- Chimera-users - RBVI Mailing Lists

Multiple Docking Using Chimera
by SOBAHY, TURKI MOHAMMED 02 May '16

02 May '16

Hello, I have a protein of interest that I need to perform molecular docking on by multiple ligands (~1000,000). The protein is in PDB file format, while ligands are in a SDF file format. Initially, the ligands were divided into multiple SDF files (mini) for hardware sake. Then, a python script was developed to handle the docking of each mini SDF file against the protein of interest. This works nicely, however docking scores (tables) have no ligands IDs associated to distinguish each score. So, basically I have scoring tables without any key IDs!! Kindly, I want to know if you have encountered the same problem and what approach you took to solve this. Thanks,? ______________________________ Turki Sobahy Research Associate Research Center (J-04) King Faisal Specialist Hospital & Research Center (Gen.Org.)-Jeddah Branch PO Box 40047, Jeddah 21499, Saudi Arabia Tel# +966 667 7777 ext. 66736| MCD# 40716 Mobile# +966 505837027 email tsobahy(a)kfshrc.edu.sa<mailto:ESan-Diego@kfshrc.edu.sa>

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Solicitud Información
by luz Martinez 02 May '16

02 May '16

Cordial Saludo Soy estudiante de licenciatura en Química de la UNIVERSIDAD PEDAGOGICA NACIONAL. Colombia, Cordialmente solicito información acerca del modelo matemático general que el programa UCSF Chimera utiliza, lo anterior con el fin llevar a cabo una investigación en el espacio académico de Química Computacional que curso. Agradezco la atención y pronta respuesta Luz Angela Martinez M. Estudiante Decimo semestre

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Thank you and a suggestion
by Mohamed Elrobh 01 May '16

01 May '16

Dear UCSF Chimera, Just wish to say big thank you for your program. If you kindly allowed me to ask if there is a possibility to make a live webinar tutorial on Mohamed Elrobh, Ph.D., Assistant Professor, Room 2A 66 B5, Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia Phone +966 114675944, Fax +966 114675791, Mobile +966 502072937 Email melrobh(a)ksu.edu.sa<mailto:melrobh@ksu.edu.sa> Site http://fac.ksu.edu.sa/melrobh<http://faculty.ksu.edu.sa/elrobh> ________________________________ Disclaimer: This communication is intended for the above named person and is confidential and / or legally privileged. Any opinion(s) expressed in this communication are not necessarily those of KSU (King Saud University). If it has come to you in error you must take no action based upon it, nor must you print it, copy it, forward it, or show it to anyone. Please delete and destroy the e-mail and any attachments and inform the sender immediately. Thank you. KSU is not responsible for the political, religious, racial or partisan opinion in any correspondence conducted by its domain users. Therefore, any such opinion expressed, whether explicitly or implicitly, in any said correspondence is not to be interpreted as that of KSU. KSU may monitor all incoming and outgoing e-mails in line with KSU business practice. Although KSU has taken steps to ensure that e-mails and attachments are free from any virus, we advise that, in keeping with best business practice, the recipient must ensure they are actually virus free.

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Manually adjusting alignment
by Visvaldas K. 30 Apr '16

30 Apr '16

Dear All, I wasn't able to adjust alignment in the Alignment window, and search did not find an answer (because I get great number of false negatives)...I tried shift-arrow, ctrl-shif-arrow and many times but only once the region moved "by accident", and I wasn't able to repeat this feat. To simplify the task, let's say I have in the alignment window: seqA NQDF.RFRDseqB MKTFIEHKD I want to move "RF" by one residue to the left so that the top part becomes NQDFRF.RD What would be the sequence of keys, clicks/drags and so on to do that (also, how is the active region which is ready to move signified: green, green in a dashed frame, or perhaps white dashed frame)? Sincerely yours, Vis Kairys

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need help joining existing pdb files with new sequence
by John Hess 28 Apr '16

28 Apr '16

HI folks, I have asked Elaine a couple questions about this project of mine. She’s been very helpful, but I’m such a beginner, I feel guilty wasting her time and the rest of the folks reading the entire chimera list as I ask how to connect this and move that. I would like to take at least 2 existing pdb files and link them to some additional peptides sequence that would be between them. The resulting pdb would describe a structure that looks like this: > protein 1 -> peptide linker -> protein 2 I’m dealing mainly with alpha helices (in coiled-coils), and I know how I want them positioned. I joined a helical peptide sequence (made using Build Structure) to one pdb file but the orientation was way off and I’m wondering how to “grab” the entire helical peptide region and move it where I want it (sorry, in the past, I have tried to modify structures with Foldit and have had a collaborator who used Rosetta to try and model my data.). Is anyone else on this list from UC Davis and willing to get together for some tutoring? Does anyone not at Davis have time to answer my questions and help? If we work well by email and I make progress, I think that this could be a $ for time or co-authorship situation. thanks, John Hess jfhess(a)ucdavis.edu

