient is much much slower than steepest descent, so >>> it probably pays to use steepest descent to get near the minimum before >>> starting conjugate gradient. You can look at the reported energy values >>> reported to decide whether the minimization is proceeding as expected. >>> Chimera energy minimization is not highly optimized, so it may take a >>> while to run for a large system. If only one portion of the model is >>> "interesting", e.g., an active site, it might be faster to select just >>> the region of interest (plus a buffer around it) and only optimize that >>> part. >>> >>> Hope this helps a bit. Better answers should come later in the week. >>> >>> Conrad >>> >>> On 5/11/2013 6:50 PM, aixintiankong wrote: >>>> Dear, >>>> i am a newer use the chimea, i have some question to consult to you, >>>> please help me. >>>> Frist, after Homology modeling using the chimera modeller, should i >>>> optimizate the modle by energy optimization or Molecular dynamic >>>> simulations? The next step i will use the model to make docking. >>>> Second, i want to use chimera to minimize the structrue of my modle. >>>> i select Tools>Structure Editing>Minimize Structure to perform my >>>> work, but my modle include protein and a organic molecule NAD+, so i >>>> don't know how to select the force fileds for the minimiztion of the >>>> modle. please help me. >>>> Third, if i olny want to use the conjugate gradient to perform the >>>> minimiztion, should i only need to set the steepest descent steps to 0? >>>> in general, how many conjugate gradient s! teps and size should be ? >>>> Thank you very much!

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Error reading PubChem3D SDF Files
by Jon Fuller 15 May '13

15 May '13

I tried to read an SDF file directly downloaded from pubchem into Chimera. However, I ran into the following problem (link to example file used, and reply log below). Is this expected behaviour, or a bug? Additionally I tried to import the pubchem CID 71739 (same compound) from the fetch structure by ID tab, and got the error message: Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH HERE!' Many thanks in advance, Jon http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=2385389770715… You are now running Chimera version 1.8 (build 38642). Your previous version was 1.5 (build 32133). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) Error while processing CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_3672_e5800000001_conf.sdf: Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data

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energy optimization of the modle from homology modeling
by aixintiankong 15 May '13

15 May '13

Dear, i am a newer use the chimea, i have some question to consult to you, please help me. Frist, after Homology modeling using the chimera modeller, should i optimizate the modle by energy optimization or Molecular dynamic simulations? The next step i will use the model to make docking. Second, i want to use chimera to minimize the structrue of my modle. i select Tools>Structure Editing>Minimize Structure to perform my work, but my modle include protein and a organic molecule NAD+, so i don't know how to select the force fileds for the minimiztion of the modle. please help me. Third, if i olny want to use the conjugate gradient to perform the minimiztion, should i only need to set the steepest descent steps to 0? in general, how many conjugate gradient steps and size should be ? Thank you very much!

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desmond in chimera
by lecan 15 May '13

15 May '13

Hi to everybody. Can the newest version of Chimera use the .cms files from desmond by schrodinger to analyse trajectories and make movies? Regrads, Luis L.

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surface
by Gesa Volkers 13 May '13

13 May '13

Hi chimera users/developers, I have a problem with a surface calculation from one monomer of a structure that I want to show. As you can see in this image http://imageshack.us/photo/my-images/801/testss.png/ it looks like the surface calculation failed (?) because the surface is missing in the middle (note the chewed up structure of the surface). Most of the surface is smooth but for whatever reason not this part of the structure. I have played around with probeRadius, vertex density and zone and they all increase quality but do not add the missing surface part (I'm not even sure if zone is applicable to surfaces at all or only to electron density maps). Any suggestions which parameter I am missing? Thanks for suggestions, Gesa

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Contour maps or step-gradient of volume map?
by Bullitt Esther 13 May '13

13 May '13

Hi, Is it possible to choose n levels of gray for a volume map? I'd like to make a known-thickness slice using clip, and then see that slice as a defined number of colors. I can kluge it by displaying the map 4 times at 4 contour levels, but is there a better way? thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics Boston University School of Medicine 700 Albany Street, Room W302 Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041 http://www.bumc.bu.edu/phys-biophys/faculty/bullitt

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mask using volume contour surface
by gongpu zhao 13 May '13

