- Chimera-users - RBVI Mailing Lists

How to study residue-residue interactions in Chimera?
by Ahmad Khalifa 17 Jan '19

17 Jan '19

How to study residue-residue interactions in Chimera? How can I show the bonds of the interacting residues? Regards.

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[MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany
by Harald Lanig 17 Jan '19

17 Jan '19

Dear list subscribers, we are very delighted to announce this year’s “33rd Molecular Modelling Workshop (MMWS)” (http://mmws2019.mgms-ds.de) that takes place on April, Monday 8th to Wednesday 10th, 2019, at the Friedrich-Alexander-University in Erlangen, Germany. The MMWS has a long history of giving young scientists (especially graduate students) the opportunity to present their work and dive into discussions with each other and the "older experts" of the field to gain valuable feedback from academic as well as industrial colleagues. Oral and poster contributions are welcome from all areas of molecular modelling – from the life sciences, computational biology and chemistry, cheminformatics, to materials sciences. Starting with the scientific program on Monday after lunch should allow to avoid travelling on weekend keeping the expenses at a minimum. A hearty workshop dinner and a traditional joint evening in Erlangen’s Steinbach-Bräu brewery complement the scientific program. The workshop is organised by the German Section of the Molecular Graphics and Modelling Society (MGMS-DS e.V.). ####### Satellite symposium in honour of Tim Clark's 70th birthday ####### Directly after the MMWS, there will be a one-day symposium on Thursday April 11th, 2019 to celebrate the occasion of Tim Clark's 70th birthday. You are invited to attend this meeting and extend your stay in Erlangen by an extra day. There will be invited lectures only and no contributed talks. There is no registration, conference desk, or extra fee. Nevertheless, we expect that you indicate your interest in attending on Thursday by checking the corresponding field during registration for the MMWS. For further information about our Birthday Symposium, please refer to "Tim-Clark-Day" via https://mmws2019.mgms-ds.de/index.php?m=113 ####### Pre-conference workshop ####### For the second time at our Molecular Modeling Workshop, Schrödinger is offering a pre-conference workshop entiteled "Structure-based Drug Design using the Schrödinger Suite". If you are interested in participating at the software session, please checkmark the corresponding field upon filling the registration form. ####### Plenary Speakers ####### We are very happy to announce that four outstanding researchers accepted our invitation to present a plenary lecture at the Modeling workshop: Matthias Bremer (Merck KGaA, Darmstadt) "The Role of Quantum Chemistry in the Development of Liquid Crystals for Display Applications" Ruth Brenk (University of Bergen) "Structure-based design of riboswitch ligands and selective NMT inhibitors" Bernd Meyer (University of Erlangen) "Chemistry at the solid-liquid interface" Rochus Schmid (Ruhr-University Bochum) "Force fields for porous coordination polymers - a tricky business" ####### Poster and Lecture Awards ####### As in the past years, there will be two poster awards of EUR 100 each and three lecture awards for the best contributed oral presentations: 1st winner: Travel bursary to attend the Young Modeller's Forum in London, UK, plus a speaker slot option at YMF (travel expenses are reimbursed up to EUR 500) 2nd winner: EUR 200 travel expenses reimbursement 3rd winner: EUR 100 travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. ####### Registration and poster/talk submission ####### Submit talks and/or poster titles via the registration form accessible on the workshop website https://mmws2019.mgms-ds.de/index.php?m=register The deadline for all submissions is February 22nd, 2019. ####### General information ####### Website http://mmws2019.mgms-ds.de will provide all necessary information about the meeting. We are looking forward to meeting you in Erlangen! - Paul Czodrowski, Scientific Committee Workshop Organisation 2019 - Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.de) -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen Fon +49 9131-85 20781 harald.lanig(a)fau.de Fax +49 9131-85 20785 http://www.zisc.uni-erlangen.de ------------------------------------------------------------------------

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transparency in BILD format
by Kovács Bertalan 14 Jan '19

14 Jan '19

Dear Chimera Users, I drew a polygon and a sphere in BILD format, and I was trying to make the polygon transparent so that when the sphere is behind it, it does not hide the sphere completely. I noticed however, that the .transparent command in BILD does not actually make the polygon transparent, it just makes it more pale by making its color resembling more and more to the background. Generally, that is what you would expect from 'transparency', but it still hides the objects (the sphere) behind it, which I was trying to make visible even through the polygon in the first place. Did anyone else had this problem? I attach my code below. Thanks, Bertalan Ková cs Pázmány Péter Catholic University ------------------------------------------------------------ .color red .sphere 0 0 5 1 .color blue .transparency 0.8 .polygon 5 0 0 0 5 0 -5 0 0 0 -5 0

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An Enquiry
by ONYEMA AUGUSTINE 10 Jan '19

10 Jan '19

Hi, I am Onyema, Augustine Chimezie; an MSc students in the department of Biochemistry, University of Nigeria Nsukka, Nigeria. I tried downloading chimera for ubuntu 16.04 for a 64 bits computer. I went to your site and tried the version for my computer but refused to download on opera mini. On trying Google Chrome the site didn't open at all. Is there something am not doing write. Kind regards, Onyema, A. C.

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Select density of particular sidechains
by BuddySphinx 08 Jan '19

08 Jan '19

Dear Chimera users, I have an EM map and pdb coordinates. I am trying to show density fit of some of my sidechain. I want to display a particular sidechain fitting into the density. I was trying to use zonesel feature: zonesel #0 (reference pdb):2 (residue #2) 3 (cutoff 3A) #1 (EM map) show sel But somehow it did not show the EM density of residue #2, rather the entire map. I am wondering what I did wrong? Best, Yangqi Sent from Mail for Windows 10

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Re: [Chimera-users] metadata mrc files
by Elaine Meng 07 Jan '19

07 Jan '19

Hi Tom, There is a “dumpHeaders” option of the volume command to send info to the Reply Log, e.g. vol #1 dump true <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> I believe that group/ungroup models is only in the Model Panel. Undoubtedly it could be done with python, but someone else would have to help with that. (Best to send questions to the list since the “group knowledge” exceeds mine!) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 4, 2019, at 5:36 AM, Tom Marlovits <thomas.marlovits(a)cssb-hamburg.de> wrote: > > Elaine, > one more question … is there a command file to also group models? > Thx > Tom > >> >> Hi Elaine, >> is there an easy solution to read out the header metadata of an .mrc file in chimera and report it to a text file? >> Thx >> Tom >> >> Number of columns, rows, sections ..... 80 80 80 >> Map mode .............................. 2 (32-bit real) >> Start cols, rows, sects, grid x,y,z ... 0 0 0 80 80 80 >> Pixel spacing (Angstroms).............. 0.6370 0.6370 0.6370 >> Cell angles ........................... 90.000 90.000 90.000 >> Fast, medium, slow axes ............... X Y Z >> Origin on x,y,z ....................... -25.48 -25.48 -25.48 >> Minimum density ....................... -0.80182E-01 >> Maximum density ....................... 0.11564 >> Mean density .......................... 0.19742E-03 >> tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 >> Space group,# extra bytes,idtype,lens .

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FW:
by Williams, Joanne 04 Jan '19

04 Jan '19

From: Ako Karimi <akokarimi111(a)yahoo.com> Date: Thursday, January 3, 2019 at 11:52 AM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: <no subject> Hello Good time Excuse me How should the form of compounds in software chimera be shown below?

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Re: [Chimera-users] [EXTERNAL] Re: fitting antibody and envelope protein structures to EM map of virus: C3 and icosahedral symmetries
by Tom Goddard 03 Jan '19

03 Jan '19

Hi Mike, Probably you would just fit a single antibody then replicate it 2 more times to make the C3 symmetry. You probably don’t need to do the symmetric fitting that takes into account clashes because the antibodies probably do not contact one another. I can only guess since I know nothing about your data. For finding the axis for the C3 symmetry I assume your map was computed with C3 symmetry so usually you know the exact axis because you know how the map was computed. For example if the map is a single spike, then usually the axis would be the z axis. If you don’t know how it was computed and you have to rederive the axis then you take two copies of the map, rotated one copy by hand approximately 1/3 turn and fit it into the first copy then use the rotation axis reported in the reply log for that fit, or use the "measure rotation” command to find the rotation axis between these two copies of the map. Tom > On Jan 3, 2019, at 10:14 AM, Kent, Michael S wrote: > > Tom, > > Thanks very much for your response. I have tried to fit a single spike with 3 antibodies that have C3 symmetry but I have not been able to correctly specify the axis vector. Can you give me some guidance on how to do that? > > Thanks, > > Mike Kent > > > From: Tom Goddard > Date: Wednesday, January 2, 2019 at 1:31 PM > To: "Kent, Michael S" > Cc: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: [EXTERNAL] Re: [Chimera-users] fitting antibody and envelope protein structures to EM map of virus: C3 and icosahedral symmetries > > Hi Mike, > > An icosahedral capsid has twenty 3-fold symmetry axes. Are the 3-fold symmetric spikes aligned with the 3-fold symmetry axes of the icosahedron? If they are then imposing the icosahedral symmetry will make the antibody binding to each spike 3-fold symmetric. If the spike 3-fold symmetry axes are not aligned with the icosahedron 3-fold symmetry axes (seems unlikely) then you would need to know where the spike 3-fold symmetry axes are and in that case I’d suggest fitting an antibody to a single spike using C3 symmetry with an explicitly specified axis vector. > > Tom > > > >> On Dec 26, 2018, at 4:43 PM, Kent, Michael S wrote: >> >> I have an EM map for a virus that includes an antibody bound to the envelope proteins. The envelope proteins are trimers of dimers with C3 symmetry that form spikes on the surface of the virus. I fit an atomic model for the spikes to the map using icosahedral symmetry, following the very helpful symmetric fitting video tutorial <http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/>. Now I am trying to fit a model for the antibody into the spike regions of the map. I need to impose C3 symmetry for the antibody for the fit into each spike, in addition to imposing icosahedral symmetry to include all the spikes. How can I impose both of these in the fit? >> >> Thanks, >> >> Mike Kent >> >> >> >> _______________________________________________ >> 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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how to interpret the output result
by Preksha Depani 03 Jan '19

