- Chimera-users - RBVI Mailing Lists

Minimizing the structure in Chimera
by Veijola Elias 31 Jan '18

31 Jan '18

Dear Mr. or Mrs. I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error

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Adding Missing residues
by ARMIN HODAEI 31 Jan '18

31 Jan '18

Dear Chimera Users, I am trying to add missing residues to the protein with the ID: 1u54 But unfortunately for chain A, I cannot do the adding. I go to "Tools > Structure Editing > Model/Refine Loops". Then I choose "chain A" and I select "all missing structure" and then "apply". But I got an error. Is there any other way for it? for "chain B" it works. Best Wishes, Armin -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

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launch behavior query
by Oliver Clarke 29 Jan '18

29 Jan '18

Hi, I have Chimera listed as the default app on my Mac to open MRC and PDB files. It used to be that if I double clicked on a pdb, and I had Chimera open, the pdb would open in that instance of chimera. Now, it always spawns a new instance of chimera. Is there any way to revert to the old behavior? Cheers Oli

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Quantification of electron density volume
by Priyamvada Acharya 27 Jan '18

27 Jan '18

Hi everyone, I am wondering if there is a way to extract the values plotted under Tools > Volume Data > Values at Atom Positions? Specifically, I would like to quantify the electron density surrounding a domain and compare it to another domain. This can be easily done if the values in the Histogram plotted under the tool mentioned above can be tabulated on a per-atom basis (perhaps within a PDB file, in the B-factor column). If anyone knows other methods to achieve this goal, that would be helpful as well. Thank you very much in advance for your feedback and suggestions! Best regards, Priyamvada

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Alignment of repeated domains
by Benitez De La Fuente, Francisco 26 Jan '18

26 Jan '18

Hello, I'm using the tool MatchMaker to align different structures. My reference protein has 3 domains very similar and I would like to show an alignment of other 3 proteins with each one of those 3 domains. The problem is that the 3 protein always align to the same domain (one of the 3, instead of each one with a different domain). How can I do so I can exclude the part of the protein already aligned in new alignments? I hope I explained myself and thank you in advance. Francisco Benitez.

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How do i rectify this error
by Niasha Tauro 25 Jan '18

25 Jan '18

Hello Chimera Users Can you please help me rectify the following error showing on chimera (1.11.2 version) during molecular docking: 'C:\molecular' is not recognized as an internal or external command, operable program or batch file. ----- Application stdout ----- [no output] ----- I have installed Autodock Vina and i am using the local executable location: vina.exe your assistance will be greatly appreciated kind regards Nyasha Tauro <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Turning models on/off on a perframe basis
by Esser, Lothar (NIH/NCI) [E] 24 Jan '18

24 Jan '18

Hi, in a short animation I would like to turn on/off a second model that is overlapping with the main model. The idea is to show differences by showing/hiding side chains of the second model. I know I can turn off models with ~modeldisp #1 but I don't know how to do that properly in a perframe statement turn y 2 180 perframe "modeldisp #1 " range 0,1 frames 180 # pseudo code wait clearly range does not quite work and $1 is presumably not setup to be ~ or nothing. I want to turn #1 on/off say every 6 degrees. How can this be done ? Thanks, Lothar

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mouse hovering not working
by Fabian Glaser 23 Jan '18

23 Jan '18

Dear all, The mouse hovering is not working for me, I use a Mac, and tried several version of Chimera, but the residue / atom number automatic labelling does not appear when hovering over. Any suggestion? Thanks a lot , Best, Fabian Fabian Glaser PhD Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web http://bku.technion.ac.il/ Tel +972 (0) 4 8293701

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chimera website
by 陈柳青 22 Jan '18

22 Jan '18

hi i can not log chimera website . can not download the software. what's problem? sincerely liuqing chen | | 陈柳青邮箱：519198561(a)163.com | 签名由网易邮箱大师定制

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Re: [Chimera-users] question about AutodockVina /CHIMERA
by Elaine Meng 22 Jan '18

22 Jan '18

Hi Osvaldo, Without more information, I have no idea, sorry. If you are sure that the process finished (click the “i” icon near the bottom right corner of the Chimera window to make sure), I can only say to check in the Reply Log (open from Chimera Favorites menu) and see if it says anything else useful. The Autodock Vina process does not run on our system, so there is nothing I can check here; Chimera just has an interface to send and receive results from a web service that is run by another lab, as explained in the help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> For the future, please send Chimera questions to the chimera-users(a)cgl.ucsf.edu address (CC’d here) to ensure they come to our attention. 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 19, 2018, at 4:04 PM, ogs <ogs(a)ibt.unam.mx> wrote: > > to whom it may concern, > > hi! > I am having some problems using AUTODOCK-VINA / CHIMERA. > > I recently docked a linand, but I did not get the name.pdbqt file as result (I only got the name.receptor.pdb and pdbqt and the name.ligand.pdb and pdbqt) > > The software show a message telling me that the process has ended and I need to check the files (but I did not see the name.pdbqt file) > > What is happening? What could I do to solve this problem? > Thanks a lot. > Osvaldo Gómez Secundino

