- Chimera-users - RBVI Mailing Lists

graphics problems after update from UCSF-Chimera64-1.5.3 to UCSF-Chimera64-1.6.2
by Dieter Blaas 21 Aug '12

21 Aug '12

Hi, I replaced the previous version of Chimera, UCSF-Chimera64-1.5.3 with the new one UCSF-Chimera64-1.6.2 on our cluster running Linux l22 2.6.32-131.17.1.el6.x86_64 #1 SMP Wed Oct 5 17:19:54 CDT 2011 x86_64 x86_64 x86_64 GNU/Linux whereas everything was perfect so far I now get the error message: X Error of failed request: GLXBadContextTag Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1352 Current serial number in output stream: 1352 followed by a crash. This is annoying since I need the new version for compatibility with some sessions saved with the new version on another machine. Thanks a lot for hints, 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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a problem with silhouettes
by Alja Oblak 20 Aug '12

20 Aug '12

Dear Chimera users, I am trying to create an image for a publication using Chimera 1.6.1. Whenever I turn on "silhouette" dark spots appear on the screen and on the saved image. They seem totally random but they move along with the structure when rotated. When I zoom on them they look like small "umbrella-shaped" discs. The "show shadows" option is turned off. Does anybody know what are those spots and how to get rid of them? Thank you very much for any help. Regards, Alja Oblak

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how to use antechamber?
by 何永辉 16 Aug '12

16 Aug '12

Hello, Can you show me how to use the ambertool antechamber in Chimera? Thanks! Yonghui Dr. Yonghui He Central South University 932 Lushan South Road Changsha, China.

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em fit refinement
by Bala subramanian 15 Aug '12

15 Aug '12

Friends, I used "fit" command to fit a structure onto a EM map and obtained a list of fits. Now i want to choose the best fit and refine it further. I would like to know if there is any way to refine a fit produced by fit command in Chimera. Or can i use any other software for the same, which can take chimera's fit as input and refine it further. Thanks, Bala -- C. Balasubramanian

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Mountain Lion
by John (Jack) Johnson 13 Aug '12

13 Aug '12

Are there any issues with the current Mac version of Chimera (1.6.2) and Mac OS 10.8 (Mountain Lion)? Also, for a MacBook Pro (latest version) should one be using 32 or 64 bit version of Chimera. Thanks, Jack John E. Johnson Elden R. Strahm Professor of Structural Virology PHONE 858-784-9705 Department of Molecular Biology, MB31 FAX 858-784 -8660 The Scripps Research Institute EMAIL jackj(a)scripps.edu<mailto:jackj@scripps.edu> 10550 N. Torrey Pines Rd. La Jolla, CA 92037 http://johnsonlab.scripps.edu/ Virus Partcle ExploreR (VIPER) http://viperdb.scripps.edu/ ******************************************************************************** Olive Ireland PHONE 858-784-2947 Administrative Assistant EMAIL ireland(a)scripps.edu<mailto:ireland@scripps.edu>

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Elongating TMV capsid
by Jeremiah Gassensmith 13 Aug '12

13 Aug '12

Hello, I've downloaded the tobacco mosaic virus structure from the PDB and used Multiscale Models to build the biological unit. Unfortunately, only about 45 or so of the 2200 protein monomers show up. Is there a way I can multiply the biological unit to elongate the TMV structure? I don't need all 2200 monomers, but something a bit longer would be helpful. Thanks! Jeremiah Dr. Jeremiah J. Gassensmith Stoddart Mechanostereochemistry Group Northwestern University 2145 Sheridan Road Evanston, IL 60208-3113 Phone (W) +1(847)467-5936 Fax +1(847)491-1009

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Chimera inquiry: .py to .u3d conversion
by Will Jones 13 Aug '12

13 Aug '12

Hello, My name is Will. I'm a researcher at the University of Iowa. Our group has been using your Chimera software to visualize a model of our protein of interest. It's been very helpful but I've run into a small issue that I'd like to ask your advice on. I'm trying to convert the 3d image of the saved .py file into a universal 3D file (.u3d). I have tried several types of conversion software including polytrans/nugraph, 3DVIA Composer, and CS5 Adobe Photoshop with no success. Could you please tell me if conversion of .py to .u3d is possible, and if so how I might go about it. Thank you, I appreciate your time. Sincerely, Will -- Department of Biochemistry University of Illinois Urbana-Champaign Class of 2012

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Saving Images
by Hobbs, Merlin Eric 09 Aug '12