03 Jan '19

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Rendering by arbitrary attributes in external file
by Healey, Joe 03 Jan '19

03 Jan '19

Hi chimera team, I use the Render by Attribute function frequently for models, but to date, I have only ever used it for rendering attributes determined 'internally' by chimera (hydrophobicity, AA conservation from an MSA etc). Is there a way to render residues by an arbitrary set of parameters? Imagine for instance, I have a csv that maps a residue number to a value (between 0 and 1). In my case this is antigenicity. ResNum, Res, Value 1, A, 0.927 2, T, 0.872, 3, W, 0.738 ... Can I read this file in via python/chimera commands and apply these values from an external file? Many thanks Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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fitting antibody and envelope protein structures to EM map of virus: C3 and icosahedral symmetries
by Kent, Michael S 02 Jan '19

02 Jan '19

I have an EM map for a virus that includes an antibody bound to the envelope proteins. The envelope proteins are trimers of dimers with C3 symmetry that form spikes on the surface of the virus. I fit an atomic model for the spikes to the map using icosahedral symmetry, following the very helpful symmetric fitting video tutorial<http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/>. Now I am trying to fit a model for the antibody into the spike regions of the map. I need to impose C3 symmetry for the antibody for the fit into each spike, in addition to imposing icosahedral symmetry to include all the spikes. How can I impose both of these in the fit? Thanks, ?Mike Kent

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MD animation of electrostatic map
by Bala subramanian 02 Jan '19

02 Jan '19

Dear Chimera users, I have a series of structures (tens of snapshots from MD) for which i have calculated the electrostatic potential (with APBS). I would like to know if there is any way,for instance using MD-movie plugin, to map the elect. potential corresponding to each structure so that i can actually visualize the changes in surface potential. All structures have been already fitted to a reference structure, hence there wnt be any rotation or translation. Any idea or trick to achieve such mapping would be greatly appreciated. Thanks, Bala -- C. Balasubramanian

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Adding Heme ligand to protein pdb
by Yangqi Gu 01 Jan '19

01 Jan '19

Dear Chimera users, I have a pdb file of my protein, but not showing the binding ligand (Heme). I know where the binding motif is and I am wondering is there a way I can add ligand to the binding motif and write out the new pdb file in Chimera? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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H bonds
by kloe brathon 31 Dec '18

31 Dec '18

Dear Chimera users, I want to calculate H bonds between the ligand of my protein and its nearby residues. Could you give any suggestions on how to select this residues and calculate H bonds between them and the ligand? Kind regards,Kloe

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Visualizing SwissDock clusters.dock4.pdb
by Francesco Pietra 31 Dec '18

31 Dec '18

Hi all I am trying to open sequentially with chimera the various clusters generated by SwissDock (file clusters.dock4.pdb in the output). I was only able to extract clusters from clusters.dock4.pdb and view them, one by one, with chimera. Or a way to highlight the varius pdbs from loading clusters.dock4.pdb and target.pdb, in order to see where they are located. The web gui by SwissDock was much too grob. Thanks for advice francesco pietra

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Re: [Chimera-users] Help on removing ligand on a pdb file with protein in complex with ligand and viewing the conformational change
by Elaine Meng 26 Dec '18

26 Dec '18

Dear Kei Onn, When you open the structure in Chimera, the conformers are already separate submodels, and it looks like they are already superimposed. Also you can delete the ligand residue in all submodels at the same time using the ligand residue name, which is “PKA” according to the the information for this structure at the RCSB PDB: <http://www.rcsb.org/structure/2MGY> I.e.Chimera command: delete :pka However, you need to consider what makes scientific sense. If you just delete the ligand, Chimera is not going to predict the change in the rest of the structure, so it will just look exactly the same as it did before except without ligand. Instead you should search the PDB for a structure of the same or similar (e.g. homolog in different species) protein that has been solved without the ligand. Then you would actually have something different to compare to the structure(s)with the ligand. One way to search is with Blast Protein in the Chimera menu under Tools… Sequence. You have to look through the results and figure out which ones do and don’t have ligand. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/blast.html> I’m sure there are other ways to look for related structures, so you could certainly use other programs or websites to do that. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 24, 2018, at 6:55 PM, #LAI KEI ONN# <KEIONN001(a)e.ntu.edu.sg> wrote: > > Dear Elaine, Eric, Chimera Team and fellow users > > Thank you very much for the great work in developing Chimera! > I was wondering if there's a way in Chimera for me to visualise my protein of interest without the ligand bound to it and for me to visualise it's original unbound conformation ( so that i can compare bound and unbound protein). > > In addition, i realised that the PDB file has 20 conformers of the protein-ligand complex. > Therefore I thought that my steps/strategy would be > • split the 20 conformers into submodels > • del ligand and to do a loop on it for the 20 submodels. > • superimpose all 20 conformers (unbound) vs 20 conformers (bound with ligand) > > Please advice if my steps are right or I am missing something. > > PDB file is 2MGY > > Thank you! > > Once again really appreciate all the work and technical advice provided for Chimera > Best > Kei Onn

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Changes in protein stability
by kloe brathon 25 Dec '18

25 Dec '18

Dear Chimera Users, I am studying on aprotein and its interactions with its ligands and I want to explore what wouldbe the effect on protein thermodynamic stability if some parameters were changed such asaddition, removal of hydrogen bonds or other forces. Any idea on how to dothat? I am new on this. Thank you on advance! Kloe

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Topology error
by Gonzalez Fernandez, Cristina 19 Dec '18

19 Dec '18

Dear Chimera users, I want to perform molecular docking by using Swiss Dock. Therefore, I have used Chimera to remove the molecules that I don't want from the PDB file, add hydrogens and save as mol2. However, when I tried to upload the mol2 file in SwissDock I get this error: "Ligand setup failed. Please check that your structure file has a correct topology. No extra info available". Does anyone know what I am doing wrong? Thank you in advance, C.

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Script to minimise the binding site
by Miro Moman 18 Dec '18

18 Dec '18

Hello, I would like to minimise the binding site including ligands, cofactors and water molecules. I have the following script: ___ runCommand("open " + pdbpath + pdbid + "_chimera.pdb") runCommand("findclash 'ligand | solvent' test '~ligand | ~solvent' overlapCutoff -1.0 hbondAllowance 0.0 intraMol false selectClashes true") runCommand("sel up") runCommand("namesel tomin") runCommand("minimize spec tomin fragment true cache true prep true freeze :@ca cgsteps 0") runCommand("write format pdb #0 " + pdbpath + pdbid + "_min.pdb") runCommand("write format mol2 #0 " + pdbpath + pdbid + "_min.mol2") ___ I am facing two issues: 1) Water molecules are deleted by prep. Is there as way of preventing this. I have tried creating a custom preferences file like: echo "{'AddCharge': {'charge method': 'Gasteiger'}," > ${DIR}/chimera_preferences #echo " 'DockPrep': {'delete solvent': 'false'}," > ${DIR}/chimera_preferences echo " 'DockPrep': {'incomplete side chains': 'rotamers'}}" >> ${DIR}/chimera_preferences However, the second option is not recognised. Does it exist and, if so, what would be the correct syntax? 2) The second problem is that the selection is ignored and every atom except CAs is minimised. Another option I have tried be setting prep to false and running it beforehand: models = chimera.openModels.open(pdbpath + pdbid + "_chimera.pdb") prep(models, delSolvent=False) But, again, if I do this, the selection is also ignored. Best, Miro -- Edelmiro Moman, PhD South Ural State University - SUSU Южно-Уральский государственный университет - ЮУрГУ Phone: +7 902 614 73 77 E-mail: miromoman(a)gmail.com https://www.linkedin.com/in/edelmiro-moman-3a9979a/

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Measuring the distance between an atom and the protein surface
by Sergio Garay 18 Dec '18