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MD movie residue network analysis
by Neha Gandhi 22 Jan '18

22 Jan '18

Dear List, I am loading gromacs trajectory in Chimera using .tpr and .xtc files. The residue number in gro file starts from 83 and not from 1. When I perform residue network analyis using chimera and cytoscape, the numbering of residues starts from 1. Is there a way to change the residue numbers either in .tpr file or in cytoscape? Changing the residue numbering after the trajectory is loaded doesn't help. Thank you for your attention. Regards, Neha -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Inactive atoms
by Nazahiyah Rodzli 22 Jan '18

22 Jan '18

Dear Chimera Users, My Chimera seems to display atoms and side chains in dimmed dark colour (picture below). I’ve tried to change the colour but they don’t work. I also can’t select any of the atoms/sidechains by mouse click+ctrl unless I pick select all from the select menu. I am using Chimera 1.10 version. Could you help me how I can change the settings perhaps? Best regards, Naza

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Rotate and transform command
by 大帅 22 Jan '18

22 Jan '18

Hi, Therefore, we used UCSF Chimera to have a map's smmetry axes (approximately) parallel to the XYZ axes. The procedure followed by the relion tutorial we used for that was to read in InitialModel/symC1/run_it003_class001.mrc; use the duplicate option under the File menu of the Volume viewer. Then to deactivate map #1 on the Model Panel; rotate map #0 to have it’s symmetry axis more or less parallel to the XYZ axes; and then to use in the Command Line entry field: run_it003_class001.mrc; and save this model in the InitialModel/symC1/ directory with the name inimodel.mrc I have done as the above tutorial in relion, but the saved inimodel.mrc file does not change its position or orientation at all. So, my question is what commend can save a map after rotating or transforming its x,y,z coordinate ? What is the procedures to do so ? Thanks Dashuai

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emails
by Aga Szydlik 20 Jan '18

20 Jan '18

May I please ask to be unsubscribe from all "chimera users questions" emails, thank you Aga Szydlik PhD Candidate, School of Pathology, University of the Witwatersrand National Institute for Communicable Diseases, a Division of the National Health Laboratory Service Centre for HIV & STI's: HIV Virology Section (Morris Laboratory) 1 Modderfontein Road Sandringham, 2131 South Africa email: agas(a)nicd.ac.za<mailto:agas@nicd.ac.za> | www.nicd.ac.za<http://www.nicd.ac.za/> [cid:image003.png@01D2F0EE.60CC2540] Practice Number: 5200296 The views expressed in this email are, unless otherwise stated, those of the author and not those of the National Health Laboratory Service or its management. The information in this e-mail is confidential and is intended solely for the addressee. Access to this e-mail by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted in reliance on this, is prohibited and may be unlawful. Whilst all reasonable steps are taken to ensure the accuracy and integrity of information and data transmitted electronically and to preserve the confidentiality thereof, no liability or responsibility whatsoever is accepted if information or data is, for whatever reason, corrupted or does not reach its intended destination.

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Adding Menu items to Python Shell
by Batra, Vinod (NIH/NIEHS) [C] 16 Jan '18

16 Jan '18

Hi How to add menu items to IDLE-> Python Shell opened with Chimera 1:1x running on OS X. Vinod Batra NIEHS

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Command line selection in Chimera
by Jerry Honts 16 Jan '18

16 Jan '18

Is there any easy way to select *a range of chains* in complex models like the ribosome in Chimera at the command line? I haven't been able to work out the syntax for this type of complex selection at the command line. For example, what is the syntax of the command to select chains 1G through 1Z and chains 10 through 19 in PDB file 5DOY [without explicitly listing them one by one]? I may be missing something simple, and I have not been able to get it to work or find an example in documentation. I have been able to do this in Chimera X but not the current version of Chimera. Thanks, Jerry E. Honts -- Jerry E. Honts, Ph. D. Associate Professor of Biology Drake University 2507 University Avenue Des Moines, IA 50311-4505 Science Connector Building 210 (faculty office)

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Re: [Chimera-users] Pseudobonds in mmCIF
by Elaine Meng 16 Jan '18

