- Chimera-users - RBVI Mailing Lists

I Can't Open My ZDOCK Output File Into Chimera
by Nissa Nabila 22 Aug '17

22 Aug '17

Hello and hi! My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem? Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review. Thank you in advanced!

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Helix voxels labeling
by natan geier 22 Aug '17

22 Aug '17

Hello, I am currently studying the connection between density maps and the secondary structure elements. I have a density map file for a certain protein, giving for each voxel a density value, and what I am missing is a "helix map", giving a binary value for each voxel, representing wether it is a part of a helix or not. In order to build this "helix map", I need to use the .pdb file of that protein, but I am not really sure how to extract an appropriate 3D boolean matrix out of this file. Any suggestions would be greatly appreciated. Thanks

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Regarding generating a .pdb file of peptide (Diglycine)
by Dilip H N 22 Aug '17

22 Aug '17

Hello, I have install chimers in ubuntu 14.04.. I am finding difficult to get the .pdb format for diglyicne peptide... 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:- Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590) 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error.. So can anybody kindly help....i am a novice here.. Thank you... -- With Best Regards, DILIP.H.N Ph.D Student <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dili…>

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biounit
by Arthur Szabo 18 Aug '17

18 Aug '17

When one fetches structures from the PDB data base what is the difference between fetching using the PDB only selection and the pdb biounit selection? Arthur G. Szabo

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move different map to the same origin of coordinate
by C.J. 18 Aug '17

18 Aug '17

Dear specialists, I open a map(#1) and make icosahedron surface(#1) using Tools-> Higher-Order structure->icosahedron surface. But the model #0 and #1 don't have the same center, how could I center them into the origin of same coordinate? Thanks! -- Best regards! Jianhao

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advanced option for WebGL?
by Albert 17 Aug '17

17 Aug '17

Hello, I noticed that Chimera can export a scene as HTML file which is based on WebGL. However, we can no longer change the displaying styles through this .html file since there is no any menu or option button in the page. Would it be good if Chimera could provide this function? As far as I know, PyMOL has similar function, but the generated .html provide a menu to change the scene styles. see here https://pymolwiki.org/index.php/Pymol2glmol Thank you very much. Albert

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Draw Line
by Catherine Jenifer Rajam Rajendran 17 Aug '17

17 Aug '17

Hi Eric, Can you please tell me what are the ways to draw an axis. I have a directional vector - x, y, z coordinates (e.g., 0.407 -0.747 0.526) and a point (14.395, 37.07, -12.029). How to draw an axis in chimera tool with these two data? Thanks, Catherine

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command line minimization
by Milo Westler 16 Aug '17

16 Aug '17

We are trying to automate the minimization of a series of compounds using the system command line. Since we have quite a few compounds, we are interested in using the Gasteiger method for assigning charges. The command line minimize includes the AM1-BCC method.. Is there a way to run an automatic minimization using the Gasteiger method? Currently we use: chimera --nogui --silent R.mol opt.cmd Where opt.cmd is: minimize write #0 R_min.pdb -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo(a)nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========

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Match->Align commandline
by sonal rashmi 10 Aug '17

10 Aug '17

sir/mam, i want to use chimera Match->Align feature using the commandline or nogui script (python) to align multiple protein sequences (pdb files) to generate the alignment on MultiAlignViewer and save it as clustal (.aln) file. I tried out the python codes posted on the portals but non of them are giving proper alignment. kindly advice as to what i can do? Is there any commandline available for it? Thanking You Sincere User

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Problem with added ions in Amber
by George Tzotzos 08 Aug '17

08 Aug '17

In MD movie I loaded complex.prmtop and complex.inpcrd files In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I’m attaching a snapshot showing the Na+ ions in red). I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 NOTE: I unticked the Removed existing ions/solvent box I obtained the following Warning “Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA I generated complex_solv.prmtop and complex_solv.inpcrd files When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below). > resinfo #Res Name First Last Natom #Orig #Mol 1 ASP 1 14 14 1 1 2 THR 15 28 14 2 1 ——————— 250 LEU 3988 4006 19 250 3 251 VAL 4007 4023 17 251 3 252 KBR 4024 4062 39 252 4 253 WAT 4063 4065 3 253 5 ———— 10272 WAT 34084 34086 3 10272 10024 10273 WAT 34087 34089 3 10273 10025 Is this what should be expected? Should I consider the solvated complex charge neutralised? Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions Thank you in advance for any suggestions.