18 Dec '18

Dear Chimera Users I want to measure the distance between an atom (or group of atoms) and the protein surface. I need a sort of residue depth, so the shortest distance between an atom and the molecular surface would be fine for me. I found that command "measure distance" could help, but it does not appear to be working, because every atom that I choose give aproximately the same value. For example (I have only one molecule loaded in Chimera) :. measure distance #0:1@ca #0 log info: minimum distance from #0:1.B@CA to 1752 atoms, 1 surfaces = 1.4814 measure distance #0:58@ca #0 minimum distance from #0:58.B@CA to 1752 atoms, 1 surfaces = 1.4484 The second selected atom is clearly deeper inside the protein Thank you in advance Sergio -- *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Re: [Chimera-users] Chimera
by Elaine Meng 16 Dec '18

16 Dec '18

> On Dec 16, 2018, at 6:05 AM, Xhoela Bame <xhoelabame(a)yahoo.com> wrote: > > Hello, > > I hope this message finds you well. > > I had posed a question in chimera website but maybe it did not come to you. > > I am studying ligand interaction with a protein and there are pi pi interaction. I am not sure on what is the principle I have to use to show that there is this type of interaction and illustrate that with chimera. > > Also, when showing H bonds, I want to show residue side chain as well in the picture as open structures. Any suggestion on that? > > I am quite new in using chimera and I would be extremely helpful if you would help me on these questions. > > Best, > Ann Hello, In the future, please send questions to chimera-users(a)cgl.ucsf.edu rather than to me directly, and put something useful about the topic in the Subject line like “showing side chains” or “pi-pi interactions.” I did reply to you already about the pi-pi question but perhaps you did not see the answer. I changed the subject line because “Chimera Usage” was not descriptive. Here is that previous answer: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015270.html> To show the side chains, turn on this option of FindHBond before running the H-bond calculation: "If endpoint atom hidden, show endpoint residue” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo…> If you click Help on the FindHBond dialog it would show you that page. Or if you are using the commands, command “help hbonds” would show you the “hbond” command help and its “reveal” option to do the same thing. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Question about Gaussion filtering
by CAO, Sheng 13 Dec '18

13 Dec '18

Dear Sir/Madam, I am a Ph.D student from The Chinese University of Hong Kong that have just begun to learn structural biology. I found that the Gaussion filtering in Chimera has a much better result than other programs. And I an quite interested in it. Could you please share the principle of the Gaussion filtering algorithm used in Chimera? Thank you. Best Regards, Cao Sheng Postgraduate of The Chinese University of Hong Kong Major: Chemistry E-mail: 904323223(a)qq.com<mailto:904323223@qq.com> Address: G55, Science Centre South Block, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong P.R.China

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Trajectory superposition question
by Samo Lešnik 13 Dec '18

13 Dec '18

Dear Madam/Sir, I have a long MD trajectory (dcd files), and before performing analysis on it I would like to superimpose every frame to the protein from the first frame or the protein from the average one. I am not sure how can this easily be performed. Thank you for your answer, Samo Lešnik

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An oddity in ribbon.
by Yehuda Halfon 13 Dec '18

13 Dec '18

Hi, I have an oddity when showing ribbon. When I show the loop (see figs) in ribbon I get the small thing in the middle and when I show it in atom the loop is longer. In coot the loop looks fine. Is it in the PDB? is in a chimera error? It only happens in this loop in this PDB. The same loop in other PDBs is fine. Thanks, Yehuda Halfon

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Color subunits for map density
by BuddySphinx 12 Dec '18

12 Dec '18

Dear Chimera developers, I have a quick question about coloring. I have a filament map with multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament? Best, Yangqi Sent from Mail for Windows 10

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Chimera Usage
by Xhoela Bame 12 Dec '18

12 Dec '18

Hello, I am new in using chimeraand new in this group. I was wondering if I can ask questions related to thetechniques here. I want to study the pi-pi interactions between a protein andits ligand. Any suggestions on how to do that using chimera? Thanks! Ann

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Programmatic selection and minimisation
by Miro Moman 10 Dec '18

10 Dec '18

Hello, I am trying to use Chimera programmatically in order to automatise a number of tasks. I have tree questions: 1) When I select a zone around the ligand (for instance "runCommand(select #0:501.A zr<5)" the selection level is either atoms or, in this case, residues. Is there a way to select molecules? Because the problem I am finding is that if I run "runCommand(select up)", depending on the PDB file, sometimes I need to do it twice and sometimes three times in order to select the entire molecules (be them proteins or not). I would like to have more control over this function. The purpose being deleting molecules that are far away from the ligand. 2) Right now I am running "DockPrep" followed by "minimize" (without further "prep"). The reason is that "DockPrep" enables me to set options, whereas for "minimize" with "prep" this possibility, if it exists, does not seem to be documented. Is that the case? 3) Finally, in "DockPrep", is there a way to select the charge model explicitly? For instance, to choose Gasteiger charges in order to save time. Kind regards, Miro -- Edelmiro Moman, PhD South Ural State University - SUSU Южно-Уральский государственный университет - ЮУрГУ Phone: +7 902 614 73 77 E-mail: miromoman(a)gmail.com https://www.linkedin.com/in/edelmiro-moman-3a9979a/ <https://www.linkedin.com/in/edelmiro-moman-3a9979a/> <edelmiromoman(a)rcsi.ie>

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Questions about the electric fieldline
by xmgign＠126.com 07 Dec '18

07 Dec '18

Hi I want to make the electric fieldline but there are always some problems. I did this as follows, 1. run add charge to the system 2. run APBS, the I get the electrostatic surface and a file named 1.dx 3. open 1.dx 4.measure fieldLines #0 lines 500 startAbove 10 color pink linewidth 2 then I get the problem : no volume specified I have check the userguide of measure fieldlines, but there is nothing about the volume. measure fieldLines map-model(s) [ lines N ] [ startAbove cutoff ] [ step s ] [ modelId model-number ] [ color line-color ] [ lineWidth width ] [ tubeRadius radius ] [ circleSubdivisions M ] [ markers true|false ] what should I do next? Thanks. Qiao Xue xmgign(a)126.com

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changing atomic radii in Chimera
by Elaine Meng 07 Dec '18

07 Dec '18

Hi Yu Guo, (including chimera-users in the message since it is a general question that other people might be interested in) You can change atomic radii as shown in sphere style with command “vdwdefine,” for example <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> vdwdef -0.2 Ca (subtract from current size) vdwdef 1.0 Ca (set size to specific value) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> Maybe the single O atoms (those without bonds) are in stick style, however, so you would also need to change them to sphere style to see a difference. Since the molecule also has O you wouldn’t want to use “O” in the commands or you would change them all. Instead you could select them (Ctrl-click on atom) and then use “sel” in the command, e.g. repr sphere sel vdwdef 0.8 sel Actually, if you select the atom(s) another way is to use Selection Inspector (open by clicking green magnifying glass icon near the bottom right of the Chimera window) to change their display style and radius. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 7, 2018, at 11:05 AM, Yu Guo <yg2(a)kth.se> wrote: > > The movie is fine now! I am now wondering how can I change the atomic radii in Chimera? I find Ca is much too big, and O is too small. See the attached movie.

1 0

mmcif, auth_xx information versus label_xx information
by moocow＠mindless.com 07 Dec '18

07 Dec '18

2 3

Re: [Chimera-users] Breaking down symmetry in Chimera
by Elaine Meng 06 Dec '18

06 Dec '18

Hi Anne, It is recommended to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d here) since others may be able to provide better answers or benefit from the exchange. My guess is that you might instead want to use symmetrical fitting, in which multiple copies of the atomic structure automatically maintain the specified symmetry. Symmetrical fitting is available in the “fitmap” command (not the GUI). See documentation <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#symmetric> and video tutorial <http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/> The video is >6 minutes but worth watching, because like in that video you may need to first just fit one copy (not using symmetry), then use command “measure symmetry” to annotate the map with its symmetry, and then use command “sym” with “update true” to generate the symmetry copies of the atomic model. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 6, 2018, at 10:32 AM, Jecrois, Anne <Anne.Jecrois(a)umassmed.edu> wrote: > > Dear Dr Meng, > I have a 5A cryoEM map with D3 symmetry, howeve I am having some problem with rigid body fitting since I don't know where one assymmetric unit starts or ends . I was wondering if there is way to break down the symmetry in chimera and extract 1/6 of the map and use that for fitting? > Thanks, > Anne Jecrois > PhD Candidate > UMass Medical School > Schiffer Lab/Royer Lab > 364 Plantation St, LRB 970L > Worcester MA 01605

3 3

Saving mrc EM-map
by Ibrahim M. Moustafa 06 Dec '18

06 Dec '18

Hi All, I'm trying to do the fitting of a model into EM (mrc map) for real-space-refine in phenix.First I read the map and clicked "center" in the Volume viewer. Then I saved the centered map, assuming that the header info will be updated in the saved map.I did the fitting and saved the model relative to the map. Reading the saved map and fitted model back looks OK. However, when I do the real-space-refine in Phenix, the CC-value during the run is really low (0.01) suggesting something is not properly done. I checked the header (using mrcfile) of the saved "centered" map and compared it to the original map and it is the same "0,0,0". Which means chimera did not update the header after centering. I'm not if there is a more proper way to do this! Any advice? Thank you for your help. Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park, PA16802 Tel (814)863 5940 Fax (814)865 7927