16 Jan '18

Just for the benefit of the list, the problem with spurious bonds between residues in Chimera was solved by adding sequence information to the input mmCIF file. Elaine > > On Jan 11, 2018, at 1:35 PM, Henry Nguyen <nguyen.henry.c(a)gmail.com> wrote: > > > > Thanks everyone for all the help. My problem is fixed by running mmtbx.prepare_pdb_deposition with the sequence information. The new cif file is displaying pseudobonds correctly and can be toggled on/off. > > > > Thanks again! > > Henry > > > > On Thu, Jan 11, 2018 at 11:43 AM, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: > > Hi Henry, > > > > Sorry about the problems with mmCIF in Chimera. Those problems are a major reason why we wrote ChimeraX. So please check out ChimeraX, http://www.rbvi.ucsf.edu/chimerax/. The mmCIF reader is several orders of magnitude faster than Chimera's and presents the author numbering to identify residues instead of the internal mmCIF numbering. The graphics in ChimeraX are better too. If there is some feature in Chimera that isn't in ChimeraX yet that you need, please let us know. ChimeraX also works with VR headsets. > > And while ChimeraX shows your structure "correctly". It could do a much better job if the missing sequence information were in the mmCIF file. In Phenix, that is done by running the mmtbx.prepare_pdb_deposition program, i.e, by preparing the mmCIF file so that is suitable for submission to the PDB. That would probably help Chimera too. > > > > HTH, > > Greg

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Does Chimera support stereo with a Nvidia Quadro M4000 graphics card?
by xzhang1999＠zju.edu.cn 13 Jan '18

13 Jan '18

Hi, Does Chimera support stereo on the Nvidia Quadro M4000 graphics card? I have a workstation with a Nvidia Quadro M4000 graphcs card (64bit, win10&ubantu), but cannot successfully have Chimera displaying sequential stereo? Any suggestion would be greatly appreciated. Thanks a lot. Best regards, Xing

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Output of distance measurements
by Marco Sette 13 Jan '18

13 Jan '18

Dear all, I have a very primitive script to measure distances, like distance :1.a@ha :5.b@ha distance :1.a@ha :4.b@ha distance .... etc. I run the script in File --> Open and get the distances in the Structure Measurements panel and then Save. The output file list all the distances but, for my analysis, it would be better to keep the lines separated by a blank line, or something like this. Maybe this is possible by some change in my primtive script but I have no idea... Thanks for your help, Marco

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Pseudobonds in mmCIF
by Henry Nguyen 10 Jan '18

10 Jan '18

Hi, I am trying to disable all pseudobonds between gaps in my structure in an mmCIF file. I've tried: In the Pseudobond Panel, there is only one group (distance monitor) and it has 0 pseudobonds in the group. Hiding that group doesn't change anything. I also tried disabling them using setattrr ("setattr p display false"/ "setattr p display false") but neither didn't change anything. If I select a psuedobond and examine it using the Selection Inspector, the Pseudobond tab is unselectable under Inspect. Only if I go to the Bond tab can I hide it. I have to use mmCIF format as I have too many chains for a pdb. Thanks, Henry

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Re: [Chimera-users] importing chimera module question
by Mysteray Rice 10 Jan '18

10 Jan '18

Get organized with Yahoo Mail

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write prmtop, source leaprc.ff14SB
by stu118506 08 Jan '18

08 Jan '18

Dear Chimera users, I'd like to save a prmtop file of my protein after preparation for molecular dynamics simulation. I tried to do it by using Tools - Amber - write Prmtop . I get this reply log entry: _command: ['/gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap', '-f', '/scratch/tmpOlw0GO/solvate.cmd']_ _Running sleap command: /gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap -f /scratch/tmpOlw0GO/solvate.cmd_ _(writeprmtop) [gtkleap]$ source leaprc.ff14SB_ _(writeprmtop) Error: can not find file leaprc.ff14SB in all the search path._ _Failure running sleap_ I guess that it should source oldff/leaprc.ff14SB because the file seems to be in the directory oldff. But I don't know if that is right and were I have to change the path. Additionally, addions works perfectly although leaprc.ff14SB is also needed. So there the path seems to be set correctly. Is there anything I can do about it? Thank you Freia Krause Christian-Albrechts Universität zu Kiel,Germany

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Inquiry about hydrogen bond analysis- important
by Mohamed S. Nafie 08 Jan '18

