- Chimera-users - RBVI Mailing Lists

[ViewDock] wrong bonds
by Aurelien GROSDIDIER 29 Aug '05

29 Aug '05

Hi all ! I'm currently trying to use the ViewDock plugin to visualize results coming from our in house docking program, which dumps PDB files. These PDBs are them transformed into in a DOCK3/DOCK4 compliant format. First, I should say I haven't seen a clear description of this format, and the script gathering together PDB files is very empirical. The problem I see might come from a mistake of our docking program. Urls to fock3/4 specifications are thus welcome :) Problem context: ---------------- The problem happens when dealing with ligands having several distinct residue numbers or if the docking coordinates do not consist only of a ligand, but also a set of sidechains of its receptor (also with distinct residue number). Problem symptoms: ----------------- The representation loaded using ViewDock show bonds between each and every atoms of the ligand (and the sidechains, if any), no matters their atom type or how far they are. This is kinda of weird, as the representation is perfect when these PDB are loaded from individual PDB files (not using ViewDock). I am a newbie on this mailing list, and unfortunately this problem should be solved withing a few days or so. I would like to apologize in advance in case this help request should go somewhere else. And in case you need a clearer description of the problem (with figures, input files and so on), feel free to contact me either directly or using the ML :) Thanks a lot for your help, Aurélien Grosdidier

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regarding coloring
by moumita dutta 24 Aug '05

24 Aug '05

Dear Sir, How can I use more than one color to highlight different area using the UCSF chimera software in a 3d refined model of a virus ? Regards, M.Dutta --------------------------------- Start your day with Yahoo! - make it your home page

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problems reading delphi phi map under XP
by Boaz Shaanan 24 Aug '05

24 Aug '05

Hello, When I try to read a delphi phi map under XP I get the error message: Return code: -2147483641 and the program exits. The same map would be read OK under linux and under Win2k. I'm using the latest win32 snapshot (the same happens with the official release though). I would appreciate if you could let me know what has gone wrong. Thanks, Boaz

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ATI catalyst 5.7 drivers with R9600SE video card crash winxp when creating surfaces (or running surface benchmark) in chimera-1.2143
by Sabuj Pattanayek 22 Aug '05

22 Aug '05

Hi, I had upgraded ATI's catalyst drivers from 5.4 (or 5.5) to 5.7 for my R9600SE video card under winxp sp2. In Chimera-1.2143 when I tried to create a surface representation or tried the surface benchmark the screen would go black (monitor led goes from green to orange) and the system would crash (no longer responds to pings). Downgrading to catalyst 5.6 fixed the problem. I sent a trouble ticket to ATI. Has anyone had a similar problem with Radeon (non-firegl) cards? Thanks, Sabuj Pattanayek

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Re: [chimera-dev] accelerators and stereo
by Eric Pettersen 18 Aug '05

18 Aug '05

Hi Justin, Chimera doesn't have a function to directly save a stereo image. Instead, what you do is save separate left-eye and right-eye images and place them appropriately in your presentation or paper -- for a cross-eye image that would be the left-eye on the right and vice versa. You save the images by bringing up the Side View (under Favorites) and clicking on the "Camera" tab. There is a "camera mode" menu under that tab that lets you select left-eye/right-eye views. Then just use the regular image-saving process. This is also described in the Images tutorial (near the end): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html We want to make this easier to do but haven't gotten to it yet. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu On Aug 18, 2005, at 7:06 AM, Justin Wu wrote: > Hi > Would you please let me know how to make a cross-eye figure from > Chimera? I do not where to look for this function. > Thanks > Justin > ************************************************ > Justin Wu > Rm 752, Biological Science Building > 484 West 12th Ave, > Columbus, OH 43210 > Tel: (614)247-5040, Fax: (614)292-6773 > ************************************************ > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

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Re: [Chimera-users]
by Eric Pettersen 09 Aug '05