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Labeling and coloring chains
by Elaine Meng 28 Apr '16

28 Apr '16

> On Apr 28, 2016, at 8:15 AM, Deniz Simsek Buck <simsekd(a)stanford.edu> wrote: > > Hi Elaine, > Thank you for your reply. > > I already changed the chain IDs to different names. I am working with ribosome structure: 44 chains are large subunit and then I want to color them the same color. > If I already changed chain A to L23, lets say, how do I choose them? > > Also, is there a way to choose different colors than the available ones and also how do I make the label the same color as the chain? > > Thank you very much, > Deniz > Hi Deniz, I do not know how you changed the chain names, so it is hard to say. In PDB format there is only one column allotted to chain ID in the ATOM lines, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#co…> ...so it can only be one letter or number, as far as I know. So it would depend on what Chimera thinks are the chain IDs…. for example, it may have only read the single character in column 22 as the chain ID. You could probably tell by putting the mouse over some atom in the chain and see what information is in the pop-up balloon. But maybe you used some other format that allows more characters of chain ID. Nevertheless, it might not be possible to use the range syntax I showed in my previous message (first example included below). You could try it, but if ranges didn’t work, you’d have to specify all the IDs (again, all of what Chimera thinks are the IDs) in one long command, or in multiple separate coloring commands. > color red,r :.A-D > (meaning: color red ribbons-only in chains A-D in all models) > > color green,a #0:.B,.D > (meaning: color green atoms-only in chains B and D of model #0) Instead of changing chain IDs I would recommend using “alias” to give new names to the set of atoms and then use these new names in the coloring commands, e.g. alias L23 :.X (meaning assign the name L23 to chain X) color hot pink,r L23 … of course you could assign the name to a collection of multiple chains if you wanted, e.g. alias L23 :.X,.Y,.H You could also use alias with your existing changed chain IDs providing you can figure out what Chimera thinks they are. As for colors, you can specify an infinite number of colors as RGBs or hexadecimal or first define new color names and use those names, if the built-in set of named colors doesn’t have what you need. Color specification is described in the same “color” manpage I mentioned before. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> Also described in that page are how to specify coloring labels, e.g. color orange,r,l (meaning coloring ribbons and labels only) Again I’ve CC’d the recommended address for chimera questions, chimera-users(a)cgl.ucsf.edu 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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Three-dimensional structural model of the VP7 trimer
by Dr Omer Naseer 28 Apr '16

28 Apr '16

Hi I am s student of PhD and working on the Rota virus A, I want to created "three-dimensional structural model of the VP7 trimer". by using "UCSF Chimera", can you please tell me How to do this? because I tried a lot but unable to produce a structure like yours. Regards Dr, Omer Naseer Ph.D Scholar University of Veterinary & Animal Sciences, Lahore, Pakistan. +92 321 640 89 56

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The question about fitting
by Zhongjun Hu 28 Apr '16

28 Apr '16

Hi, everyone: Once I fit one map to the reference map, there will be some fitting result. I want to use this fitting result to align the map to the reference map using another software, for example, EMAN. How do I this? It seems that I am not clear about the fitting result, could anyone give some idea? or, is there other protocol/software to do this? Thank you! Best, Zhongjun

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electron density map
by 陈柳青 28 Apr '16

28 Apr '16

Hi! I display the 2Fo-Fc map in chimera, but i wonder what the meaning of step 1, step2,etc in volume viewer. The other question is what the relationship between the level in chimera volume viewer and Coot map level ? Best regards -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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Re: [Chimera-users] electron density map
by Oliver Clarke 28 Apr '16

28 Apr '16

Dear Liuqing, Step size refers to whether every point in the map is displayed (step 1), or every second point (step 2), or every fourth point (step 4) and so on - basically, the coarseness of the grid. Loading a map at a larger step size will have less detail, but will be faster to load and manipulate. See here (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#sampling) for details. The level in Chimera is the same as in coot in absolute terms (e-/Å^3) - it is just that in Coot, by default, maps are adjusted in steps of r.m.s. (often called “sigma”), whereas the default behaviour in Chimera is to deal directly with absolute electron density levels. You can mimic the Coot behaviour, however, by adjusting the volume level on the command line with the option sdlevel, for example “volume #1 sdlevel 1” will set the volume with id #1 to 2xr.m.s. See here (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#level) for details. For convenience (really due to my forgetfulness), I use an alias to do this, as follows: "alias ^map_sig volume $1 sdlevel $2" so then one can use the command “map_sig #1 5” to adjust map #1 to 5xr.m.s., which should match the corresponding level in coot. If you want to mimic how maps look in coot, adjusting some of the mesh options is handy, as follows: "alias ^cootmode volume $1 capfaces false style mesh meshlighting false squaremesh false color "#08882eefa222" step 1; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1; background solid white; cofron” Where “cofron" is an alias that mimics the centering and navigation behaviour of coot: "alias ^cofron set showcofr; cofr view; clip on” Cheers, Oli.

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