08 Jan '18

Chimera team. I made the hydrogen bond analysis for the co-crystallized ligand for 1DB1 receptor. it makes on the PDB 6 hydrogen bonds through both oxygen and hydrogen of the hydroxyl group (three of both) with the amino acids residues in the binding site, Also chimera forms 6 but through oxygen of hydroxyl group only. This my first question why? The second question is the structure of the Co crystallized Ligand is not correct, when I adjust the bond order of it by Maestro and save it as pdb and reopen it by Chimera, it forms only two hydrogen binds why? Please try to help me in this question, because I need it necessary Thanks Mohamed S. Nafie Assistant lecturer Chemistry Department, Faculty of Science, Suez Canal University Ismailia, P.O(41522), Egypt Mobile: +201065072524

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regarding opening mouth or poc file on chimera
by Ming 05 Jan '18

05 Jan '18

Hi Chimera team, I have a quick question regarding opening CASTp file on Chimera. I downloaded the pdb file together with mouth and poc file and saved them in the same folder. I also made sure the names are consistent among these files. However, I am still getting error messages as following. Error reading 3mbg.poc: ValueError: Mouth info header missing or IDs not consecutive File "/home/ming/.local/UCSF-Chimera64-1.11.2/share/CASTp/__init__.py", line 88, in processInfoFile " IDs not consecutive" % label.capitalize()) See reply log for Python traceback. I looked up the Chimera manual online and it looks pretty straight forward to open either the mouth or poc file but I am not sure why I keep getting the error messages. Any help will be appreciated. Thanks, Ming

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How to set volume view step size in "vop morph" command
by Zheng Liu 04 Jan '18

04 Jan '18

I want create a morph volume between 2 maps (#0, and #1), as a command I wrote:vop morph #0,1 step 1 playStep 0.04 frames 200 step 1 However, the new model #4 morph was display in step "8", not step "1" in the volume view window. How to set the step size in the vop morph command? Thanks!

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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

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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

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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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box cut out is not a cube!
by Dieter Blaas 20 Dec '17

20 Dec '17

Dear all and Elaine, I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box! Thanks for help, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Question about docking in Chimera
by Ulrich, Rebecca 20 Dec '17

20 Dec '17

Hello, I am trying to do some docking studies in chimera and I have been following a protocol given to me in a drug discovery class that walks me through the dock prep and autodock vina options in chimera. I have tried to run some docking and it will tell me "execution complete- check outputs to verify successful execution" but I don't get any popups with any information about the docking. Is there a way to get the docking values to show? I have done this assignment before and didn't have issues, but now as I am redoing it to prep for some other docking studies, I can't get it to work. Thanks, Rebecca

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Re: [Chimera-users] [Chimera] Failure preparing structure for Autodock Vina
by Elaine Meng 20 Dec '17

20 Dec '17

Dear Jutapat, The chimera-users address (CC’d here) is recommended for questions, for your future reference. Email to me only might fall through the cracks. It is hard to tell what the problem is without having your data, but the message says it cannot figure out the atom type of some atom Ha, so maybe the hydrogen atoms in your input structure have weird names or the names are in the wrong columns of the file. You might try deleting all hydrogens (e.g. command: delete H) before running the tool. However, if that doesn’t work you probably need to correct some error in your input file (the file format or atom names in the file). 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 20, 2017, at 1:30 AM, Jutapat Romsuk <jutapat_rom(a)bio.eng.osaka-u.ac.jp> wrote: > > My problem is show below > Wrote prteinA.receptor.pdb > Traceback (most recent call last): > File "/Applications/Chimera.app/Contents/Resources/share/vina/ws.py", line 393, in prepareReceptor > execfile(scriptPath, d) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/Utilities24/prepare_receptor4.py", line 172, in <module> > delete_single_nonstd_residues=delete_single_nonstd_residues) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 533, in __init__ > version=version, delete_single_nonstd_residues=delete_single_nonstd_residues) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 140, in __init__ > self.addCharges(mol, charges_to_add) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 226, in addCharges > chargeCalculator.addCharges(mol.allAtoms) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/MolKit/chargeCalculator.py", line 80, in addCharges > babel.assignHybridization(atoms) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 127, in assignHybridization > a.babel_atomic_number = self.get_atomic_number(a.babel_type) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 103, in get_atomic_number > (name,_name) ) > ValueError: Could not find atomic number for Ha Ha > Receptor preparation for AutoDock Vina failed; please look inReply Log to see error messages. > cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors. > > I would like to know how to fix this problem. Help me please. > > --------------------------------------------------------------------------------------- > Jutapat ROMSUK > Biotechnology Global Human Resource Development Program > > Cell Technology Laboratory > Department of Biotechnology, Graduate School of Engineering, Osaka University > C2-111, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan > Laboratory phone: +81-6-6879-7423 >