2 2

join models
by Stewart Morley 05 Dec '18

05 Dec '18

I cannot for the life of me get join models to work. 1. I have two structures. 2. The structures overlap. 3. I align them using matchmaker. 4. I delete the overlapped residue from one chain. 5. I select the appropriate C and N terminal residues 6. I try to use join models under Build structure 7. The apply box remains gray, no matter what residue or atom I select. What are common problems that cause join models to not work? Stewart Morley Brigham Young University

2 2

needing help for separating structures
by Yu Guo 30 Nov '18

30 Nov '18

Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY? cluster and all its ligands? Thank you very much! Best wishes

4 12

UCSF import Error
by Cackett, Gwenny 28 Nov '18

28 Nov '18

Hi so I am running Linux Fedora 29 and since updating from Fedora 28 I have noticed my Chimera installation has stopped working - the icon does not open the program. And when I try to run from the command line I get the code below, which I gather is an issue with python importing a module: Traceback (most recent call last): File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/chimeraInit.py", line 628, in init import chimera File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/chimera/__init__.py", line 2758, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/home/gwenny/.local/UCSF-Chimera64-1.12/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var Any help would be appreciated. Thanks and best wishes, Gwenny Cackett PhD Student RNAP Lab Institute of Structural & Molecular Biology University College London Gower Street, London, WC1E 6BT Phone: 020 7679 3899

2 1

Chimera Interface to Modeller
by Alisson Oliveira 28 Nov '18

28 Nov '18

Good night, I would like to construct a human DDX3 homology model in its closed conformation. However, I can not perform a proper alignment. I target the sequence Uniprot ID: O00571 and as models the PDB structures: 2I4I and 2DB3. However, the generated models present unsatisfactory results in terms of their quality. Attached is the image of the alignment. Can you help me??? [cid:3ddc1e68-24f3-40bf-8654-0fea58f849dc] [cid:e60c81ce-40de-4d0e-8e3a-a071a3aca2d0] Att. Alisson Felipe de Oliveira Farmacêutico CRF/RS: 18468 Mestrando em Ciências Farmacêuticas - UNIPAMPA

2 1

Matching of small molecules
by Cassandra Ceccopieri 28 Nov '18

28 Nov '18

Dear Sir/Madam, I would like to ask how to overcome the following problem that I faced trying to perform an alignment of small molecules. Writing in the command line section the following instruction: match #0 at c5,c4,n7,c8,c9,s10 #1 at c9,c8,n11,c12,c13,s14 I obtain, as output, an error message saying: Error in "#0 at c5,c4,n7,c8,c9,s10" must be an integer. I checked the tutorial but the instruction for the command line seemed in the same format as mine. Therefore, I would like to ask assistance to be able to perform my analysis. Kind Regards, C.

2 2

Using Per-Frame commands to recolor structures with attribute data is very slow
by David Slochower 27 Nov '18

27 Nov '18

Hi, As a follow up to this thread (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003712.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003712.html>) from 2009, I’d like to color a model by a custom attribute that changes from frame to frame. Using the workaround mentioned in that thread, we are able to use Per-Frame commands to load a new attribute file each frame, and then color the structure by the attribute, but this awfully slow (probably over 1 second per frame). Is there a way to cache the attribute data? Or a way to improve the performance of defining the attributes and re-coloring the structure? I know that I could use a Python script to load each coordinate frame with its associated attribute data, save images, and then stitch them together for a movie, but the current goal is for data exploration.

2 2

Announcement: Release of DOCK 6.9
by Scott Brozell 27 Nov '18

27 Nov '18

We are pleased to announce the release of DOCK 6.9. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.9 is available for download and free for academic users at http://dock.compbio.ucsf.edu/. This is a release of the new ligand searching method DOCK_DN: De Novo design using fragment-based assembly. De novo design can be used to explore vast areas of chemical space in computational lead discovery. DOCK_DN is an iterative fragment growth method, in which new molecules are built using rules for allowable connections based on known molecules. For full information on what is new in DOCK 6.9, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.9.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

1 0

chimera --nogui --script option not doing anything!
by Ahir Pushpanath 27 Nov '18

27 Nov '18

Dear Chimera crew, I am having serious trouble running my script using chimera --nogui --script option. I tried running a simple script that just prints a comment, and i dont get anything returned on the cmd, let alone the actual script. The cmd does not flag up any errors , it just does nothing and return back to the prompt. I have chimera 1.13.1 and its added to the system path - "C:\Program Files\Chimera 1.13.1rc\bin\". I can launch chimera fine from the command line showing its added to path fine. I am completely stumped! Also, the script works fine within the IDLE of the GUI. See code below: import os > print "Script is running" > from chimera import runCommand as rc # use 'rc' as shorthand for runCommand > from chimera import replyobj # for emitting status messages > # change to folder with data files > os.chdir("C:/Users/JM/Documents/Public Qsync/Jenny > Taylor/IREDs/Structures/") > # gather the names of .pdb files in the folder > file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] > # loop through the files, opening, processing, and closing each in turn > for fn in file_names: > res = "tyr" > if fn == ""2NAD.pdb": > print fn > replyobj.status("Processing " + fn) # show what file we're > working on > rc("open " + fn) > for b in range(1,300): > rc("sel #0" + ":"+str(b)) > rc ("swapaa "+res + " sel criteria p") > rc ('write format pdb #0'+ " " + fn > +"_"+res+'mutated.pdb') > rc("close all") > # uncommenting the line below will cause Chimera to exit when the script > is done > rc("stop now") -- Dr. Ahir Pushpanath* PhD.* Senior Biologist, Johnson Matthey.

2 1

dsv to Chimera format
by Tavangari, Simin 27 Nov '18

27 Nov '18

Hello, I do not know how to open a discovery studio visualizer (.dsv) file in Chimera. Can you please help me with that? Thank you. Best regards, Simin

2 4

needing help for separating structures
by Elaine Meng 26 Nov '18

26 Nov '18

P.S. I recommend you do not use that PDB file because it is missing much of the information that is in the original mmCIF file Elaine

1 0

Basic question re: nucleotide sequence
by Pecot, Chad V. 26 Nov '18

26 Nov '18

Hello, I am trying to use Chimera to predict the structure of a nucleotide sequence that does not have a PDB ID. This is an unstudied protein, and I’m hoping to get some structure information and to visualize it using the software. I tried using the tutorials, but the best I can tell it appears to work off of already available PDB IDs. Is there a way I can enter the nucleotide sequences as a starting point? If so I’d really appreciate a few step/steps on how to do this. Best, Chad _______________________________________ Chad V. Pecot, M.D. Assistant Professor UNC Lineberger Comprehensive Cancer Center Thoracic Medical Oncology 450 West Drive, Office 32.048 Chapel Hill, NC 27599 Office: 919-966-4779 Cell: 615-305-3955 Fax: (919) 966-6735 pecot(a)email.unc.edu

2 2

A script for deleting discontinuous/disconnected parts of a map, similar to the hide dust function in Chimera
by CHI-MIN HO 24 Nov '18

24 Nov '18

Hello Chimera Team, I would like to write a script that can automatically remove smaller blobs (disconnected parts) of a volume, exactly likely how the hide dust function works in chimera, except I want it to be automated. I would like a script that can automatically determine a good threshold, then rank the parts/volumes in the box by size, and then remove all but the largest volume, and save the result as a new volume. Do you have any existing code or sample code that accomplishes anything like this that you could point me toward? Or if not, would you be able to advise me as to the best way to achieve this? Thank you in advance! Best wishes, ~Mimi

2 1

Running AddCharge from the command line
by Samuel FreemanFox 21 Nov '18

21 Nov '18

Hi, I am attempting to automate Vina with a python script and want to use addH and addCharge before running Vina, however I cannot run addcharge without the window opening asking me to specify net charges. I was wondering if you could advise on the correct way of writing this command Many thanks, Samuel Freeman-Fox ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Porton Biopharma Ltd, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. *******************************************

2 1

Dual transparency in chimerax
by Yehuda Halfon 21 Nov '18

21 Nov '18

Hi all, I want to make a picture with one protein in transparency 90 and one of its subunits in transparency 40. On thier on this works fine. But when I try them together the 40 is gone inside the whole protein. Is there a way to do it in chimerax? Yehuda Halfon

2 5

Enquiry docking
by Thuluz 20 Nov '18

20 Nov '18

Dear Chimera users and technical assistance, I would like to ask you about molecular docking issue. We are performing a number of blind dockings, always by posing the grid box at the centre of a given molecule, the box had always the same size. Our question is why sometimes we get docking results very close to the centre and sometimes further away from it? is it only random or depends on physic-chemical properties? thanks in advance for any help on this matter, my best regards -- *Dr. Thuluz Meza Menchaca*