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chimera batch process
by y.turgay＠bioc.uzh.ch 08 Aug '17

08 Aug '17

Dear chimera users, I was wondering if you could help me automate the following procedure in order to batch process all my tomograms. What I want to do is to open a segmented tomogram, apply parameters like surface, the step size (1 of 8) to increase the connectivity of what has been segmented, to hide the dust (size: 50) and to threshold the tomogram to 0.5. Afterwards I would select all remaining objects and open a script to invert the surface and execute "mask #0 sel invert true" using the command line in chimera to substract the background from the tomogram. Finally I would save this as new map. Can anyone help me with the commands I have to write in the Terminal to iterate through 200 tomogram folder and automate and batch process this. Best Yagmur Turgay

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looking for help in UCSF Chimera
by Ch Bilal 07 Aug '17

07 Aug '17

Respected Sir/Madam. Its Bilal here and i m doing research on a protein "rstA". I am UCSF Chimera user and i am facing an error while energy minimization i got a pop up windows with this error "No MMKT name of atom "HN1" in standard residue "LYS", please help me out i am attaching my complexes with this mail as well please find the attachment. Thank you!

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Automatically changing rotamers
by Ali Malay 07 Aug '17

07 Aug '17

Dear all, I have a large, capsid-sized structure. Is there an easy way (e.g. using a script) to automatically change all of the rotamers of a particular residue type? For example, I would like to modify all cysteine residues such that they all correspond to the Dunbrack rotamer with Chi1= -61; could this be done using the swapaa command? Thank you in advance! Ali

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surface calculation failed on new laptop
by Paul van Erp 03 Aug '17

03 Aug '17

Dear chimera users and developers, Recently I purchased a new laptop. One of the primary uses of this laptop is rendering structures using chimera and running VR simulations of these structures. I've used the new ChimeraX successfully for this. However I also use the old version of chimera for structure visualization, coloring according to attribute lists and I create morph models between structures. The new laptop is unable to calculate virtually any surface. I've gone through the various troubleshooting pages and tried many things. None seem to be effective. Is it possible that the surface calculation would be more successful on a different computer? Also would this depend on the hardware? or might a similar computer from a different brand suffice? Any help you could offer would be greatly appreciated. Thanks in advance, Regards, Paul van Erp

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Volume transparancy
by Matzov Donna 02 Aug '17

02 Aug '17

Hello, I'm trying to make a movie such that a ribbon model would appear while its maps (represented as surface) is already shown and is partially transparent. For that I wanted to set the ribbon transparency to 100 and then use the following command: transparency 0,r frames 100 The problem is that when when the ribbon in 100% transparent, the shape is still apparent in the partially transparent map. the ribbon shapes are not seen only when the map is not transparent at all. Is there a way to fix that? Thanks, Donna

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put outline box at the center of a marker
by Dieter Blaas 01 Aug '17

01 Aug '17

Hi, I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? Thanks a lot for help, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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QUESTION
by Arthur Szabo 31 Jul '17

31 Jul '17

I am working with a stretch of dna oligos bound to proteins. I selected all the nucleotides on one strand, showed the atoms as sticks. Then I realized I had wiped out the original colors of the atoms, oxygen, red and nitrogen, blue. How can I restore the atom colors by selecting those nucleotides, and changing the atoms back to their typical colors - as a group. I know how to change the colors of the atoms by first showing them as balls and sticks and then selecting the atoms I want to color. But with 10 nucleotides that is a bit of a pain, selecting them on the screen image. I seem to recall that there is a way to do color all the same atoms at once, but forget how. If I hide the nucleotide side chains, then show them again, I get back to the view where the atoms are not selectively colored. Thanks Arthur G. Szabo