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[MGMS-DS]: Molecular Modelling Workshop March 12-14, 2018 in Erlangen, Germany
by Harald Lanig 14 Dec '17

14 Dec '17

Dear list subscribers, we are very happy to announce next year’s “32nd Molecular Modelling Workshop (MMWS)” (http://mmws2018.mgms-ds.de) that takes place on March, Monday 12th to Wednesday 14th, 2018, at the Friedrich-Alexander-University in Erlangen. 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.). ####### Pre-conference workshop ####### For the first 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 workshop: Bernd Engels (Institute of Physical and Theoretical Chemistry, University of Würzburg) "Towards the Rational Design of Covalent Inhibitors" Pavel Hobza (Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague) "Protein-Ligand Interactions and Drug Design" Gerhard Wolber (Institute of Pharmacy, Free University of Berlin) "Exploring Protein - Ligand Binding Using 3D Pharmacophore Patterns" Marc Hamm (Henkel AG & Co. KGaA) "Facets of Materials Modelling at Henkel" ####### 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://mmws2018.mgms-ds.de/index.php?m=register The deadline for all submissions is February 16th, 2018. ####### General information ####### Website http://mmws2018.mgms-ds.de will provide all necessary information about the meeting. We are looking forward to meeting you in Erlangen! - Achim Zielesny, Scientific Committee Workshop Organisation 2018 - Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.org) -- ------------------------------------------------------------------------ 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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Edition of the pdb/trajectories via Chimera
by James Starlight 04 Dec '17

04 Dec '17

Dear Chimera Users! I have a pdb file for the 16 monomers of the coarse-grained GPCRs and its corresponded trajectory in dcd. In both files all the monomers are defined as the same letter of the chain (X). My question: are there an easy way to assign a unique letter to each of the monomers in the both files via Chimera to facilitate the further analysis ? Thanks so much! James

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fail to install chimera 1.12
by Haoming Zhang 01 Dec '17

01 Dec '17

Hello, I would appreciate your help for some problems with installation of chimera 1.12 in rhel 7.4 linux. Although we have installed chimera in rhel 5.4 before, this time we upgraded OS to rhel 7.4 and run into the problem. Basically I downloaded the binary file from your website and run the bin file in the Download directory. But the process failed. I have included the error message in the attachment and would appreciate your help. Sincrely, Haoming Zhang PhD Research Assistant Professor The University of Michigan Ann Arbor, MI PS. I have troubled attaching the file. SO I paste it below: root@boxx Downloads]# ./chimera-1.12-linux_x86_64.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/root/Downloads' inflating: chimera_install_aelQQu/installer inflating: chimera_install_aelQQu/chimera.bin Enter install location: /opt/UCSF/Chimera64-1.12 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /opt/UCSF/Chimera64-1.12' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu (icon has to be done by user)? yes Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.12/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/opt/UCSF/Chimera64-1.12/share/chimeraInit.py", line 628, in init import chimera File "/opt/UCSF/Chimera64-1.12/share/chimera/__init__.py", line 2758, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/opt/UCSF/Chimera64-1.12/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/opt/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: libXss.so.1: cannot open shared object file: No such file or directory ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_aelQQu' Installation is done; press return. When I run chimera in the installed directory, I got this error. root@boxx bin]# ./chimera Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.12/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/opt/UCSF/Chimera64-1.12/share/chimeraInit.py", line 628, in init import chimera File "/opt/UCSF/Chimera64-1.12/share/chimera/__init__.py", line 2758, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/opt/UCSF/Chimera64-1.12/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/opt/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: libXss.so.1: cannot open shared object file: No such file or directory

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question on visualization
by C.J. 01 Dec '17

01 Dec '17

Hi specialists, I have a problem when adjusting the level of a map. If the level > 0, it seemed OK, but when it is less than 0, it showed a solid box. This is different from EMAN2. In EMAN2, the threshold less than 0 also works. I'm not sure whether the defining of level is the same as the threshold in EMAN2. Or is there any other way to show the density of a map as in EMAN2 with threshold less than 0? Some snapshots of the visualization in both programs are attached to the post. Thank you! regards, Jianhao

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Mutating to Lysine neutral
by Alireza Shaneh 30 Nov '17

30 Nov '17

Hello, I wanted to know if there would be a way to mutate the positively charged Lysine to Lysine neutral in Chimera. Thanks in advance, Alireza

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hiding the structure elements
by chemocev marker 26 Nov '17

26 Nov '17

Hi Is there is way to hide all those structure elements which are not selected in chimera. best Jiri

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Analysis of the protein-protein binding interphaces in MARTINI models
by James Starlight 26 Nov '17