13 May '13

Hi All, I have a question about volume contour surface in chimera. I have a density volume of a shell shape. I plan to use the outer contour surface of the volume to mask out all density encased by the outer surface in a tomogram. But instead, I could only mask out the density within the shell. I am wondering if I can make a surface model only using the outer surface. Thanks a lot. Gongpu

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About Morph Conformations
by 吕柯 13 May '13

13 May '13

Dear Sir./Madam, I am a graduate student in Chinese Academy of Sciences. I have two PDB files: one for virus(4 chains, PDB:3VBS), the other for empty particle(3 chains, PDB:3VBU). I would like to use Morph Conformations to make movie for that. However, it turns out "Can not interpolate models: models have different number of chains". Could you please show me what should I do next? Thanks a lot. Yours, Lyu Ke -- Lyu Ke, Ph.D. student Structural Virology Unit Institut Pasteur of Shanghai Chinese Academy of Sciences No.411 Hefei Road Shanghai, 200025, P.R. China Tel: +86-21-54920652

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Re: [Chimera-users] saving sessions
by Tom Goddard 08 May '13

08 May '13

Hi Thomas, There is no session saving option that copies density map files to the same directory as the session file. All other Chimera models including PDB files are included (not linkied) in the session file. The reason maps are not put into the session file is because they are sometimes very large, Gbytes in size. Some day I intend to add an option to include the maps in the session file so you can have a self-contained session if you want. Copying the files could be another approach but it has problems. What if there is already a map with the same file name in the current directory? Could modify the copied file name I guess. Maybe better put all the map files in a new subdirectory. But are you really going to make copies of all the map files on every session save? If you only do it sometimes it doesn't solve the problem of moving data to a new computer. It will be slow to copy the files and it makes many redundant copies which then can become confusing as to whether two files with the same name really are identical. Hard links could be used to avoid copying the file, but that won't work when a session is on one file system and data on another. I think the way to handle moving data files to a new computer is to keep all your data including sessions under one directory tree so the whole thing can be easily copied. If instead the goal is to occassionally make a self-contained session then copying the map files and session file to a new directory would be a nice option similar to embedding all files in the session. I've noted this in the feature request for embedding the map files. http://plato.cgl.ucsf.edu/trac/chimera/ticket/9763 The sphere/axes display idea is one way to see the axes of a displayed model. The transparent sphere would cause problems in Chimera some of the time because Chimera can only correctly display one transparent model at a time. The current default is to show a single transparent layer, so any transparent model inside the sphere would disappear. This is a longstanding and hard problem to fix. But a mesh could work. Another idea is simply to depict the x,y,z axes. I've made a feature request for this. http://plato.cgl.ucsf.edu/trac/chimera/ticket/12062 Tom On May 8, 2013, at 12:25 AM, "Marlovits,Thomas" wrote: > Hi Tom, > > I do have a question related to saving sessions, which is a great option btw. > Is there a way that one can save the session - let's say in a new folder but then have all models also saved in there. For now, as I understand, it will only save the path/filename of those models. So, whenever we switch computers, hard-drives etc … this can turn out to be a lengthy process to find those models (we often have many models open at the same time). > Ideally, also fetched files from the pdb would be great to be saved locally in this new folder. > > The second question I have is related to turning molecules around specific x/y/z angles. > I'd love to have an option to display a big sphere that encapsulated the other models displayed. Ideally, this sphere would look like a globe with cordinates in there … if this is displayed at semi-transparency, one can easily go to a specific position but get more of an idea to easier naviagte through the 3D space. Sometimes I only would like to get a rough estimate about the angles to turn molecules. Alternatively a mesh-like grid could do the same job (and if one could display the numbers of the lattidude/longitude or so that would be great too). > > Many tx, > -T. > > > ------------------------------------------------------------------------------- > > Thomas C. Marlovits, PhD, M.A.S. > The MarlovitsLab @ IMP/IMBA > http://thomas.marlovits.myresearchlab.org > > Contact/Address/Directions: > http://thomas.marlovits.myresearchlab.org/lab/Contact.html >

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Define centroid issue
by Francesco Pietra 08 May '13