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Re: [Chimera-users] QUESTION
by Rebecca Swett 31 Jul '17

31 Jul '17

Hi Arthur, Select your nucleotides and then you can either use the command line with : color byhet selected Or go to Actions > Color > by heteroatom. Cheers, Rebecca From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>> on behalf of Arthur Szabo <agszabo(a)outlook.com<mailto:agszabo@outlook.com>> Date: Monday, July 31, 2017 at 11:53 AM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] QUESTION I am working with a stretch of dna oligos bound to proteins. I selected all the nucleotides on one strand, showed the atoms as sticks. Then I realized I had wiped out the original colors of the atoms, oxygen, red and nitrogen, blue. How can I restore the atom colors by selecting those nucleotides, and changing the atoms back to their typical colors – as a group. I know how to change the colors of the atoms by first showing them as balls and sticks and then selecting the atoms I want to color. But with 10 nucleotides that is a bit of a pain, selecting them on the screen image. I seem to recall that there is a way to do color all the same atoms at once, but forget how. If I hide the nucleotide side chains, then show them again, I get back to the view where the atoms are not selectively colored. Thanks Arthur G. Szabo This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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figured it out from the tutorial pages
by Arthur Szabo 31 Jul '17

31 Jul '17

Disregard my earlier message. Arthur G Szabo

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Help
by Marcus Mendes 28 Jul '17

28 Jul '17

Hi All, First of all I want to thanks for the great software. I'm having a problem with the surface calculation. My molecules have 384 aa, with a mutation in 9 positions between them (always in the Chain C). In some molecules there is a hole in the middle of surface (I'm using the Headless chimera). I already tried to customizing some options like probeRadius and Density, but I still have some molecules with a hole. There's anything that I can do to fix this? Best regards Marcus Mendes

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Opening DESMOND trajectories in Chimera,
by Shriyash Upadhyay 28 Jul '17

28 Jul '17

Hello, I am a researcher using DESMOND to run molecular dynamics simulations of protein-DNA interactions. However, I and others in my lab are most comfortable viewing trajectories and creating images in UCSF chimera. Is there a way to export DESMOND trajectories in a format that Chimera can open, either from maestro or some intermediate program like VMD? Thanks, Shriyash Upadhyay

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Incomplete Surface Model
by Bosung Kim 25 Jul '17

25 Jul '17

Hello, Do you know why my surface model is incomplete? I have attached picture. Thanks

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Program close during AutoDock Vina Session
by Nannette Yount 21 Jul '17

21 Jul '17

Hi, I had a computer shutdown during an Autodock Vina session (via Opal server) during the "execution in progress" stage. These sessions typically take between 5-6 days to complete, and now upon computer restart - when opening Chimera, I see no evidence that the session is still ongoing. The "get information" icon - where I could check Autodock status is also greyed out. Is there any way to get this session back - since it's probably still running on the server (process was about 3 days into the session)? Thanks, Nannette Nannette Y. Yount, Ph.D. Infectious Diseases Department of Medicine Harbor-UCLA Torrance, CA 90502

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morph interpolation
by Souroprobho Chowdhury 20 Jul '17

20 Jul '17

Hello, I am trying to use morph interpolate on two (for this post) PDBs (I2.pdb and I3.pdb, attached) but something peculiar is happening. The Hydrogen on the HIS 1082 (N1) does a ‘cork-screw’ like movement. Essentially, instead of interpolating directly from position A to B, it is taking a more round-about angle. A similar movement is observed for the O3 in the T1 O ligand. This problem has come up recurrently in my work and I am yet to find a solution. I have used most of the options that apply on morph interpolate that are mentioned on the chimera website without much improvement. I am using Maestro by Schrodinger to model my structures. Please find attached I2.pdb , I3.pdb and mov_all.pdb. mov_all.pdb is the trajectory file, works on Pymol (I am attaching a pymol script called auto-script.pml as well for selection of the correct residues, and a reasonable representation). The chimera interpolation script is also attached. Thanks! Souro

