- Chimera-users - RBVI Mailing Lists

licensing
by Schulz-Gasch, Tanja 02 Oct '09

02 Oct '09

Hi there, I have a single-user license for Chimera at Roche. Meanwhile others are interested in using Chimera as well. Could you please send me an update on licensing scemes and costs? Thanks, Tanja __________________________________________ Dr. Tanja Schulz-Gasch F. Hoffmann-La Roche Ltd Pharmaceuticals Division PRCBLM Bldg. 92/2.10D CH-4070 Basel Switzerland Tel. +41(0)61 68 88309 Fax. +41(0)61 68 86459 http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html <http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html> Email: tanja.schulz-gasch(a)roche.com "The information transmitted in this message is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you receive this message in error, please contact the sender and delete the material from any computer."

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segmentation fault
by Francesco Pietra 01 Oct '09

01 Oct '09

Hi: On Debian Linux i386 squeeze I had the X system broken while attempting to install the gnome cd burner "brasero". I purged everything about that bad code, installed and reconfigured the X system, however something is still broken. Attempts at launching CHIMERA returned "segmentation fault". That also sitting in the directory where chimera is installed ( /usr/local/chimera/bin). As I had an old version, I reinstalled chimera-1.3-linux.exe, while that did not solve the above problem. I do not remember where to put the hands in such cases. Thankful for reminding me about that. francesco@deb32:~$ gcc --version gcc (Debian 4.3.4-2) 4.3.4 francesco pietra

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Re: [Chimera-users] Solvent Accessible Surface Area
by Elaine Meng 01 Oct '09

01 Oct '09

On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > I am using Chimera for identifying the surface residues. > > I select areaSAS > 0.05 square angstroms, is this same as saying > areaSAS > 5%, I am getting confused with the numbers 5% and 0.05 sq > angstroms have these been switched some how or are they curiously > the same in the following statement? > > I just need some help in understanding. > Thank You > Sincerely > -Thiru Ramaraj Hi Thiru, In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms. Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state. See for example the GetArea server, which gives "Ratio(%)": <http://curie.utmb.edu/area_man.html> However, what Chimera reports is just the surface area of the atom or residue in your structure. To choose surface residues, I'd probably use a bigger cutoff, say select :/areaSAS>10 but it depends on what you are going to do with the results. You can try different values and see what looks reasonable. 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

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Transparent Spheres
by Waight, Andrew 30 Sep '09

30 Sep '09

Hello everyone again. I apologize for a potentially embarassing question but is it possible to display sidechains as transparent spheres with solid stick representation inside. Seeing as I also can't find an image in the Chimera gallery where it is represented as such, I am wondering if it is possible to individually color (and set opacity) on spheres. I am also aware that vdw will create dots of varying density, but is it alternatively possible to display vdw as solid surface with opacity. Thanks to all for your patience. Drew ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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Re: [Chimera-users] Chimera-users Digest, Vol 77, Issue 26
by vamsi krishna 30 Sep '09

30 Sep '09

Dear all, I am using chimera to calculate solvent accessibility of residues , may i ask you what cutoff is appropriate to identify surface residues significant for substrate binding . Thank you vamsi 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://www.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. Re: Solvent Accessible Surface Area (Elaine Meng) > 2. Re: Solvent Accessible Surface Area (Thiruvarangan Ramaraj) > 3. Re: Solvent Accessible Surface Area (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 28 Sep 2009 12:14:48 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Thiruvarangan Ramaraj <thiruvaranganr(a)yahoo.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Solvent Accessible Surface Area > Message-ID: <E24233F9-9564-4824-8D82-6D9506261ACB(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > > >> Hi Elaine, >> I am using Chimera for identifying the surface residues. >> >> I select areaSAS > 0.05 square angstroms, is this same as saying >> areaSAS > 5%, I am getting confused with the numbers 5% and 0.05 sq >> angstroms have these been switched some how or are they curiously >> the same in the following statement? >> >> I just need some help in understanding. >> Thank You >> Sincerely >> -Thiru Ramaraj >> > > > Hi Thiru, > In Chimera there is no percentage (%) measurement, it is only the area > value in square angstroms. Some other programs give % exposed for a > residue, which is a ratio of the area of that residue in your > structure to the area of the same type of residue in some theoretical > unfolded state. See for example the GetArea server, which gives > "Ratio(%)": > <http://curie.utmb.edu/area_man.html> > > However, what Chimera reports is just the surface area of the atom or > residue in your structure. To choose surface residues, I'd probably > use a bigger cutoff, say > > select :/areaSAS>10 > > but it depends on what you are going to do with the results. You can > try different values and see what looks reasonable. > 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 > > > > > ------------------------------ > > Message: 2 > Date: Mon, 28 Sep 2009 13:49:00 -0700 (PDT) > From: Thiruvarangan Ramaraj <thiruvaranganr(a)yahoo.com> > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Solvent Accessible Surface Area > Message-ID: <842106.2825.qm(a)web53905.mail.re2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thanks,? Elaine for the information. > > Also I am having problems with installing Chimera on Linux Fedora 11(32 bit version). I am able to download it and install it. When I start chimera it comes up and then crashes immediately, the only message it gives is Segmentation Fault. > > Is there anyway I could resolve this problem. > > Thank You > > -Thiru Ramaraj > > --- On Mon, 9/28/09, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Solvent Accessible Surface Area > To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Date: Monday, September 28, 2009, 1:14 PM > > On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > > >> Hi Elaine, >> I am using Chimera for identifying the surface residues. >> >> I select areaSAS > 0.05 square angstroms, is this same as saying areaSAS > 5%, I am getting confused with the numbers? 5% and 0.05 sq angstroms have these been switched some how or are they curiously the same in the following statement? >> >> I just need some help in understanding. >> Thank You >> Sincerely >> -Thiru Ramaraj >> > > > Hi Thiru, > In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms.? Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state.? See for example the GetArea server, which gives "Ratio(%)": > <http://curie.utmb.edu/area_man.html> > > However, what Chimera reports is just the surface area of the atom or residue in your structure.? To choose surface residues, I'd probably use a bigger cutoff, say > > select :/areaSAS>10 > > but it depends on what you are going to do with the results.? You can try different values and see what looks reasonable. > 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 > > > > > > >