08 May '13

Hello: I was unable to put to work define centroid radius 0.5 color red :ligand_residue_name or define centroid radius 0.5 color red #0&@serialNumber=1972 with a homodimeric protein (I am at CHARMM NAMD/XPLOR, so that the two subunits are only distinguished by either the atom sequential number or the segment name, the latter not being understood by chimera, as far as I know). In the first case, running the movie after the appropriate further steps, the centroid sequence obtained was for the centroid between the two protein ligands, as it was expected. In the second case (as I wanted to refer to the ligand in subunit A only), the command raised the error: AttributeError: 'NoneType' object has no attribute 'openState' File "/opt/UCSF/Chimera64-1.7/share/StructMeasure/Geometry.py", line 293, in _getRefInfo invXForm = lowest.openState.xform Please notice that the line command #0&@serialNumber=1972 correctly selects the ligand on subunit A (a diatomic ligand, where "1972" is the sequential number of one of the two atoms of the ligand. Here "#0" may be redundant, as it deals of a single model. However, using "@serialNumber=1972" raised the same error. I fear I am missing some obvious facet of define centroid, so that I thank you for your patience. francesco pietra

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Question about measuring volume in chimera
by Varun Kumar 07 May '13

07 May '13

Hi, Can we outline a particular area and measure volume in chimera? I wish to measure specifically the purine binding site in the ATP binding pocket of Protein kinase C. Best regards -- Varun Kumar International Graduate Student School of Biomedical Sciences Department of Biological Sciences Kent State University, Kent, Ohio, U.S

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RMSD
by George Tzotzos 04 May '13

04 May '13

Hi everybody, I am trying to measure the RMSD between a docked ligand and the corresponding ligand in an X-ray structure. I've been looking to find a way of doing this in Chimera to no avail. I'd be grateful for any suggestions on how to do this. Best regards George

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save map with the adjusted threshold
by Moumita Dutta 01 May '13

01 May '13

Hello, I'm not sure if I can do this in chimera. Once I open a density map and adjust the threshold and removed dust how can I save the map in this setting so that next time when I open it I don't have to adjust again. Thanks

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Chimera shutsdown when opening sideview
by vamsee 29 Apr '13

29 Apr '13

Hi Elaine, I have recently moved to Linuxmint 14 from Windows 7. I can open virus capsids very easily (much more easier than in Windows 7, which is pretty sweet). But, every time I try to open the Side View option from the menu, Chimera shuts down. I have tried version 1.7 and 1.8rc. Both exhibit the same behavior. The interesting thing is, I can open all the other tabs (Effects, Lighting etc.) on that window from the menu. But when I click on Side View, Chimera crashes immediately with no bug report (Its almost like the process never existed). So, I tried starting chimera from the command line with the Side View option enabled (sudo chimera --start "Side View"). That started the Side View window and that stayed even after I opened my models. I then closed the Side View and re-opened it from the menu bar this time in the same chimera session. That worked again. So, I am kind of at a loss though I seem to have a work around for now. I have used the same features on Windows 7 (I still do using a virtual machine inside Linux) and they work fine. Any reason why this would happen? My computer specifications Processor : Intel® Core™ i7-2630QM CPU @ 2.00GHz × 8 Memory : 8Gb Onboard Video : Intel® Sandybridge Mobile OS : LinuxMint 14 Thank you Vamsee

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morph conformation
by Moumita Dutta 27 Apr '13

27 Apr '13

Hello chimera-users, I'm trying to use the option morph conformations from the command line and cannot specify more than one molecule with the command morph start. How to use the morph start command for more than two molecules ? Thanks for any help. Moumita

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morph map and movie recording
by Moumita Dutta 26 Apr '13

26 Apr '13

Hello, I am trying to morph more than two maps at a time so I am using vop morph instead of Morph map. I am following the mini-video animation example script of vop morph using the recommended chimera 1.7 version 2013. The script actually recorded the movie but in the movie threshold changed from what I set and it turned some maps to x 90 degree not all and it is not showing the morph animation only the superimposed maps. Another problem is though I remove the dust after loading the maps but it came back in the morph and in the movie as well. How can I fix the problems and generate the movie ? Moumita

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Ubuntu 12.10 and Chimera update #2
by Greg Couch 25 Apr '13

25 Apr '13

Found a better solution to Chimera's problems on Ubuntu 12.10 -- just install Ubuntu 13.04! HTH, Greg

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Re: [Chimera-users] movie recording from morph map
by Elaine Meng 25 Apr '13