2 2

Helix axis and correction
by Gulsevin, Alican 20 Nov '18

20 Nov '18

Hello everyone, I have a question about the "helical correction" option for calculating helix axes. I've been trying to find the exact calculation Chimera uses to correct the helix axis, but I couldn't find anything specific in the archives and I also couldn't figure it from the source code. Where can I find a detailed description of how the helix axes and the corresponding corrections are calculated? Thanks for your help, Alican Gulsevin, PhD Postdoctoral Researcher Vanderbilt University Department of Chemistry Center for Structural Biology - Meiler Laboratory 465 21st Ave South Nashville, TN,37221 Office: MRBIII, Room: 5150C Phone: (615)-936-6594

2 3

Movie Recorder Frame Options not available
by Angela Gehrckens 20 Nov '18

20 Nov '18

Dear Sir or Madam, I am trying to record a movie in Chimera 1.13.1, but I consistently get the following error without a proper error message: "An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ". I think there might be a problem with the frame directory, but I can neither change the frame options (they are hidden) nor do I find any information on how to get the permission to change the fram options. I'd be very happy to receive help from you concerning this matter. Kind regards, Angela Gehrckens --- Diese E-Mail wurde von Avast Antivirus-Software auf Viren geprüft. https://www.avast.com/antivirus

3 2

Some UCSF Chimera marker (.cmm) bonds written as pseudobonds in pdb
by Jun Ha Song 20 Nov '18

20 Nov '18

Dear RBVI, I have UCSF Chimera marker set made by Volume Traver, and I used "Write PDB" in the model panel to transfer the .cmm file as .pdb file. However, when I opened newly created .pdb file, only about 4.3% of bonds were being shown as bonds, and the rest were being shown as pseudobonds. Is there any reason for this phenomenon? Best, Junha.

2 1

Ligand Receptor docking
by Shriwas, Pratik 20 Nov '18

20 Nov '18

Hi, I am trying to use UCSF chimera to study ligand-docking interactions. My protein is GLUT1 (4pyp - PDB) and a small molecule called DRB18 .I have used NIH pubchem browser to generate a smiles string for this compound and used the smiles string to generate a 3D structure in chimera. I have found that the compound interacts with protein in central cavity and interacts via hydrogen bonds (depending on parameters). I want to know whether my data is publishable. If docking studies performed using chimera are acceptable. People use softwares like Schrodinger/medusa among others. If you wish to see my work, I can send it in as well via email. Thank you. Regards, Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.

2 5

how to make/delete hydrogen bond and delete chains
by Paris Tzou 19 Nov '18

19 Nov '18

Hi, I have a protein-dna complex structure with protomer as A as protein and B as DNA. It is impossible in hbond function to "generate" hbonds between two chains (A and B). One have to parse protein and DNA into two files and load into Chimera as two models. Another question is that, once generated, hbonds cannot be "erased" in the chimera view. And "delete chain ID" cannot really delete one chain from protein-DNA complex. What I am doing is 5MCT, p53-DNA complex. Thanks a lot for your help. Paris

3 11

generating/saving mask files using segmentation
by Uhnsoo Cho 19 Nov '18

19 Nov '18

Hi, I am a beginner and still in the learning phase of chimera. Here is my question. I generated the mask from relion (mask creation) and open the mask in chimera. Using segmentation, I successfully split the mask into three segments and saved them individually. Then, I found that each mask file changes its box size (smaller than the original mask) and failed to run the multi-body refinement in relion. Using relion_image_handler (--new_box), I changed the box size but now the origin is shifted and all three masks are overlapping each other by losing their relative position. Is there a way to save the segmented mask maps by maintaining its original box size and relative position? Thanks. Best, Uhnsoo

2 1

Using headless chimera to create images
by Chemmama, Ilan 19 Nov '18

19 Nov '18

Dear developers, I am trying to create a bunch of images using Chimera. I wrote a script that create the scene using the following steps: mc_frame=str(INPUT_FRAME_NUMBER) rmffile=str("PATH_TO_RMF") runCommand('open '+rmffile) runCommand('set bgcolor white') runCommand('windowsize 1028 1028') runCommand('~set depthCue') runCommand('set projection orthographic') runCommand('wait 2') runCommand('scale 0.75') runCommand('copy file ./Image_'+mc_frame+'.png PNG supersample 3 dpi 300') runCommand('close all') runCommand('stop now’) While the scrips works in the headless version using PDB files, I have not been successful when using RMF files. The images when using the RMF files are just the background color (red when set to red, blue when set to blue) without the structure. I tried also to add the display .2 option as in: runCommand(‘display #0.2’) which corresponds to the RMF beads scene in the model panel. I should add that using the GUI version of chimera, the script works fine and all the images are properly created. Do you have any hints/clues on what could be done to make it work? (I am running the script the full version of chimera but the headless should be more efficient). Thanks, Ilan

2 1

Difference map
by Yangqi Gu 18 Nov '18

18 Nov '18

Dear Chimera users, I am trying to examine two cryo-EM maps and want to know if there is a subtle change between these two. I want to calculate the difference map, is it doable in Chimera? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

3 5

Can the order of map histograms on Volume Viewer be sorted?
by Jun Ha Song 16 Nov '18

16 Nov '18

Dear RBVI, Sometimes I accidentally open more than 4 maps into UCSF Chimera session without changing the number of histogram that can be shown to some value higher than the default value of first 3 maps. UCSF Chimera places new histogram on the spot where the 1st map used to be, and the histogram order shown on Volume Viewer goes from - 1st map - 2nd map - 3rd map to - 4th map - 2nd map - 3rd map from top to bottom. I know that I can bring back the histogram of 1st map by clicking on Data drop-down menu, but it doesn't bring back the 1st map to the top slot. Is there any way to manually re-sort the order of the histogram so that it would be in the order of their loading (or in the order of their model ID)? Best, Junha Song.

2 1

How can I export the list of hydrogen bonding and clash/contact?
by Paris Tzou 15 Nov '18

15 Nov '18

Hi, I have a structure of protein-DNA complex. How can I export the list of hydrogen bonding and clash/contact, please? Thanks a lot, Paris

2 2

Re: [Chimera-users] Fwd: Re: How to correct this error: ~/usr/chimera-1.12/lib/libgomp.so.1: version `GOMP_4.0' not found (required by /usr/lib/libopenbabel.so.4)
by Francois Berenger 14 Nov '18

14 Nov '18

On 11/15/18 9:51 AM, Francois Berenger wrote: > > > -------- Original Message -------- > Subject: Re: [Chimera-users] How to correct this error: > ~/usr/chimera-1.12/lib/libgomp.so.1: version `GOMP_4.0' not found > (required by /usr/lib/libopenbabel.so.4) > Date: 14/11/2018 18:42 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Francois Berenger <mlists(a)ligand.eu>, chimera > <chimera-users(a)cgl.ucsf.edu> > > That looks like a problem between libopenbabel and Chimera. The bug is > that libopenbabel.so was compiled with a newer compiler than what > Chimera was compiled with. You can try renaming > chimera-1.12/lib/libgomp.so.1 (eg., to libgomp.so.1.save) to see if it > fixes the problem. Yes, this workaround works: mv ~/usr/chimera-1.13/lib/libgomp.so.1.bck ~/usr/chimera-1.13/lib/libgomp.so.1.bck And I also needed to issue that one: mv ~/usr/chimera-1.13/lib/libz.so.1 ~/usr/chimera-1.13/lib/libz.so.1.bck > While I consider this a bug with the Python > openbabel package, it should be bundling and using a libopenbabel.so > that is compatible with the Python "manylinux1" ABI (based on CentOS 5), > we will investigate incorporating a workaround. Thanks a lot. Francois. > -- Greg > > > On 11/13/2018 5:53 PM, Francois Berenger wrote: >> Hello, >> >> On a Ubuntu 18.04.1 LTS, I get this error message when I start chimera. >> >> Is there a known fix? >> >> Am I running a too old version of chimera or should I run >> a version specially compiled for Ubuntu computers? >> >> Here is the full error message: >> --- >> # chimera >> Error while importing plipgui from >> /home/berenger/.local/lib/python2.7/site-packages: >> Traceback (most recent call last): >> File >> "/home/berenger/usr/chimera-1.12/share/chimera/extension/base.py", >> line 349, in _importExtension >> __import__(module) >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plipgui/ChimeraExtension.py", >> line 8, in <module> >> from plipgui.core import cmd_plip, cmd_unplip >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plipgui/core.py", >> line 50, in <module> >> from plip.modules.preparation import PDBComplex >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/preparation.py", >> line 13, in <module> >> from .detection import * >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/detection.py", >> line 12, in <module> >> from .supplemental import * >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/supplemental.py", >> line 26, in <module> >> import pybel >> File "/home/berenger/.local/lib/python2.7/site-packages/pybel.py", >> line 53, in <module> >> import openbabel as ob >> File >> "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line >> 21, in <module> >> _openbabel = swig_import_helper() >> File >> "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line >> 20, in swig_import_helper >> return importlib.import_module('_openbabel') >> File >> "/home/berenger/usr/chimera-1.12/lib/python2.7/importlib/__init__.py", >> line 37, in import_module >> __import__(name) >> ImportError: /home/berenger/usr/chimera-1.12/lib/libgomp.so.1: version >> `GOMP_4.0' not found (required by /usr/lib/libopenbabel.so.4) >> --- >> >> Thanks a lot, >> F. >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