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Using Chimera to read SMILES string into structure
by Miriam Gochin 29 Sep '09

29 Sep '09

I have downloaded the latest build (Aug 30, 2009) and don't seem to be able to input a SMILES string. I have tried both the Utilities -> Structure Diagram and the Structure Editing -> Build Structure tool, and in both cases I can see a box to input the SMILES string, but the copy and paste mechanism won't work. I can enter text in the box, but cannot paste it in, which I need to do. Thanks for your help. Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Zoom factor for model when first opened
by Tom Goddard 25 Sep '09

25 Sep '09

Hi Kevin, The camera settings (position, amount of zoom, angular field of view) all contribute to how much of the Chimera window is filled when you open a map. How those are initially set when you start Chimera and open a map has changed a few times over the last year or two so if you run different Chimera versions (Help / About Chimera... to check version number) you may see different initial sizes. Tom -------- Original Message -------- Subject: chimera question From: Kevin Koehntop To: goddard Date: 9/24/09 6:34 PM > Hi Tom, > > I have a quick chimera question. When I open the same EM map in two > different chimera sessions, even though the scale factor, origin, > voxel size, and isosurface threshold level are exactly the same, the > map appears much smaller in one of the windows and I can't determine > why. Is there another parameter that I need to check? Thank you > > Kevin

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Re: [Chimera-users] [chimera-dev] select opt
by Eric Pettersen 23 Sep '09

23 Sep '09

On Sep 21, 2009, at 7:27 AM, Victor MuÃ±oz wrote: > I'd like to know if there's a way to select the select mode "append" > using the > command line instead of the visual interface. Hi Victor, There isn't a way to do that, but it typically isn't necessary. The "|" and "&" characters perform union and intersection operations respectively. So for example you can add all LYS residues to the current selection with: sel sel | : LYS or you could intersect the current selection with LYS residues with: sel sel & :LYS If you really need to change the mode for some reason, let me know what that reason is and maybe we can add something. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu P.S. The "|" character is a vertical bar, not a capital i, in case that's not clear in the font you're using.

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Re: [Chimera-users] question about Chimera
by 吴雪 22 Sep '09

22 Sep '09

Dear Elaine: Thank you very much for your instruction. We'll follow your guide. Best wishes WU Xue >From: Elaine Meng <meng(a)cgl.ucsf.edu> >Reply-To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >To: 吴雪<wuxue(a)nankai.edu.cn> >Subject: Re: [Chimera-users] question about Chimera >Date: Tue, 22 Sep 2009 11:00:11 -0700 > >Dear Wu Xue, >There are several different distance and angle cutoffs that depend on >the donor and acceptor atom types. For example, the distance and >angle cutoffs for finding a H-bond donated from hydroxyl -OH to >carbonyl =O will be different than from amine -NH3 to carbonyl =O. >The cutoff values are taken from tables in this paper: > > Three-dimensional hydrogen-bond geometry and probability >information from a crystal survey. Mills JE, Dean PM. J Comput Aided >Mol Des. 1996 Dec;10(6):607-22. > >As discussed in the FindHBond documentation, > findhbond.html#criteria> > >the criteria in this paper were based on very high resolution crystal >structures of small molecules. Typically the structures in the PDB >are not so high resolution and so the criteria are relaxed. For >example, if a strict criterion from the paper is 2.8 Angstroms >cutoff, then with 0.4 relaxation the cutoff becomes 3.2 Angstroms. >We set the default relaxation amounts to what we felt gives >reasonable results on most PDB structures. However, we made them >user-adjustable so that if you don't like them, you can change the >values to whatever you want. > >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 Sep 22, 2009, at 4:18 AM, 吴雪 wrote: > >> Dear colleague: >> I have a question about the "find hydrongen bond" in Chimera. >> The dumb relax constraints in Chimera are "0.04 nm" and "20 degree". >> I don't understand the meaning of the parameter. 20 degree may >> means the angle bias the line,but I can't figure out what is the >> 0.04nm. >> The cutoff of the hydrogen is 0.4nm, and the angle is about 90 >> degree or some other parameters depending on the strength of the >> hydrogen bond. >> If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds >> are found. I don't know the criteria. Can you give me some advice >> so that I can follow your instruction? >> Sincerly Yours >> WU Xue > >

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.sld (MOLCAD, Sybyl 8.0) file import or visualisation of an inner surface (of a protein) in Chimera
by Xarana 22 Sep '09

22 Sep '09

Hi, My interest is a 4 helix protein which has a cavity inside. A colleague generated with a 1,4 Angström probe this inner surface with Sybyl for me and exported the surface as .sld file. Can I import this file into chimera somehow? Alternatively, can I generate such a surface with chimera? My knowledge of protein visualization is limited and I am very thankful for any help Thank you very much in advance. Best Wishes Natalie

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