- 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 01 Jan '19

01 Jan '19

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 11 Dec '18

11 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.

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

07 Dec '18

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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

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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

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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

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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

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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

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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

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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.

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Using Per-Frame commands to recolor structures with attribute data is very slow
by David Slochower 28 Nov '18

28 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.

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Announcement: Release of DOCK 6.9
by Scott Brozell 28 Nov '18

28 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

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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.

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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

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needing help for separating structures
by Elaine Meng 27 Nov '18

27 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

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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

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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

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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. *******************************************

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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

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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*

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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

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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

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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.

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