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Re: [Chimera-users] Define Plane
by Eric Pettersen 18 Jul '17

18 Jul '17

Hi Catherine, Remind me how exactly you are creating the axis in Chimera, and send me whatever script you are using to compute it yourself… —Eric > On Jul 18, 2017, at 8:24 AM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > Hi Eric, > > I am able to generate the axis. Like you said, we used the x,y,z axis subtracting it from centroid position and did the SVD. > For most cases, the axis is same as Chimera but for few it is little different. I checked the number of atoms used between both and it is same. > Are you using all the atoms or only specific atoms or is there any other thing I am missing? > > Thanks, > Catherine > > On Fri, Jun 30, 2017 at 7:13 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: > Chimera simply calls numpy.linalg.svd (singular value decomposition) on an array of the xyz coordinate (after the centroid position has been subtracted from them). The documentation for numpy.linalg.svd is here: > > https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.svd.html <https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.svd.html> > > It looks like it in turn calls LAPACK routine_gesdd, which is documented, in general, here: > > https://software.intel.com/en-us/mkl-developer-reference-c-singular-value-d… <https://software.intel.com/en-us/mkl-developer-reference-c-singular-value-d…> > > It’s an implementation of singular value decomposition, described in general terms here: > > https://en.wikipedia.org/wiki/Singular_value_decomposition#Relation_to_eige… <https://en.wikipedia.org/wiki/Singular_value_decomposition#Relation_to_eige…> > > The math is pretty complicated. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > >> On Jun 30, 2017, at 10:09 AM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu <mailto:catrajen@umail.iu.edu>> wrote: >> >> Hi Elaine, >> >> Thank you for helping me understand it. Can you give me more details about how PDB file is decomposed to find the plane and normal. Like, how the eigenvectors are calculated from the atomic coordinates. >> >> Thanks, >> Catherine >> >> On Thu, Jun 29, 2017 at 7:23 PM, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >> >> >> > On Jun 29, 2017, at 2:14 PM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu <mailto:catrajen@umail.iu.edu>> wrote: >> > >> > Hi, >> > >> Hi Catherine, >> >> > I am trying to understand how the plane is defined in chimera. Can you please help me with that? >> > >> > "Define a plane for the specified atoms. Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane)." >> > >> > Define a plane for the specified atoms. >> > - specified atoms, i use 'sel protein’ >> >> OK, so if using the graphical tool (Axes/Planes/Centroids) it uses the selected atoms, meaning all the protein atoms if you had used “sel protein.” If using the “define” command, you can just specify “protein” directly in the command to use all the protein atoms, without making a selection. >> > >> > Eigenvectors/values are calculated from the atomic coordinates >> > - atomic coordinates, so x,y,z coordinates of all atoms. (Can you please explain a bit more like how and what you read from PDB file to define plane). >> >> For the atoms you specified, there are ATOM lines in the PDB file with X,Y,Z coordinates. Each atom is a point in 3D (X,Y,Z). >> >> > >> > after subtracting the position of their non-mass-weighted centroid >> > - how is non-mass-weighted centroid is calculated >> >> It is the centroid of the points (atomic positions), not sure how else to say it. The average position of all the atomic points is the centroid. Non-mass-weighted just means all the atomic points are treated equally, instead of heavier atoms being treated as more important than lighter atoms. >> > >> > The plane is anchored at the centroid >> > - which centroid is this? Is the protein moved to the origin(0,0,0) position? >> > >> The centroid is the same centroid as in your previous question. Nothing is moved. >> > >> > Thanks, >> > Catherine >> >> You’re welcome. I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > >

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