25 Apr '13

On Apr 25, 2013, at 1:01 PM, "Moumita Dutta" <dutta(a)bio.fsu.edu> wrote: > Hi Elaine, > I am trying to morph more than two maps at a time so I am using vop morph instead of Morph map. I am following the mini-video animation example script of vop morph like below > > Record the movie > # > > movie record supersample 3 > > wait 1 > movie crossfade > vop morph #0,1 frames 200 > wait 200 > > movie encode morphmap.mp4 morphmap.webm morphmap.ogv bitrate 200. > > It starts recording the movie but it does not stop. > Best, > Moumita Hi Moumita, The first thing to check when following a tutorial or examples is your version of Chimera. The top of the mini-examples page <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html> says that they were made with Chimera version 1.7 from March 2012 or newer. In those versions, movie recording will automatically stop when you use "movie record." In older versions, you have to use the "movie stop" command to stop recording before you do the encoding. (I cc'd chimera-users(a)cgl.ucsf.edu -- please use that address for Chimera questions unless your data are private) I hope this helps, 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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Seeking guidance on Volume-volume fitting
by ingvar 25 Apr '13

25 Apr '13

Dear Chimera, I am seeking guidance on what would be best practice in doing volume-volume fitting, and what expectations should I have on number of trial conformations. For instance would it be beneficial to resample one of the volumes to the same grid as the other volume. What about volumes with different resolutions, do this require any special handling. In the case below it would probably be more efficient to just align the principal moments of inertia of the envelopes above the contour level and then do a search from there, though this will only work well if the volumes are very similar. In an initial study I used 3 EM volumes from EMDB, (EMD-5500, EMD-5501, and EMD-2017). They are all 30S E. coli ribosomes of similar resolution (12.9, 14.0, 13.5 Å). I thought that this would be a relatively easy starting point, with the intent to then go on to fit 30S subunit in some of the many E. coli 70S EM volumes that are available. The volumes EMD-5500 and EMD-5501 are in similar orientation, while EMD-2017 is in a completely different orientation. The grids are similar but not identical, 125^3 vs 128^3. I adjusted the contour levels from the EMDB recommended values to make the enclosed volumes more similar in size. Contour levels used: EMD-5500 -2.8 -> -2.5 EMD-5501 -2.8 EMD-2017 39 -> 32 I am using scripts like the one shown here: from chimera import runCommand as rc from chimera.tkgui import saveReplyLog rc("open data/EMD-5500.map") rc("volume #0 level -2.5 transparency 0.5") rc("open data/EMD-5501.map") rc("volume #1 level -2.8 transparency 0.5") rc("fitmap #1 #0 search 50000 metric cam envelope true inside 0.2") saveReplyLog(r'/Users/ingvar/chimera/log/fit5500_5501_loc.txt') It seems correlation about mean is the best metric for volume-volume fitting, and that it is best to only use points inside the envelope. The maps EMD-5500, and EMD-5501 have the unusual feature that the density range is shifted downwards so that the average is well below 0. I was concerned about that and moved the density range, but with the fitmap parameters above that did not seem to have any significant impact (with other sets of parameters the density range appears to be an issue). In this case, it is relatively easy to see when you have found the "good" fit, all other fits have clearly worse statistics. What I was surprised about was the number of trial conformations needed to be reasonable certain to find the "good" fit. 5500 in 5501 7 times in 5000 5501 in 5500 2 times in 5000 5500 in 2017 0 times in 5000 5500 in 2017 8 times in 50000 2017 in 5501 0 times in 5000 Many Thanks, Ingvar Lagerstedt

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morph map and molecule together
by Tom Goddard 24 Apr '13

24 Apr '13

Hi Moumita, You can morph both maps and molecules at the same time. You use commands instead of the morphing dialogs in order to get them to play with perfect synchronization. The basic plan is to create the molecule morph and the map morph using the dialogs as usual. Then load a simple command script that starts both playing at the same time and records the movie. I'm sure this works in Chimera 1.7, probably in 1.6, and maybe in 1.5. Here is an example command script morphing a filament map and fit molecule http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/scripts/movie2.txt and here's the resulting movie http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/images/morph1.mp4 and here is the web page where I explain how this was done http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/animate.html This was a demonstration I gave at the Bay Area Cryo EM meeting in Santa Cruz last summer. Tom -------- Original Message -------- Subject: morph map From: Moumita Dutta To: goddard Date: 4/23/13 10:16 PM > Hi Tom, > > I want to morph a set of density maps and the atomic models fitted > into them together and run the two movies concurrently so that I get a > movie that shows how the density and the atomic models change > together. I have been able to make the two different sets of data > morph independently, but thought it more informative if they morphed > together. > > I was wondering whether this can be done using chimera ? If so which > version supports it ? > > Thanks, > Moumita > > >