(1) Autodock Vina executable on windows (2) selection of submodels
by Visvaldas K. 14 Nov '18

14 Nov '18

Dear colleagues, I'd like to report a couple of issues which have cropped up. (1) On Windows, running Autodock Vina in Chimea using local executable fails due to spaces in file path (gives error something like "File "C:\Program" not found). The thing is, the university computer admins do not allow change paths or copy system files around. It should be possible to escape spaces in file names, wouldn't it? (2) The selection of submodels does not work if it is used as a part of the list. For example, "sel #1.1" selects just the submodel 1 (let's say I have a set of 20 molecules in sdf file), which is fine, while "sel #1.1,#0" selects ALL submodels in #1 in addition to #0, and that does not seem to be right. Best regards, Visvaldas

5 4

Secondary structure recognition issue in homology model
by Monika Tokmina-Lukaszewska 13 Nov '18

13 Nov '18

Dear Chimera Team, In my homology model (see attachment) it looks like there has been some issue with secondary structure recognition in one of the domains (highlighted in cyan). In .py file I added one of the protein templates (yellow) based on which the C-terminal domain was constructed. I am not sure what has happened to a final model, since template for that domain looks good. I was wondering if there is an option in Chimera which could fix that issue? Thank you for your time, Sincerely, Monika Lukaszewska -- Monika Lukaszewska, Ph.D. Senior Research Scientist Chemistry & Biochemistry Department Montana State University Bozeman MT, 59717 lab: (406) 994 5418 tokminalukas(a)montana.edu <tokminalukas(a)chemistry.montana.edu>

2 3

Chimera installation
by Gonzalez Fernandez, Cristina 13 Nov '18

13 Nov '18

Hi all, I am new in the molecular docking field and I would like to start using Chimera. I would like to install it in Linux but use a GUI as in Windows. Is it possible? Thank you in advance! Cristina

2 1

Save measured distances
by Dhananjay 13 Nov '18

13 Nov '18

Dear all, I am calculating distance between CA atoms as follows: sel #0:13@CA, #0:129@CA color red selection distance #0:13@CA #0:129@CA I want to save the measured distance between residue 13@CA and 129@CA in a file. I can do it using GUI. How can I do this within the command line ? Any help would be appreciated !! Thank you -- Joshi

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Editing mol2
by Francesco Pietra 13 Nov '18

13 Nov '18

Hi all: Is it possible editing .mol2 files with chimera? thanks francesco pietrta

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Drawing vectors depicting the movement of one conformer to another
by Beth Stroupe 12 Nov '18

12 Nov '18

Hi, I would like to make a figure depicting the movement of an RNA molecule from one conformation to another. It is not a simple rigid body rotation or translation but a rolling motion where some parts of the molecule move more than others. I would like to show vectors to show the rotation that are colored coded by the distance of the move. Is there a straightforward way to do this in Chimera? Thank you, Beth

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how to create using Chimera?
by Paris Tzou 10 Nov '18

10 Nov '18

Dear Sir, I am studying PDB id: 5MCT (p53-dna) complex. There is a "BIOMT TRANSFORMATIONS" required to generate the biological unit. Would you please guide me how to do this? Thanks a lot, Paris

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Re: [Chimera-users] 1up opt
by Elaine Meng 09 Nov '18

09 Nov '18

Hi Zhengzheng The format of your PDB file is not standard because all the H atoms are all at the end instead of with their their residues. Also they are all in a different chain (chain A) than the other atoms (chain B). Whatever program wrote this file wrote it incorrectly. You can easily see all atoms, e.g. commands: ~ribbon display (or use Actions menu to do the same things) but if you use Chimera features requiring chemical knowledge (findhbond etc.) it will not work correctly if the H and the other atoms are not recognized as being in the same residue. I tried editing so that all atoms were chain B, but it did not fix the problem, which is apparently instead caused by placing all the H atoms at the end instead of with their individual residues. You could fix it be removing and re-adding hydrogens in Chimera, but then the H atom positions wouldn’t be exactly the same. Commands: delete H addh It is recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC’ed here) in case I’m not available to answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 7, 2018, at 8:02 AM, zheng l <zhengsfriend(a)hotmail.com> wrote: > > Dear Dr. Meng > > I used Chimera software for analyzing many protein crystal structures and then modified them and it has so faithfully doing job for me. However, this structure that I attached below is very difficult to modify. > > The problem is that the hydrogens in structure are hidden. Usually when I need to, for example, replaces a carbon to a nitrogen in a Phe the nitrogen will attached with a hydrogen if I set to have 3 bond for the nitrogen. But this structure is not showing hydrogens at all > > Would you please help me find a way of show all hydrogens need for modifying the protein structure? > > Thank you! > > Best regards! > >> Zhengzheng > > <1tup chain b opt 2.pdb>

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(no subject)
by rekha pydala 08 Nov '18

08 Nov '18

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FW: Chimera [viewer] for iOS in the future?
by Williams, Joanne 05 Nov '18

05 Nov '18

From: Bryan Crawford <bryanc(a)unb.ca> Date: Wednesday, October 31, 2018 at 3:53 PM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Chimera [viewer] for iOS in the future? Hello, I use Chimera occasionally in my research, and extensively for teaching (biochemistry, cell biology, developmental biology). It is now the only remaining piece of software I use that requires me to bring a laptop computer to class. For everything else (PDFs, animations, Keynote presentations, etc.) I can use my iPad which connects by AirPlay to the projector, and screencast everything using Doceri. Furthermore, the touch-screen interface of the iPad seems ideally suited for many of the analyses and/or molecular renderings people use Chimera for. So I’m wondering if there are any plans to produce either a full or partial version (perhaps with only viewing capabilities) of Chimera that runs on iOS? If there is, I would be very happy to help with beta testing. If not, can I ask if you can recommend any software that runs on iOS that I might consider? Cheers -- Dr. B.D.Crawford Professor Matrix Dynamics Lab Department of Biology University of New Brunswick Fredericton, NB, Canada

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Automating H bond distance retrieval
by Samuel FreemanFox 01 Nov '18

01 Nov '18

Hi, I was wondering about the possibility of writing a setup.com file which is capable of opening a receptor.pdb and ligand.pdb file, locating the H-bonds between these two structures and then reporting back the lengths of the bonds? Currently I am able to open both files, execute addh, addcharge, and hbonds with my setup.com file. However I am unsure of how to proceed from there. Many thanks and I look forward to your response. Samuel Freeman-Fox ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Porton Biopharma Ltd, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. *******************************************

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Batch Processing of Molecular Attributes
by Benjamin Feinsilver 01 Nov '18

01 Nov '18

Hello, Is it possible to pass a CSV file to Chimera containing a list of SMILEs, then output their molecular attributes in a new CSV file? For example, volume, surface area, the number of surface points with positive electrostatic potential, and the energy of the molecule's current 3D conformation. If so, would you please let me know how I would accomplish this? Thanks, Ben

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Chimera use
by Hui Min 31 Oct '18

31 Oct '18

Hi there, Sorry to disturb you. I have a question of how to use the Chimera software. If I've already got a .pdb file and use SMART to predict the domains, how can I mark the 3D structure with user defined color？ Thank you in advance for your help -- *Hui Min* Postdoctoral Scholar Research, Department of Internal Medicine, College of Medicine, University of South Florida, Tampa, FL 33612 minh8(a)health.usf.edu

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How can I load a list of residues of protein?
by Paris Tzou 30 Oct '18

30 Oct '18

Dear all, I want to load a file containing a lit of residues of protein which is already shown in Chimera. I don't want to manually select the residues under investigation through "Favorite -- Sequence". Is there a way of doing this ? I know I can do it using command line like:select #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content like: 15,C 16,C 17,C 263,A 264,A 265,A Thank you very much. Paris Tzou

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Split map from command line
by armoelle 29 Oct '18

29 Oct '18

Dear Chimera Team, I am trying to call the split map command directly from a script but somehow I don’t seem to be able to get it to run - maybe you can help me? I am calling scolorzone (which works perfectly) and then ( as suggested in the mailing list) use the accelerator command ac sm to split the map. However, generally nothing happens - sometimes though (I don’t know what triggers it - and I am not doing anything different) it runs perfectly fine. I am a bit puzzled as the same is the case no matter if I run form command line or I use the keyboard shortcuts gui. Many thanks for your help! cheers Arne ________________________________ Dr. Arne Moeller Independent Research Group Leader Department of Structural Biology Max-Planck-Institute of Biophysics Affiliated Researcher DANDRITE, Aarhus University, DK www.moeller-lab.com www.biophys.mpg.de/en/moeller.html Arne.Moeller(a)biophys.mpg.de 0049 69 63033057 Max-von-Laue-Strasse 3 D-60438 Frankfurt am Main Office L.1.015