09 Aug '12

We are having trouble saving images to look a certain way. More specifically we are trying to make an image with the distance from a residue to a metal ion shown. The problem arises when we save the image the 'thickness' of the distance line doesn't change on the actual saved image. So no matter what the thickness is on chimera the image will always show the distance line as being less thick. Thanks Eric -- Merlin Eric Hobbs | Graduate Student, Biochemistry and Biophysics | Raushel Lab | Rm 2510 | Texas A&M University | College Station, TX 77842 | 979-845-9163 | eric0zero(a)tamu.edu

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Re: [Chimera-users] Rapid Access - a different question/request
by Eric Pettersen 08 Aug '12

08 Aug '12

On Aug 8, 2012, at 2:25 PM, Boaz Shaanan wrote: > OK Eric, thanks. I'll wait for the scroll bar since my window is already stretched to the limit. Okay, there will be a scrollbar in tonight's daily build. Worked fine in my tests. Speak up if it turns out I botched something! --Eric

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Rapid Access - a different question/request
by Boaz Shaanan 08 Aug '12

08 Aug '12

Hi Eric, I actually find the Rapid Access very convenient, however I wonder: is the list limited to the n most recent sessions/pdb ? I actually am missing the option of paging further down the list to jobs that are not in the list but which are quite recent. Is there already an option to do this? The browse button does other things (at list in my hands). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Monday, August 06, 2012 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 112, Issue 6 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Modelling of missing regions ussing Chimera (Gleb Novicov) 2. (no subject) (Merced Malabanan) 3. Re: Rapid Access file list (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Sat, 4 Aug 2012 15:44:12 +0400 From: Gleb Novicov <gnovikov87(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Modelling of missing regions ussing Chimera Message-ID: <CAN=J6WkT9_GH8YYT8U=Nbt-3hhor_YvNHrndwXK6L4ix75uHvA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear Chimera's users! I need to model some missing segments ( In particular case I need to build missing N and C termi ) of my protein ussing Modeller's options. Could you tell me about possible solution of that issue ? On my win7 I have installed Chimera as well as Modeller v 9.10 suite. I've defined Modeller pathways in the Chimera's Model pool options but when I've selected option Prune seection to define region of interest I didnt obtain anythinf from both of Chimera or Modeller. On other hand the option Structure -> Modeller tools also not available for me. Does it means that I've installed modeller incorrectly ? Also I've used runmod.dat script with defined variables from which I obtained the below C:\Users\own\Desktop\worktemp>runmod.bat usage: mod9.10 script [...] Doest this means that all work fine ? By the way after executing of that script I could not launch modeller by means of mod9.10.exe from modeller folder. The error from modeller was C:\Program Files\Modeller\bin>mod9.10.exe FATAL ERROR: MODINSTALL9v10 environment variable not set: incomplete MODELLER in stallation Could you explain me whats I've done wrong and how I could fix this problem? Thanks for help Gleb

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Modelling of missing regions ussing Chimera
by Gleb Novicov 08 Aug '12

08 Aug '12

Dear Chimera's users! I need to model some missing segments ( In particular case I need to build missing N and C termi ) of my protein ussing Modeller's options. Could you tell me about possible solution of that issue ? On my win7 I have installed Chimera as well as Modeller v 9.10 suite. I've defined Modeller pathways in the Chimera's Model pool options but when I've selected option Prune seection to define region of interest I didnt obtain anythinf from both of Chimera or Modeller. On other hand the option Structure -> Modeller tools also not available for me. Does it means that I've installed modeller incorrectly ? Also I've used runmod.dat script with defined variables from which I obtained the below C:\Users\own\Desktop\worktemp>runmod.bat usage: mod9.10 script [...] Doest this means that all work fine ? By the way after executing of that script I could not launch modeller by means of mod9.10.exe from modeller folder. The error from modeller was C:\Program Files\Modeller\bin>mod9.10.exe FATAL ERROR: MODINSTALL9v10 environment variable not set: incomplete MODELLER in stallation Could you explain me whats I've done wrong and how I could fix this problem? Thanks for help Gleb

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Re: [Chimera-users] Chimera-users Digest, Vol 112, Issue 2
by vamsee 07 Aug '12