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Hide bonds
by Masaki Uchida 23 Apr '13

23 Apr '13

Dear Chimera users Is it possible to hide bonds between spheres (atoms/bonds view)? I have a "pdb" file which is a bead model of a protein generated by SAXS analysis. When I open the file and changed a view to "sphere" under "atoms/bonds", bonds between beads are shown. I believe the bonds are meaningless in this case and would like to show just spheres (beads). Thank you in advance for your help -- ********************************************** Masaki Uchida Department of Chemistry&Biochemistry Montana State University **********************************************

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dock
by LW 23 Apr '13

23 Apr '13

Dear all, As attached, I have a structure of Saposin C in the presence of SDS micelle solved using NMR. I took the first model out of its 20-structure ensemble and generated SapC_one_model.pdb. I also have a PDB file(as attached )built to model SDS micelle surrounded by water. Does Chimera allow people to dock these two molecules and generate a combined PDB file for further analysis? While the structure of Saposin C in the presence of SDS micelle, NMR data indicate that the open hydrophobic core is in contact with SDS micelle. Is it possible to use Chimera to determine the relative orientation of the two molecules where (i), they are in intimate contact, (ii), there is no clash, (iii), the shape complementarity is at its optimal? Any clue would be much appreciated. Levi

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batch production of images
by Benjamin SCHWARZ 23 Apr '13

23 Apr '13

Dear list, I am considering to use chimera to render (a tons of) pictures of models that I generated and issued in nice markerSet (.cmm) files. 1. If I understand well, the only way to do that is through the linux headless version, and there is no way to do that under MacOS X for the moment 2. I should then use the "copy" command. Something like : chimera --nogui --script "myscript.py" where myscript.py should contain something like "from chimera import runCommand; runCommand('copy file pipo.png')" 3. All my models were produced in a same cartesian, and I'd like to keep the orientation and "picture frame" similar for all pictures. What I mean here, is that I'd like to be able to set my camera somewhere, looking in a specified direction, which I would probably do under the chimera GUI; and then, shoot all my pictures from that point of view on a batch mode. How shall I do that (set a point of view for the camera and use it on a batchmode) ? Thanks a lot again for your great job, and your constant answers --Ben

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stereo viewing with consumer graphics cards
by Greg Couch 22 Apr '13

22 Apr '13

In the past, Chimera has always needed a workstation-class graphics card (e.g., AMD FirePro or NVIDIA Quadro) to view molecules in 3D stereo and read dialogs at the same time. Now that there are 3D HDTVs, that has changed. I have just confirmed that with a computer running Microsoft Windows 8, with an AMD Radeon HD 7850 graphics card, and a Panasonic 3D HDTV, that 3D stereo worked without fiddling with any display settings. That is awesome -- "without fiddling with any display settings". Windows 8 is a requirement, Windows 7 will not work. I am unaware of any effort to get Linux to work. There is a good chance that Apple Mac OS X will work and we plan to test that soon. Any recent AMD Radeon HD graphics card with HD3D, or NVIDIA GeForce graphics card with 3D Vision support, should work. I hope to test a NVIDIA graphics card soon to confirm that. And supposedly, any 3D HDTV will work. The 3D HDTV in the test was a Panasonic TC-P50GT25, from 2010/2011, and I expect that any 3D HDTV that support a full resolution stereoscopic 3D format will work well. Non-full resolution formats would work for the 3D stereo images, but the associated 2D dialogs would be unreadable. Happy 3D viewing! Greg

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Distance between atoms at the interface
by Mehdi Talebzadeh Farooji 22 Apr '13

22 Apr '13

Dear Chimera Users, I was wondering if there is a way to show distances between two objects (two chains) and filter them; for instance to display all of the distnaces between atomes of two interacting protein chains which are less than 6 A. Any help would be much appreciated, Mehdi

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View Dock plugin
by James Starlight 22 Apr '13

