December 2017 - Chimera-users - RBVI Mailing Lists

about select and label a residul with another different from the color of the whole model
by 张雷 13 Apr '19

13 Apr '19

Hi the experts of Chimera, Good noon! I had selected a residul and labeled it with the commands sel #0:500 rlabel #0:500. Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot! Sincerely, Lei Zhang Peking University, Beijing, China

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Hidden water molecules
by Michael Sharkey 11 Apr '19

11 Apr '19

Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike --

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Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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Error in Windows saving a session
by Joel Mackay 21 Apr '18

21 Apr '18

Hi all Have other people seen (and solved!) this error before (below)? I'm having it crop up pretty much all the time now when I try to save a session (on my Win7 machine - running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: <function command at 0x00000000155434A8> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay(a)sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/

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substituting atoms
by simon chapman 03 Apr '18

03 Apr '18

Hello...for my Master's dissertation, I need to substitute a sulphur atom for an oxygen in a Molecular Dynamics simulation. The run works fine with my target molecule 1KF1.pdb uploaded into Chimera, but the substituted version sends quite a few error messages and won't run. It doesn't appear to recognise the novel S atom. Any help would be much appreciated...I've been stuck on this for nearly a week! Best wishes Simon

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Re: [Chimera-users] Analysis of the protein-protein binding interphaces in MARTINI models
by James Starlight 14 Feb '18

14 Feb '18

Thank you so much for the suggestions, Elaine! Indeed, I have turned off the both flags but the intra-models contacts are still recognized. it seems that in order to determine carefully the per-residual contacts between monomers, I should to make a backmapping of the CG models to AA. James 2017-11-27 9:23 GMT+01:00 <sdimicco(a)unisa.it>: > Grazie mille > > > Il 2017-11-23 04:47 James Starlight ha scritto: > > Thank you for the suggestions, Elaine ! > > I have already tried "Find Clashes/Contacts" plugin. In generally, it > works good, however its application on more complex oligomeric > patterns (e.g if I deal with 10-20 GPCRs in one system) is a bit > complicated. Briefly, if I select only one monomer and than try to > find its contacts with the rest of the atoms ( I have changed the > contact threshold to -1.2 for the MARTINI) - it works fine. However, > If I selected all of the atoms (even excluding inter-residue and > inter-molecular contacts) and changing the search criterium "against > themselves" - it found alot of contacts within the monomers. Does > anybody use any tricks for the MARTINI models to fascilitate the > contact searching? > > > James > > 2017-11-22 17:52 GMT+01:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > > Dear James / Gleb, > This question seems too broad, perhaps. I don't know that much about > MARTINI, so I'm guessing instead of atoms you just have a bunch of points > that each represent multiple atoms. In that case you could probably use any > analysis that does not directly use exact atomic locations, atomic radii, or > atomic point charges. Analyses that DO use those things include > surface-area calculations, Find Clashes/Contacts, FindHBond. > > Maybe you should just first think about what Chimera analysis you want to > use, then just try it on your GC model and see if it works rather than > trying to get some exhaustive list of what might work. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Nov 22, 2017, at 2:23 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: > > Dear Chimera users! > > I would like to make some analysis of the protein-protein binding > established in coarse-grained MARTINI simulations. Briefly Chimera has > recognized a coarse-grained pdb file of 16 martini models of GPCRs. > What Chimera tools (e.g. contact maps, clustering of interphaces) > should work with CG models? What tricks should be used to make this > analysis easier? Because I am working with several proteins in one > system, I would like to work with its CG models without the conversion > to all atomistic representations. > > I thank you so much for the help! > James > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Chimera software error
by محمد عوض على خالد 02 Jan '18