26 Nov '17

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

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Coulombic (Mailing list question)
by RYDER WHITTAKER HAWKINS 22 Nov '17

22 Nov '17

My Question of the Day: - I am running an MD movie in Chimera - I want to display the solvent excluded surface colored by coulombic potential. - I would like to implement this command as a script at each frame. What is the command? I am getting error after error... >coulombic -10 red 10 blue How could I put this in a Per-Frame analysis? Thanks for any suggestions. The documentation is not so clear for this coulombic function. Ryder Whittaker Hawkins MSc Candidate PI: Dr. Luc Vallières ryder.whittaker(a)crchudequebec.ulaval.ca ca.linkedin.com/in/ryderwh Work: (418) 525-4444 Cell: (613) 979-7729 Dept. of Molecular Medicine Université Laval (CHUL) 2705 Laurier Blvd Québec, QC G1V 4G2

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Axes/Planes/Centroids for the OPM membrane visualization
by James Starlight 22 Nov '17

22 Nov '17

Dear Chimera Users, I have a question regarding Axes/Planes/Centroids for the visualization of the membrane plane predicted by OPM. Firstly, I have uploaded my structure with DUM atoms. Than, I selected the DUM atoms in both layers and try to show the membrane plane via defining of a plane for it. As the result, a cylindrical surface oriented perpendicular to the imaginative membrane has been emerged. What should I change in options to obtain it aligned along the membrane normal in a correct way? Is it possible to make more flexible selection of the DUM atoms only in the selected layer? Thank you for the help! Gleb

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TERs in PDB ?
by Marek Maly 21 Nov '17

21 Nov '17

Hello, is it possible to save the given molecular model (which is open in Chimera) in PDB format but with the TER string between consequent residues ? example: --------------------------- ATOM 1 Si1 CEN A 1 56.395 15.633 50.147 1.00 0.00 Si TER ATOM 2 C1 RE1 A 2 54.892 16.772 50.453 1.00 0.00 C ATOM 3 H1 RE1 A 2 54.289 16.821 49.538 1.00 0.00 H ATOM 4 H2 RE1 A 2 54.219 16.552 51.290 1.00 0.00 H ATOM 5 C2 RE1 A 2 55.394 18.185 50.780 1.00 0.00 C ATOM 6 H3 RE1 A 2 55.896 18.665 49.932 1.00 0.00 H ATOM 7 H4 RE1 A 2 56.038 18.053 51.659 1.00 0.00 H ATOM 8 C3 RE1 A 2 54.181 19.075 51.202 1.00 0.00 C ATOM 9 H6 RE1 A 2 53.674 18.496 51.984 1.00 0.00 H ATOM 10 H5 RE1 A 2 53.589 19.325 50.313 1.00 0.00 H ATOM 11 Si3 RE1 A 2 54.714 20.646 51.949 1.00 0.00 Si ATOM 12 C4 RE1 A 2 53.140 21.420 52.746 1.00 0.00 C ATOM 13 H8 RE1 A 2 53.430 22.271 53.376 1.00 0.00 H ATOM 14 H7 RE1 A 2 52.690 20.675 53.413 1.00 0.00 H ATOM 15 H9 RE1 A 2 52.466 21.649 51.911 1.00 0.00 H ATOM 16 C5 RE1 A 2 55.491 21.841 50.620 1.00 0.00 C ATOM 17 H12 RE1 A 2 56.423 21.426 50.217 1.00 0.00 H ATOM 18 H10 RE1 A 2 55.768 22.733 51.196 1.00 0.00 H ATOM 19 H11 RE1 A 2 54.875 22.300 49.836 1.00 0.00 H TER ATOM 20 C1 RE1 A 3 57.436 16.272 48.673 1.00 0.00 C ATOM 21 H1 RE1 A 3 58.039 17.117 49.028 1.00 0.00 H ATOM 22 H2 RE1 A 3 58.209 15.633 48.228 1.00 0.00 H ATOM 23 C2 RE1 A 3 56.488 16.820 47.464 1.00 0.00 C ATOM 24 H3 RE1 A 3 55.675 17.467 47.819 1.00 0.00 H ATOM 25 H4 RE1 A 3 55.960 16.034 46.910 1.00 0.00 H ATOM 26 C3 RE1 A 3 57.354 17.603 46.475 1.00 0.00 C ATOM 27 H6 RE1 A 3 58.241 17.015 46.210 1.00 0.00 H ATOM 28 H5 RE1 A 3 57.812 18.464 46.978 1.00 0.00 H ATOM 29 Si3 RE1 A 3 56.645 18.300 44.851 1.00 0.00 Si ATOM 30 C4 RE1 A 3 55.474 17.030 44.146 1.00 0.00 C ATOM 31 H8 RE1 A 3 54.666 17.578 43.646 1.00 0.00 H ATOM 32 H7 RE1 A 3 54.864 16.542 44.918 1.00 0.00 H ATOM 33 H9 RE1 A 3 55.893 16.349 43.396 1.00 0.00 H ATOM 34 C5 RE1 A 3 58.034 18.987 43.812 1.00 0.00 C ATOM 35 H12 RE1 A 3 59.000 18.584 44.141 1.00 0.00 H ATOM 36 H10 RE1 A 3 58.180 20.062 43.974 1.00 0.00 H ATOM 37 H11 RE1 A 3 58.009 18.601 42.786 1.00 0.00 H TER ATOM 38 C1 RE1 A 4 57.426 15.522 51.783 1.00 0.00 C ATOM 39 H1 RE1 A 4 58.370 14.991 51.606 1.00 0.00 H ATOM 40 H2 RE1 A 4 57.769 16.539 52.007 1.00 0.00 H ATOM 41 C2 RE1 A 4 56.787 14.966 52.995 1.00 0.00 C ATOM 42 H3 RE1 A 4 57.587 14.881 53.741 1.00 0.00 H ATOM 43 H4 RE1 A 4 56.321 13.982 52.869 1.00 0.00 H ATOM 44 C3 RE1 A 4 55.776 15.938 53.682 1.00 0.00 C ATOM 45 H6 RE1 A 4 54.722 15.759 53.439 1.00 0.00 H ATOM 46 H5 RE1 A 4 55.920 17.004 53.467 1.00 0.00 H ATOM 47 Si3 RE1 A 4 55.756 16.172 55.603 1.00 0.00 Si ATOM 48 C4 RE1 A 4 57.359 16.942 56.191 1.00 0.00 C ATOM 49 H8 RE1 A 4 57.601 17.853 55.629 1.00 0.00 H ATOM 50 H7 RE1 A 4 58.242 16.306 56.061 1.00 0.00 H ATOM 51 H9 RE1 A 4 57.248 17.148 57.263 1.00 0.00 H ATOM 52 C5 RE1 A 4 55.827 14.369 56.251 1.00 0.00 C ATOM 53 H12 RE1 A 4 56.581 13.702 55.818 1.00 0.00 H ATOM 54 H10 RE1 A 4 54.854 13.866 56.186 1.00 0.00 H ATOM 55 H11 RE1 A 4 56.205 14.393 57.280 1.00 0.00 H TER . . . --------------------------- If yes, how to do it ? Thank you in advance for your advice. Best wishes, Marek -- Vytvořeno poštovní aplikací Opery: http://www.opera.com/mail/

