- Chimera-users - RBVI Mailing Lists

how to get chimera to use the auth_seq_id in .cif format files
by Carmen San Martin 21 Jan '19

21 Jan '19

Hi all, I am using chimera to display a structure with a 10-residue gap. When I use a pdb format file, the gap appears as a dashed line and everything is fine. However, when I convert the coordinate file to cif format, chimera draws a very long bond across the gap. Further, the residue numbering seems to have changed, so that now instead of skipping the 10 figures in the gap, the residues at both sides are consecutively numbered, and therefore the numbering in the rest of the protein is wrong. I understand this happens because chimera is using the cif column "label_seq_id" instead of "auth_seq_id" to identify the residue number. Is there a way to make chimera use the auth_seq_id column instead? Sorry if this has already been answered, I googled it and saw similar questions but not the actual answer to this one. Best, ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen(a)cnb.csic.es Phone: 34-91-5855450 Fax: 34-91-5854506 <http://www.cnb.csic.es/> http://tinyurl.com/carmensanmartinlab https://sites.google.com/site/adenonet/ ------------------------------------------------------------

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I-TASSER secondary structure
by nadineh.1991＠web.de 21 Jan '19

21 Jan '19

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match command
by Hernando J Sosa 20 Jan '19

20 Jan '19

Dear Chimera, Can somebody clarify the syntax of the match command. I am specifically trying to move several atoms (residues or ligands) to match their location in another model *without* moving the rest of the model. e.g. match #0:ADP.A #1:ADP.A works fine but moves the whole model #0 But match #0:ADP.A #1:ADP.A atoms Or using any other option after the atom specifications generate the following error: "an even number of space-separated atom specs are required" According to the user-guide website the syntax is: match atom-spec1 atom-spec2 options Not sure what the problem is. Thanks H.

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question
by Willenbring, Holger 18 Jan '19

18 Jan '19

Hello, Can UCSF Chimera be used to model the structure of an AAV capsid starting from the DNA sequence? Best, Holger Willenbring

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Volume blob and sum internal map value(s)
by Esser, Lothar (NIH/NCI) [E] 17 Jan '19

17 Jan '19

Hi, I seem to remember that the following is possible but I cannot figure it out anymore: One can read, say, an electron density map, contour it at desired level and in "Measure and Color Blobs" one can individually select blobs that are of interest and determine their volume and surface area. That works well. What I don't remember is how to integrate the map values inside the blob. I think it was implemented once but it currently escapes me. Any advice welcome. Thanks, Lothar

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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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