02 Jan '18

Hello everyone. I am interested in using the builtin vina docking tool in Chimera. I get stuck several times at the following Error: ( Running AutoDock Vina for 5x5d failed; see Reply Log for more information: Application stderr ----- 'C:\Program' is not recognized as an internal or external command, operable program or batch file. ----- Application stdout) I check for several tutorials but got the same error, the version I used is Chimera 1.12 and Ulpha version 1.13 in windows 10 platform (64bit) Thank you? Mohammed Khalid Department of Chemistry University of Taif Saudi Arabia ' ________________________________ هذه الرسالة ومرفقاتها (ان وجدت) تمثل وثيقة سرية قد تحتوي على معلومات تتمتع بحماية وحصانة قانونية, ان لم تكن الشخص المعني بهذه الرسالة يجب عليك تنبيه المرسل بخطأ وصولها إليك وحذف الرسالة ومرفقاتها (إن وجدت) من الحاسب الالي الخاص بك ولايجوز لك نسخ هذه الرسالة او مرفقاتها (إن وجدت) أو اي جزء منها أو البوح بمحتوياتها لأي شخص أو استعمالها لأي غرض علما بأن الإفادات والاراء التي تحتويها هذه الرسالة تعبر فقط عن رأي المرسل وليس بالضرورة رأي جامعة الطائف ولا تتحمل جامعة الطائف أي مسئولية عن الأضرار الناتجة عن أي فايروسات قد يحملها هذا البريد . The information in this email and in any files transmitted with it is intended only for the addressee and may contain confidential and/or privileged material. Access to this email by anyone else is unauthorized. If you receive this in error, please contact the sender immediately and delete the material from any computer. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. Statement and opinions expressed in this e-mail are those of the sender, and do not necessarily reflect those of the Taif University. '. If the disclaimer can't be applied, attach the message to a new disclaimer message. ' ________________________________ هذه الرسالة ومرفقاتها (ان وجدت) تمثل وثيقة سرية قد تحتوي على معلومات تتمتع بحماية وحصانة قانونية, ان لم تكن الشخص المعني بهذه الرسالة يجب عليك تنبيه المرسل بخطأ وصولها إليك وحذف الرسالة ومرفقاتها (إن وجدت) من الحاسب الالي الخاص بك ولايجوز لك نسخ هذه الرسالة او مرفقاتها (إن وجدت) أو اي جزء منها أو البوح بمحتوياتها لأي شخص أو استعمالها لأي غرض علما بأن الإفادات والاراء التي تحتويها هذه الرسالة تعبر فقط عن رأي المرسل وليس بالضرورة رأي جامعة الطائف ولا تتحمل جامعة الطائف أي مسئولية عن الأضرار الناتجة عن أي فايروسات قد يحملها هذا البريد . The information in this email and in any files transmitted with it is intended only for the addressee and may contain confidential and/or privileged material. Access to this email by anyone else is unauthorized. If you receive this in error, please contact the sender immediately and delete the material from any computer. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. Statement and opinions expressed in this e-mail are those of the sender, and do not necessarily reflect those of the Taif University. '. If the disclaimer can't be applied, attach the message to a new disclaimer message.

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Coloring specific amino acid residues in Chimera
by Mariano Carossino 27 Dec '17

27 Dec '17

Hi, I have two trimer structures for the VP7 protein of two different rotavirus strains and I would like to highlight specific amino acid changes between these two. Could you please indicate me how can I color the amino acid residues that differ between these two structures using Chimera? Thank you, MC

2 1

B-factor values
by ARMIN HODAEI 25 Dec '17

25 Dec '17

Dear Chimera Users, I am trying to define new attributes in Chimera, and I have written a new set of scores for every residue (for b-values) but after adding I get this error message. It seems that I have to change the numbering of the residues on the PDB, to get correct colors. Sincerely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

2 1

Electrostatic Potential
by chemocev marker 21 Dec '17

21 Dec '17

Hi I am just calculating the Electrostatic Potential, and I wanted to know your opinion which force field is better for metallo proteins.And what is criteria to choose and not to choose the pKA... As I am doing the reaction at different pH and what I see in the PDB the proteins are crystallized at different pH then the reaction conditions. Structures are solved at low pH but the reactions are done at high pH. best Jiri

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Chimera-users December 2017