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Re: [Chimera-users] will chimeraX support the BILD file format?
by Francois BERENGER 21 Nov '17

21 Nov '17

On 11/17/2017 09:53 AM, Greg Couch wrote: > We've been debating that. The bild format has many commands. Which ones > do you use? I ask because I have code that implements the transforms, > color, and shape commands, but not any of the line drawing, polygon or > marker commands. Does that work for you? I use most of the drawing commands, to create graphical annotations (arrows, boxes, spheres). And I love the fact that they can be colored and made transparent. The whole format is potentially useful to me. This is a big advantage of Chimera over pymol for example. Don't loose that. Pymol is a mess for that and it forces you to go down to Python. Going through a simple specialized text format like BILD is a huge win. The BILD file format is trivial to generate by hands (for quick test) and via any programming language (when in production). Regards, F. > -- Greg > > On 11/16/2017 04:35 PM, Francois BERENGER wrote: >> Hello, >> >> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html >> >> I am a huge fan of this chimera feature, so I hope it will >> not disappear (trivial to create graphical annotations by hand >> or via a program). >> >> Regards, >> F. >> _______________________________________________ >> 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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Fwd: Does volume outline is bigger than actual volume?
by Elaine Meng 21 Nov '17

21 Nov '17

> > From: Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> > Subject: Does volume outline is bigger than actual volume? > Date: November 21, 2017 at 6:00:17 AM PST > > Hello, > > I need to understand precisely what Chimera do. Please look at the attached screen shoot. The arrows are anchored in point (0,0,0), and they are point in direction [(1,0,0),(0,1,0),(0,0,1)] red, yellow and blue respectively. > > I set my volume to minimum (grey cube), I checked "Show outline box using color", and I noticed it does not cover the shape of my volume. > > There are "margins" in the top, and the bottom visible in the image and much smaller on the sides. > > Why they are there? What is its exact size? Where does volume actually begins in the (0,0,0), or slightly below that point? > > -- > best wishes, > Michał Kadlof <m.kadlof(a)cent.uw.edu.pl <mailto:m.kadlof@cent.uw.edu.pl>>