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CUDA on Mac OSX 10.14 Mojave
by David Bhella 26 Oct '18

26 Oct '18

Dear All I just learned (after updating) that nVidia CUDA support is not in place for the latest Mac OS X release. I have a 2010 Mac Pro with a Quadro 4000 card in - which is still fine as a desktop. Chimera throws an error now - complaining about the graphics settings being incorrect: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." Presumably because the graphics driver is not working correctly. Has anyone succeeded in resolving this? Or do I need to roll back to 10.13? A quick scan of the Mac/nVidia Forums suggests that CUDA support may not be forthcoming anytime soon, but I thought I would check if anyone has resolved this before going through the hassle of downgrading. Thanks, D Dr David Bhella Director - Scottish Centre for Macromolecular Imaging MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella

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Dynamic Protein
by Alex Nazlidis 25 Oct '18

25 Oct '18

Dear Elaine, is there any way in chimera to produce a clip similiar to this ( https://www.youtube.com/watch?v=zm-3kovWpNQ at 5:44)? You know animating the dynamic nature of a protein and its folding process. Thank you very much in advance, Alex

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defining planes and axes based on existing ones
by ChuHui Fu 25 Oct '18

25 Oct '18

Hello, I am trying to define planes and axes that are orthogonal to the planes and axes that I have previously defined. I have an alpha helix, and I only managed to define one plane and two orthogonal axes around the helix. Is it possible to define the rest of the axes and planes? Thanks! -- ChuHui Fu B.S.Candidate in Chemistry Haverford College, Class of 2019 cfu(a)haverford.edu

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Saving a moved PDB only moved in a new session
by Marta Perez Illana 25 Oct '18

25 Oct '18

Hi all I am working with chimera, and I have a map and a pdb. 1) I have split the pdb into several fragments in order to fit them into the map 2) I have successfully moved the PDBs and fitted them into the map 3) I have "write each PDB" "relative to the map, which seems to make sense :) 4) In the current session I keep the map and the moved PDB open ...plus I open the just saved "wrote PDB" (intended to be on the same position I moved it). To me both, the opened PDB (which I have moved) and the just saved PDB, might be in the same position, fitting into the map... But... the just save-written PDB is clearly somewhere else... :( 5) But... If I make a NEW session, opening the map and the "wrote PDB", everything make sense, and the PDB is where I in fact moved to keep it fitted... Why is that that in the current session the written-PDB is not where it was "moved"; but when a new session is opened it is displayed where it was moved? It seems that everything works fine, it is just a bit confusing to me. Thanks in advanced! Marta

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Help SASA
by Andrea Yimena Cardona Barreto 25 Oct '18

25 Oct '18

Good afternoon, my name is Andrea Cardona and I´m a student of a magister in Human Genetics at Universidad Nacional de Colombia. In my thesis I´m interested in obtain the surface accessible solvent area of a homotetrameric protein (fumarate hydratase) but I have some troubles with Chimera. Can you give some help? -- Andrea Yimena Cardona Barreto Maestría en Genética Humana Universidad Nacional de Colombia

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Accessible surface area and ASA per residue
by anastasia＠campus.technion.ac.il 25 Oct '18

25 Oct '18

Dear User, I'll appreciate your help. I've worked with Chimera previously, but have not used it recently. Now I try to repeat some of the analysis I've done, but I don't see the option ,solvent accessible surface, in the software (I guess I've installed a newer version). I would like to color all the exposed (to the solvent) residues like in the image below and export a table with these values per atom and residue. [cid:7c648fa9-c7cf-4dab-bf40-f0b4a95b8f47] What I tried to do this time is : 1. Show a molecular surface.. 2. Depiction --> render by attr , when attr is set to areaSAS on residues [cid:f46b071c-36ab-4792-bfc2-31eb50fc2be3] The result I got was: [cid:6b44e796-b2c2-42f8-aac8-1ab725121d38] Am I doing it right? how can export the calculated areaSAS per atom and residue from chimera? How the SAS values calculated in Chimera? Does the higher value means that this residue is more exposed? Thank you for your help, Anastasia

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Chimera bug report submission
by Anas 23 Oct '18

23 Oct '18

The following bug report has been submitted: Platform: osx_x11 Chimera Version: (None given) Description Hello, I am trying to superpose a .pdb file on a density map (.mrc), and save it as .pdb. Chimera saves the file, but when I open it it doesn’t display any density map. Just the pub file which was superposed. I am doing it to start model building, but I am stuck at this. Kindly help.

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MacOS Mojave
by Eric Pettersen 22 Oct '18

22 Oct '18

Hi all, A fix for the non-showing buttons problem on MacOS Mojave (10.14) is now in the Chimera daily build and the 1.13.1 release candidate. If you encounter any problems with the new version please use Chimera’s Help→Report A Bug to let us know about them. Note that the fixed version only runs on Mac OS 10.10 or later, whereas the previous version also ran on 10.8 and 10.9. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [Chimera-users] Chimera problems
by Elaine Meng 20 Oct '18

20 Oct '18

> On Oct 19, 2018, at 8:41 PM, Shriwas, Pratik <ps774614(a)ohio.edu> wrote: > > Hi, > I am trying to use USCF chimera for studying docking between my compound and the receptor called GLUT1 (PDB - 4pyp or 1SUK). My concerns are: > > • I find different scores everytime I use the same compound and receptor Hi Pratik, Sounds like you are using the Autodock Vina interface of Chimera. Chimera does not calculate the docking, it just sends/receives data from an outside web service that is running the Autodock Vina program. It may be that the docking process uses some random numbers, and because the web service does not allow a high amount of sampling, it cannot always find the same top score(s). However, I do not know the details of Autodock Vina and you would have to look at its website <http://vina.scripps.edu/> and/or paper to learn about that. I’m guessing you are using Chimera’s Autodock Vina GUI to enter inputs, not the “vina” command. However, if you are using the command make sure you get a recent version of Chimera, because some problems with the command were fixed. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> > • I am not able to show my hydorgen bonds between compound snd receptor in GUI. Although I can see them in the list box. Maybe the atoms are not shown (for example, if the sidechain is not shown, the H-bond to the sidechain won’t be shown). To make sure the H-bonding atoms are shown, in the H-bond parameters dialog turn on the option “If endpoint atom hidden, show endpoint residue.” However, if that is not the problem, then maybe the graphics on your computer has trouble showing lines. You could try updating your graphics driver, or try showing the H-bonds as sticks instead of lines with command: setattr p drawMode 1. Or maybe it can draw lines but they are too thin for you to see. In that case, in the H-bond parameters dialog increase the “Line width” value. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo…> > • I am not able to find exact binding energy. This is the central problem of docking! Firstly docking scores are not binding energies, only approximations, and secondly, one has to do a lot of conformational and positional sampling to find the most accurate position. The Autodock Vina website does not allow a high amount of sampling, as it is a shared resource provided for free. If you want to do more intensive docking you can download Autodock Vina (or some other docking progam like DOCK, Gold, ...) and run it directly. > • My ligand is not on pubchem/NIH servers. What is best way to find its smiles string. Different websites have different smiles string and I get different interactions. Usually there are multiple ways of writing the SMILES string for the same compound. As long as the compound looks right to you (has the correct covalent structure, the right elements connected in the right way) then the results should be equally valid even though the coordinates might be slightly different (e.g. rotated or translated or different conformation). Any slight change in inputs will change docking outputs, since sampling is not exhaustive, but the change does not mean one answer is “wrong” and the other is “right". > > Regards, > Pratik Shriwas > Phd Candidate, > Molecular and Cellular Biology program, > Edison Biotechnology Institute, > Ohio University. For future reference, Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC’d here). For Autodock Vina questions, see <http://vina.scripps.edu/questions.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Finding files my session is showing
by David Sáez 19 Oct '18

19 Oct '18

Hello everyone. I saved some sessions time ago. Now I found the .py files, and they work fine, but I do not remember what files I am opening when I restore the session. In the .py file I could not find any information about loaded topologies or pdb files. Can these data be recovered from a session? Thanks in advance

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Saving PDBs
by Elliott, Jabari 17 Oct '18

17 Oct '18

When attempting to save PDBs of multiple models into one file, I end up with a pdb file with no data (0-600 bytes). When attempting to open files in pymol, they are blank. Please advise. Thank you.