22 Apr '13

Dear Chimera users! I have a question about the View Dock plugin. >From some servers usually I've obtained pdb file of the target protein as well as separate file consisted of all predicted posses which I can visualize in Chimera. So I wounder to know 1- How I could hide hydrogen bonds as well as protein's side chains of the residues which are in contact with the ligands ( on the default both of that two options are turned ON) 2- How I could properly save some poses as the separate pdb models ? E.g when I chose to same target.pdb with the #1_pose from the chimera saving menu I obtain protein and ligand with the surrounded residues as two models in one pdb file ( so I must manually merge it in one model and delete residues from the second model). Does it possible to obtain protein-ligand complex as one model as the output? Thanks for help, James

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multiple volumes' orientation in space
by Yunji Wu 22 Apr '13

22 Apr '13

Dear all -- I am a total newb to Chimera, and I have an issue which I feel like can be easily resolved with your help. I am trying to make a 'structure-based schematic' with the purpose of clarifying the locations of the domains of a complicated crystal structure. There are 12 domains in this structure that I want to represent as 'blobs', and they are oriented in space in a very confusing way, especially if represented as the standard ribbons or cartoons. I used pdb2mrc (in EMAN2) to create 25Å maps from my .pdb files for (with the command e2pdb2mrc.py -R 25 H.pdb K.mrc). These show up fine individually in Chimera, but the separate maps are not oriented properly in space. It looks like the map volume files have no instructions about where to be in space relative to the coordinate files that generated them. If I take a single .pdb file with all 4 chains and generate a single .mrc file, I obviously get something that has the chains correctly oriented. This is less useful and satisfying, since I'd like to make separate chains into separate map volumes so I can color them separately (for example: chains H,K,L,M as H.pdb, K.pdb, L.pdb, M.pdb into H.mrc, K.mrc, L.mrc, M.mrc). When these 4 volumes are plotted in Chimera, they appear to be semi-randomly piled in the middle of the viewing field, with no correlation to the original pdb coordinates (attached screenshot of volumes from 4 chains, calculated from 4 individual pdb files). Is this just a result of a preset in Chimera that I am not aware of that needs to be adjusted? If I plot the original pdb file with the 4 chains from which these volumes were generated, there is no spatial correlation between the structure and the volumes. In trying to solve this, I know that "Fit to Map" will allow the coordinates to be fit into the map volume, but I cannot seem to fit the separately map to the individual chains, which would be a longer way around the issue. Is there some way to do this, or to just create maps that are oriented properly in space relative to each other? Thank you so much for your help, Yunji Wu

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Radius of gyratiion
by George Tzotzos 22 Apr '13

22 Apr '13

Hi everybody, I've search the archive to find a script for measure protein radius of gyration. I came across the following link: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007257.html I'm now trying to find the actual script <radius-of-gyration.py>. Any ideas how to retrieve it? Many thanks in advance George

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euler angle
by Jingchuan Sun 19 Apr '13

19 Apr '13

Hi, After I rotate a volume to a specific orientation, and "save map as" in "volume viewer", the saved volume are still in the original orientation. Could I save it in the new orientation. If I could display the current euler angles, I can rotate it in other software. But how could I display euler angle after rotation? Thanks! Jim

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Doubt
by Víctor J. Gallardo López 19 Apr '13

19 Apr '13

Good Morning Mr./Ms., I have a bit problem with the molecular modeling. I have a dímer (the two chains of this protein are the same sequence) and I want to put 34 residues at the N-terminal in each chain. I load my fasta (with this residues addition) in chimera and I blast a protein structure in the PDB that has the same residues as my protein without this addition. When I modeller (homology) my fasta, the programm only gives me one of the chain with this addition but I need the whole protein (with the two chains and with this residue addition for each chain as well). How can I do it? I hope you resolve my problems. Thanks you for you attention. Sincerely, Víctor J. Gallardo

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Generating trajectory of a user-defined plane
by Lili Peng 18 Apr '13

18 Apr '13

Hi, I am interested in measuring the deviation of an helical segment with respect to the initial structure in a GROMACS trajectory. I have already uploaded my *.tpr and *.trr files into MD Movie and have defined a plane through the helical segment within the initial structure. Is it possible to define another plane through the same helix and track the intersection angle throughout the trajectory? Thank you, Lili

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python script running OUTSIDE chimera possible?
by frederick lee 18 Apr '13

18 Apr '13

hello chimera experts, as far as i know, python scripting for chimera is done within the context of chimera like chimera --nogui myscript.py parameters ... is it possible to run myscript.py without the need of the chimera executable and use import statements of some sort to access the chimera module(s) like python myscript.py parameters best regards, fred

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