07 Aug '12

Hello, I am trying to script distance measurements (distance monitor) between the Calpha of a residue and a few Hydrogens. I have pretty much everything working except that I am not able to figure out how to change the attributes (color, line style etc..) of the distances (pseudo-bonds). I know it can be changed using the GUI but I would rather script it. Any suggestions? Thank you Vamsee On Thu, Aug 2, 2012 at 1:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. combining mrc maps (Daniel Murin) > 2. Re: combining mrc maps (Elaine Meng) > 3. Re: combining mrc maps (Tom Goddard) > 4. double bonds visualization ? (Marek Maly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Aug 2012 18:58:53 -0700 > From: Daniel Murin <cmurin(a)scripps.edu> > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] combining mrc maps > Message-ID: > < > 83025BE3F3B8D644AA9F8CAA21F2640801A3D700C402(a)EXCH-CCR01.lj.ad.scripps.edu> > > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I was wondering if it is possible to combine two mrc volumes into a single > volume and save that as a new mrc file? I haven't really been able to find > anything and I suspect that this may not be possible with Chimera. > > Thank you for your help, > > Daniel > > > > Charles Daniel Murin > Graduate Student - Ward/Ollmann-Saphire Labs > Department of Molecular Biology > Kellogg School of Science and Technology > The Scripps Research Institute > 10550 North Torrey Pines Road, CB 227 > La Jolla, CA 92037 > > Work: 858.784.9053 > Fax: 858.784.8218 > email: cmurin(a)scripps.edu > > > > ------------------------------ > > Message: 2 > Date: Thu, 2 Aug 2012 10:06:36 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Daniel Murin <cmurin(a)scripps.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] combining mrc maps > Message-ID: <20D05B2F-142C-4433-B4A3-A8BAB0242919(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Daniel, > You can add or subtract maps to make a new map using the "vop" command: > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html> > > That command has various other filtering and scaling options that may also > be of interest. You can save the new map to a file using the Volume Viewer > dialog (its File menu) or the "volume" command. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Aug 1, 2012, at 6:58 PM, Daniel Murin wrote: > > > Hi, > > I was wondering if it is possible to combine two mrc volumes into a > single volume and save that as a new mrc file? I haven't really been able > to find anything and I suspect that this may not be possible with Chimera. > > Thank you for your help, > > Daniel > > > > > ------------------------------ > > Message: 3 > Date: Thu, 02 Aug 2012 10:07:18 -0700 > From: Tom Goddard <goddard(a)sonic.net> > To: Daniel Murin <cmurin(a)scripps.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] combining mrc maps > Message-ID: <501AB3C6.2050900(a)sonic.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Daniel, > > Yes, just add the two map with the volume operation command > > vop add #1,2 > > This will extend the grid of map #1 to cover map #2 then interpolate map > #2 on that grid and add it. You may also want to scale the values of > one map so that the two maps have comparable density ranges using the > "scaleFactors" option. > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#add > > Tom > > > > Hi, > > > > I was wondering if it is possible to combine two mrc volumes into a > single volume and save that as a new mrc file? I haven't really been able > to find anything and I suspect that this may not be possible with Chimera. > > > > Thank you for your help, > > > > Daniel > > > > > > > > Charles Daniel Murin > > Graduate Student - Ward/Ollmann-Saphire Labs > > Department of Molecular Biology > > Kellogg School of Science and Technology > > The Scripps Research Institute > > 10550 North Torrey Pines Road, CB 227 > > La Jolla, CA 92037 > > > > > > ------------------------------ > > Message: 4 > Date: Thu, 02 Aug 2012 20:00:51 +0200 > From: "Marek Maly" <marek.maly(a)ujep.cz> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] double bonds visualization ? > Message-ID: <op.wifdnpi4lc8gdf(a)pocitadlon.ujep.cz> > Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes > > Hello, > > I am just curious if it is possible to visualize double bonds > as double bonds now similarly like in case of rings one > can visualize them nicely (aromatic ring/disc). > > Thanks for the info in advance, > > Best wishes, > > Marek > > > -- > Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: > http://www.opera.com/mail/ > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 112, Issue 2 > ********************************************* >

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(no subject)
by Merced Malabanan 06 Aug '12

06 Aug '12

Hi, I'm trying to get used to the new Rapid Access interface of chimera. But how do you remove the list (or items on the list) on the right side of the interface? Thanks.

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SASA vs. MSA
by Nikolay Igorovich Rodionov 05 Aug '12

05 Aug '12

Hi all, I was wondering if you could help me conceptualize what is going on in this situation. I ran both solvent accessible surface area and solvent excluded (molecular) surface area calculations. When I compared the output for both of these calculations I found that, overall, atoms that contribute to the SASA are buried 1-3 angstroms deeper in the protein than those that contribute to the MSA. I don't really understand how this could be unless the deeper buried SASA atoms have a much larger van der waals radii than MSA atoms (I get that some atoms contribute to both). Thanks!