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Match command question
by Yann STERCKX 21 Nov '17

21 Nov '17

Dear Chimera users, I've been struggling with the match command and was hoping you could help me out. I'm working a tetrameric enzyme. When the enzyme binds ligands, its domains rotate over a pivot point in the monomer. What I would like to do is superpose different liganded structures of the enzyme on the four monomer pivot points. Here's what I've done so far: * Each liganded state of the tetrameric enzyme is a single model * I use the match command to superpose the structures on the monomer pivot points (residues 430-433 in the structure). I used the following command match #model1:430-433 #model2:430-433 What is strange is that I obtain exactly what I want for 2 out of 4 models. Using this command I get an rmsd of 0.77A. But for the other 2 models, match does not seem to work as I obtain an RMSD of 27A and the superposition is clearly off. Including the iterate option does not alleviate the problem. I don't want to use matchmaker because this feature will, at least in my understanding, try to optimally fit two chains (or selections within two chains) on top of each other. If I do that, I do not get to see how the enzyme rotates around the monomer pivot points. How come match works really well for 2 out of 4 structures, but fails to perform the same task for the rest? Any pointers on what I might be doing wrong? Many thanks and kind regards, Yann PS: I've browsed through the archive, but could not really find a thread related to this problem (unless I overlooked it).

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Coordinates of atoms and volumes
by Michał Kadlof 20 Nov '17

20 Nov '17

Hi, 1. is there any way to get the exact Cartesian coordinates of any atom directly in Chimera? 2. Is there any way to get exact value from exact place inside density volumetric data? -- best wishes Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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PipesAndPlanks coloring not accurate
by Andrew Hagen 17 Nov '17

17 Nov '17

Hello, I have a protein model that I colored according to region: N-terminal domain (green), a domain that I inserted (gray), and the flanking (GGS)2 linkers (tan). When I apply PipesAndPlanks, the tan regions are changed to either green or gray, which is not desired (and apparently, the PipesAndPlanks' color cannot be changed once rendered). Is this a bug or am I doing something wrong? To add a little more detail, I manually Frankensteined this model together. At the genetic level, it's just a domain insertion, flanked by linkers, but in Chimera I did this by: Opening my wt protein model (green), splitting the chain into two models at an internal site, generating GGSGGS linkers de novo in Chimera and joining these to the new models, and then finally joining those two fragments through a "bridge" of another model. There was lots of manual torsioning and minimizing using FoldIt in this process. I can imagine a work around is just to overlay two PipesAndPlanks renders and masking different regions, but this seems inelegant. Any assistance/advice is appreciated! --Andrew

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Re: [Chimera-users] visualisation of volumes
by Elaine Meng 16 Nov '17

16 Nov '17

Hello Michał, The answer is actually shown in the command line of your screenshot image! You would use the “volume” command to set levels and colors. Instead of a color name you could give r,g,b,a values (red, green, blue, alpha=opacity, each on a scale 0-1). Just like you can say “level” multiple times in the same command, you can also give “color” multiple times. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> 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 16, 2017, at 6:22 AM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > > Hello, > > how can I achieve the effect visible in attached image from command line? > > I need to add several semi transparent isosurfaces for a single volume. > > <Zaznaczenie_139.png>

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Command line for labelling specific residues in a zone
by Mark Rosenberg 16 Nov '17

16 Nov '17

I am not sure if this request was missed. I am having difficulty finding the syntax to write a line command in Chimera to label the non-polar or polar residues in say a 5 Angstroms zone. I would be grateful if you could advise me how to code the command line for labelling these residues with a 1-letter code please ? Once I see the format then I can readily adapt this to other situations. Thank you in advance. Mark

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Chimera/Modeller to add missing residues
by Daipayan Sarkar 16 Nov '17

16 Nov '17

Hello Elaine, I am using Chmiera-Modeller GUI to add the missing residues for my PDB file: (https://files.rcsb.org/view/1YPH.pdb) >From the mailing list, I am following the procedure listed in: http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009174.html However, once the missing residues for chains A and B are included, I save the new PDB file using File > Save PDB... > under save models selection "selected all three files" and clicked OK. The resulting PDB file includes the original header with additional 'MODEL 1', 'MODEL 2' and 'MODEL 3'. How to save the atom coordinates as a single PDB file after adding the missing residues? Any comments/suggestions is appreciated. Regards, Daipayan

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