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Alias commands for volume pieces
by Benjamin Looker 17 Oct '18

17 Oct '18

Hello! I have recently received emails from Tom Goddard and Elaine Meng on this subject, but I believe it can be further clarified. The research group I am a part of routinely generates Gaussian cube files for molecular orbitals using the DFT program ORCA, we then manually use Chimera to change the level and color of the two phases of the resulting wave function, *which appear in Chimera as two **surface pieces* belonging to the same surface. In the volume viewer menu Data, *and* in the Model Panel, there is no way to see a #0.1 #0.2 model subnumber, and Group/Ungroup returns the error "Cannot group a single molecule." Is there a way to refer to volume pieces in the command line? Such that an alias can be written to do this formatting in a more efficient manner? Best, -- Benjamin G. Looker Graduate Student Lancaster Group

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Re: [Chimera-users] [chimera-dev] Chimera orbitals alias question
by Elaine Meng 16 Oct '18

16 Oct '18

> On Oct 13, 2018, at 2:34 PM, Benjamin Looker <bgl44(a)cornell.edu> wrote: > > Hello! > My name is Benjamin Looker, I am a chemistry graduate student at Cornell University, and our group often uses Chimera to visualize the orbitals output from the DFT software ORCA. > > When these .cube files are opened in Chimera, the two phases of the wavefunction surface are given different colors and bars in the volume viewer. > > My question is, when using an alias command, how would one set the level and color of only one of these phases, ie: to perform actions on only one of the bars and colors, instead of homogenizing the whole function? > > An alias such as: > alias ^orbitals volume all level 0.05 color #2d2d00000b0b style surface > > Is great, but that pesky "all" undermines the point of the operation. I have tried referencing model numbers, such as #0, #1, and #2 instead of "all," but Chimera returns an error. I do not know the label of the object that I am trying to affect. > > Any help would be greatly appreciated! > Best, > -- > Benjamin G. Looker > Graduate Student > Lancaster Group Hi Benjamin, I don't have an example cube file to test with, but from your description I'm guessing it has signed data and that is why Chimera automatically shows two isosurfaces when you open a single file. The levels are the same magnitude, just the opposite signs. How the initial display values are set is described in the “surface and mesh display” section of the Volume Viewer documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> "For unsigned data types, an initial threshold is set so that 1% of voxels (1% of the volume encompassed by the data region) lie above it; for signed data types, positive and negative thresholds are placed symmetrically about zero." In that case, there is no way to specify in the command line changing only one isosurface and not the other. You can see in the Model Panel (open from Favorites) that the entire dataset is listed as one model. Although you could open the data twice and use your volume command on only one copy (specified by the model number as shown in the Model Panel) that would still leave both the isosurfaces on the other copy as initially shown. However, there is nothing magical about the initial display setting other than it is meant to be easily viewable. There is no knowledge used about the type of data (i.e. it doesn’t care or know that orbitals are what you’re showing) so you may want to go ahead and set all the isosurfaces using your values rather than relying on initial display. You can specify level and color multiple times in the volume command for multiple isosurfaces, e.g. volume #0 style mesh level 0.8 color red level 1.2 color 0,.5,.8 This is one of the examples in the “volume” command manpage <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. for future reference, the chimera-dev list is mainly for programming questions. General usage questions are better sent to chimera-users(a)cgl.ucsf.edu CC’d here

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Visualize 3-10 helix
by BuddySphinx 15 Oct '18

15 Oct '18

Dear Chimera users, I am wondering if there is a quick way in Chimera to visualize 3-10 helix? Or showing the dihedral angle of the peptide bonds? Best, Yangqi Sent from Mail for Windows 10

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problem with autodock vina page
by ammad aslam 13 Oct '18

13 Oct '18

I wonder, is there any problem with autodock vina website vina.scripps.edu/download.html ? I and my friends here cannot open it. Can anyone update me about the real problem. Regards, Ammad

2 1

Morphing code
by Minh Le 12 Oct '18

12 Oct '18

Hello there, I'm currently having trouble with the morphing code in chimera and I don't know how to use Python to make the morph.py. Is there any way you can help me with this? Thank you, Minh

2 3

MD movie metafile
by Matthias Fellner 12 Oct '18

12 Oct '18

Good day I successfully loaded NAMD psf/dcd files into chimera (version 1.13.1) using the tools MD movie interface. As I have many runs and each has multiple dcd files I wanted to use a script to load the different runs, instead of manually picking all the files through the interface each time. I tried to follow the limited instructions of the MD Movie homepage but failed to get anywhere. I tried some versions of this command: md: D:\script.txt or movie: D:\script.txt The command md appears to try to start MDA (MultiDomain Assembler), the command movie wants some other unrelated inputs. I am also not sure if the script command would even work like this: namd(psf/dcd) D:\structure.psf structure_MD001.dcd - D:\ Any advice is appreciated Thank you Matthias Fellner

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Generating symmetry mates
by Vani Pande 10 Oct '18

10 Oct '18

Hello, I wanted to generate symmetry mates for the protein, I am not finding a way to do so in chimera.The protein is a monomer in an asymmetric unit. Thanks Vani Pande Int PhD Biological sciences IISER Pune 20162013

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C-N peptide bond within one peptide
by Emily Xu 08 Oct '18

08 Oct '18

Hello, Is there a way to join two ends of a peptide in Chimera? I am trying the create a peptide bond linking the C and N termini in a singular peptide to form a cyclotide. Is this possible in Chimera?

2 1

error opening .cif file
by Francesco Pietra 07 Oct '18

07 Oct '18

Hi With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else. cheers francesco pietra

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Recording movie at 720p
by Ahmad Khalifa 05 Oct '18

05 Oct '18

I'm recording a movie in the command line using: movie record movie stop movie encode output ~/ I tried to include the option preset dvd for movie encode, I recieved the following error: "Error reading paper_movie.txt: AttributeError: 'module' object has no attribute 'standard_formats' File "/opt/UCSF/Chimera64-1.12/share/MovieRecorder/moviecmd.py", line 124, in encode_op settings = RG.standard_formats.get(preset) See reply log for Python traceback." What am I doing wrong and how can I record my movie at 720p? Regards.

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Maps/models display/activate checkboxes? [Feature suggestion]
by Oliver Clarke 04 Oct '18

04 Oct '18

Hi, It would be very helpful to have a way to undisplay all maps, or all models, at once. This would be particularly handy when inspecting the fit of a model in a map, as the residue tooltips don’t work when there is a surface in front of the atoms. Would it be possible to add two checkboxes in addition to the model specific checkboxes and the “all” checkbox that controls whether models, maps, or both are displayed? I would envision both the model and map checkboxes working as toggles, checked by default, but one could uncheck either to temporarily undisplay all maps/models, and then check the box again to return to the previous state. I know most effort is going into ChimeraX, so please disregard if this is difficult to implement. Cheers OIi

2 1

Chimera pdb error
by 김민재 03 Oct '18

03 Oct '18

Hi! Thanks for all of your help, but I got another problem... I uploaded a picture of the Chimera error. The HG hydrogen atoms are not being shown in Chimera. When I extract just the CG and HG pdb lines and input them, Chimera works fine and can even calculate the surface. But, when I run it with the pdb file that I have right now, it keeps returning that error. I thought that maybe Chimera could only calculate the surface for atoms which are connected, and that the program was looking for mandatory bond between the atoms. I was wondering if there was a settings change I could make to fix this, or if there was any other way to go about straightening things out to calculate the solvent excluded area of this pdb file.

2 1

MacOS Mojave
by Eric Pettersen 01 Oct '18

01 Oct '18

Hi all, MacOS Mojave will be released this Monday, Sept. 24. On Mojave, Chimera buttons and popup menus are not shown until the window containing them is resized. Therefore we advise against upgrading to Mojave until we come up with a fix for this issue — which we will announce on this list as soon as it is available. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Hiding models one by one?
by Ahmad Khalifa 01 Oct '18

01 Oct '18

I'm trying to hide a range of models using ~modeldisplay #16-60. For display purposes, I want to to make them disappear one by one or in groups. I can of course write down a bunch of ~modeldisplay #16; wait 5; ~modeldisplay #17; wait 5;...etc. Is there a way to for loop that process in the command line or do it in a better way? Regards.

2 1

Calculating surface area of a single atom
by 김민재 01 Oct '18

01 Oct '18

Hey everyone! I've been trying to calculate the solvent excluded surface area of a single hydrogen atom, but Chimera keeps returning an error "miscalc code 5" message whenever I run the "surface probeRadius" command. I would really appreciate anyone's help.

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FW: Contributing to ChimeraX ?
by Williams, Joanne 01 Oct '18

01 Oct '18

From: Nicholas Yue <yue.nicholas(a)gmail.com> Date: Sunday, September 30, 2018 at 3:40 AM To: "chimerax(a)cgl.ucsf.edu" <chimerax(a)cgl.ucsf.edu> Subject: Contributing to ChimeraX ? Hi, I took ChimeraX for a spin and when I save out to OBJ, the geometries looks connected up wrongly. I was hoping I can take a look at the source code to attempt to fix it myself. I see git being mentioned in the documentation. Is there a git repo I can clone and contribute to? If I need to sign any documents before contributing, let me know :-) I have other geometry format I'd like to write out to and also I am hoping to write out quads rather than triangles for use with OpenSubdiv in rendering software like RenderMan, Arnold, Mantra etc. Cheers -- Nicholas Yue Graphics - Arnold, Alembic, RenderMan, OpenGL, HDF5 Custom Dev - C++ porting, OSX, Linux, Windows http://au.linkedin.com/in/nicholasyue https://vimeo.com/channels/naiadtools

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