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trajectory rmsd
by George Tzotzos 03 Aug '12

03 Aug '12

I'm writing to find out if it is possible to determine the rmsd of specific residues, say 20-120 (backbone atoms only) from a trajectory against the corresponding residues of an X-ray structures. I used the Movie tool to load the trajectory having loaded prior to it the reference structure. I couldn't find a way to compute what I described above. Your help as always is much appreciated Best regards George

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Inifinite lattice minimisation
by Kyle Morris 03 Aug '12

03 Aug '12

Dear all, I am trying to do minimisations on a crystal system. I wonder if when chimera knows the unit cell will it minimise as an infinite lattice or do the copies need to be explicitly created before minimisation proceeds? Really appreciate any help/insight. Best wishes, Kyle

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combining mrc maps
by Daniel Murin 02 Aug '12

02 Aug '12

Hi, I was wondering if it is possible to combine two mrc volumes into a single volume and save that as a new mrc file? I haven't really been able to find anything and I suspect that this may not be possible with Chimera. Thank you for your help, Daniel Charles Daniel Murin Graduate Student - Ward/Ollmann-Saphire Labs Department of Molecular Biology Kellogg School of Science and Technology The Scripps Research Institute 10550 North Torrey Pines Road, CB 227 La Jolla, CA 92037 Work: 858.784.9053 Fax: 858.784.8218 email: cmurin(a)scripps.edu

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double bonds visualization ?
by Marek Maly 02 Aug '12

02 Aug '12

Hello, I am just curious if it is possible to visualize double bonds as double bonds now similarly like in case of rings one can visualize them nicely (aromatic ring/disc). Thanks for the info in advance, Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Re: [Chimera-users] FW: FW: problem in visualising metal- atoms in simulated
by Mahendra B Thapa 31 Jul '12

31 Jul '12

Dear Dr. Elaine, May I send my pdb file? I could not fix the problems; I tried my best as far as I can , with possible alternatives. Thanks, Mahendra Thapa University of Cincinnati On Mon, Jul 30, 2012 at 12:58 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > > > ________________________________________ > From: Elaine Meng > Sent: Monday, July 30, 2012 10:58:32 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] FW: problem in visualising metal- atoms in > simulated > > The atom names of the ions should not be lined up with the other names, > and the last field should be CA not C. So there are at least two problems > with these lines. Please see the format description in the link in my > previous message. > > Some additional problems are that the ion lines should probably be HETATM > not ATOM, and the names CA not CO. So I would fix those things too. > Best, > Elaine > > On Jul 30, 2012, at 9:46 AM, Mahendra B Thapa wrote: > > > Dear Dr. Elaine, > > > > The last few lines of the file are as follows: > > ATOM 1212 OXT GLN 76 17.333 31.515 17.211 1.00 0.00 > O > > TER > > ATOM 1213 CO CAL 77 35.029 27.971 38.126 1.00 0.00 > C > > TER > > ATOM 1214 CO CAL 78 37.868 20.307 30.270 1.00 0.00 > C > > TER > > > > I also tried with Ca instead of C in the last column , but no > improvement. > > > > Thank you for help, > > Mahendra Thapa > > University of Cincinnati > > > > > > On Mon, Jul 30, 2012 at 12:34 PM, Thapa, Mahendra (thapamb) < > thapamb(a)mail.uc.edu> wrote: > > > > > > > > ________________________________________ > > From: Elaine Meng > > Sent: Monday, July 30, 2012 10:34:51 AM (UTC-06:00) Central America > > To: Thapa, Mahendra (thapamb) > > Cc: chimera-users(a)cgl.ucsf.edu > > Subject: Re: [Chimera-users] problem in visualising metal- atoms in > simulated > > > > Hi Mahendra, > > Probably the format is slightly wrong for the lines with the calcium ion > coordinates. For example, the name CA for the calcium ion should *not* line > up with the name CA in the protein alpha-carbon lines. > > > > In the ATOM and HETATM lines of PDB files, > > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coo… > > > > > > ...the ion name CA should be in columns 13-14, whereas the alpha-carbon > name CA should be in columns 14-15. > > > > Misalignment of ion names is a common problem with the output of many > programs. > > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#mis… > > > > > > Best, > > Elaine > > ---------- > > Elaine C. Meng, Ph.D. > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > On Jul 30, 2012, at 9:21 AM, Mahendra B Thapa wrote: > > > > > Dear Chimera Users, > > > I converted amber-12 generated rst-file in netCDF format [ > test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the > cpptraj command of amber 12. When I loaded it in chimera, the protein > structure looks fine but two calcium atoms that the protein binds could > not be visualised, although the pdb file-format looks good. > > > Let me help in this respect. > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Unable to visualize density maps
by Anindito Sen 30 Jul '12

