December 2018 - Chimera-users - RBVI Mailing Lists

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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