30 Jul '12

Dear All, With the latest Chimera version in Daily Build for Mac , I am unable to visualize any density map in the "surface" and the "mesh" mode. On playing around trying to visualize the density maps I get something like the following attached figure. However I can see the maps at the "solid" mode. I am using Snow Leopard 10.6.8. Best Andy Versions Not Working: Mac OS X chimera-alpha-mac.dmg Size: 105982078 bytes MD5: ba098e1169a7fb37f9b80bbac27cae26 Jul 28, 2012 Mac OS X 64-bit chimera-alpha-mac64.dmg Size: 93344817 bytes MD5: 22700ce0b2b0272d3efe060832933ee5 Jul 28, 2012 Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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ff dat file
by Nikolay Igorovich Rodionov 30 Jul '12

30 Jul '12

Hi, since I am able to implement various force fields, does that mean that I have the .dat files of those ff buried somewhere in my chimera directory? I want to add my custom ff parameters to PDB2PQR so I need to locate the .dat files of force fields like Amber12 and Amber99SB. Thank you, Nikolay Rodionov

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Re: [Chimera-users] FW: problem in visualising metal- atoms in simulated
by Mahendra B Thapa 30 Jul '12

30 Jul '12

Dear Dr. Elaine, The last few lines of the file are as follows: ATOM 1212 OXT GLN 76 17.333 31.515 17.211 1.00 0.00 O TER ATOM 1213 CO CAL 77 35.029 27.971 38.126 1.00 0.00 C TER ATOM 1214 CO CAL 78 37.868 20.307 30.270 1.00 0.00 C TER I also tried with Ca instead of C in the last column , but no improvement. Thank you for help, Mahendra Thapa University of Cincinnati On Mon, Jul 30, 2012 at 12:34 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > > > ________________________________________ > From: Elaine Meng > Sent: Monday, July 30, 2012 10:34:51 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] problem in visualising metal- atoms in > simulated > > Hi Mahendra, > Probably the format is slightly wrong for the lines with the calcium ion > coordinates. For example, the name CA for the calcium ion should *not* line > up with the name CA in the protein alpha-carbon lines. > > In the ATOM and HETATM lines of PDB files, > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coo… > > > > ...the ion name CA should be in columns 13-14, whereas the alpha-carbon > name CA should be in columns 14-15. > > Misalignment of ion names is a common problem with the output of many > programs. > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#mis… > > > > Best, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jul 30, 2012, at 9:21 AM, Mahendra B Thapa wrote: > > > Dear Chimera Users, > > I converted amber-12 generated rst-file in netCDF format [ > test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the > cpptraj command of amber 12. When I loaded it in chimera, the protein > structure looks fine but two calcium atoms that the protein binds could > not be visualised, although the pdb file-format looks good. > > Let me help in this respect. > > > >

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problem in visualising metal- atoms in simulated
by Mahendra B Thapa 30 Jul '12

30 Jul '12

Dear Chimera Users, I converted amber-12 generated rst-file in *netCDF format* [ test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the cpptraj command of amber 12. When I loaded it in chimera, the protein structure looks fine but two calcium atoms that the protein binds could not be visualised, although the pdb file-format looks good. Let me help in this respect. Thanks, Mahendra Thapa University of Cincinnati

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Coulombic Potential Dielectric
by Nikolay Igorovich Rodionov 26 Jul '12

26 Jul '12

Hi, I just have a question about the default dielectric coefficient in the Coulombic surface coloring function. Does the coefficient of 4 correspond to the dielectric of the solvent or the solute (the biomolecule)? I think the latter makes more sense but I just want to make sure. Thanks! Nikolay Rodionov

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Pot.dx to cartesian
by Nikolay Igorovich Rodionov 26 Jul '12

26 Jul '12

Hi all, I was wondering if anyone knows of a program that can take the gridpoint potential matrix from the APBS output pot.dx file and convert it into Cartesian coordinates. Something like: X Y Z Potential 545 5 54 +2.5484 Thanks! Nikolay Rodionov

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