09 Aug '05

Hi Sabuj, It is the indentation. In Python, indentation is meaningful and statements at the same "level" have to have the same indentation. I've appended the critical part below. Note the the "self.rulerTexts..." and "x += ..." statements are indented one space further than the preceding if/else and "text = ..." statements. To Python, the extra space starts a new indented block of statements, which is only legal after 'if' statements and so forth. Take a space away from the front of the last two statements and I think things will work. --Eric for chunkStart in range(self.seqOffset, end, 10): seq1index = self.seqs[0].gapped2ungapped (chunkStart) if seq1index is None: dispText = "?" else: dispText = str(seq1index+1) text = self.mainCanvas.create_text(x, y, anchor='s', font=self.font, text="%s" % (dispText)) self.rulerTexts.append(text) x += self.chunkGap + 10 * (self.fontPixels[0] + self.letterGaps[0])

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by Pattanayek, Sabuj 09 Aug '05

09 Aug '05

Hi all, Is there a modification I can do to the multi-align viewer code so that "-" (gaps) characters are not counted in the alignment numbering (but are still displayed for alignment purposes) from a fasta file in the multi-align viewer? The numbering should correspond to the first sequence found in the fasta file (i.e. I don't care about the numbering due to gaps in the second, third, etc sequences). Thanks, Sabuj Pattanayek

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Making and Breaking bonds in Chimera
by David Chenoweth 04 Aug '05

04 Aug '05

Dear Chimera users, Does anyone know how to make a new bond or delete a bond between two atoms within a PDB file using chimera? -Thanks DC

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Coloring by Delphi potential in Chimera
by Elaine Meng 29 Jul '05

29 Jul '05

Hi Zach, DelPhiViewer got removed because other tools can do the same things in a more general and flexible way. Unfortunately in the latest snapshot (1.2129, June) it is confusing to get to these newer features, but they are all there, and I'll explain how. I'll assume you are using that latest snapshot and that you have an electrostatic potential file in the format from DelPhi. ------------------- First, open the electrostatic potential file with File... Open. If the file is named ending in .phi you can set the File type to "all (guess type)" or "DelPhi or GRASP potential". This will automatically start Volume Viewer. (A) IF you want to look at contour (isopotential surfaces), keep using Volume Viewer. Open the Volume Viewer man page by clicking the Help button on the dialog. You probably want to go to the "Surface or Mesh" section of the man page, under "Display Panel". Otherwise... (B) IF you want to color the molecular surface or GRASP surface based on the potential, click the Unshow button on Volume Viewer and then the Close button on Volume Viewer. Open the molecule and show its surface that you want to color, or open the GRASP surface you want to color (this can also be opened with File... Open). The tool for coloring a surface by potential is Surface Color (Tools... Surface/Binding Analysis... Surface Color). Pick the surface of interest from the menu next to "Color surface" and choose the electrostatic potential data from the menu next to "Using volume data or geometry". You probably want to change the "Color scheme" to "3 color symmetric" - then you have something similar to the DelPhiViewer surface coloring interface. Click the Help button on the Surface Color dialog if you want to see the man page. -------------------- We realized this is pretty confusing and have tried to make it better (and the improvements will show up in the next release). The improvements are that you will be able to color a surface according to electrostatic potential by choosing Tools... Surface/Binding Analysis... Electrostatic Surface Coloring, and then you can open the electrostatic potential using a Browse button on that tool (avoiding Volume Viewer entirely). It will also start with the 3-color scheme when opened this way. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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[Chimera-users] coloring of nearly identical protein sequences in multialign viewer
by Sabuj Pattanayek 29 Jul '05

29 Jul '05

Hi all, I have a clustal aln file or a fasta file with two nearly identical aligned protein sequences. When I view them in the multialign viewer I would like to change the color of the consensus style. That is, residues which are both identical should be just black (rather than red and capitalized) and residues that are not identical should be red (or some other color that contrasts against black). Is there anyway to do this? Better yet would it be possible to not use the consensus at all and color the entire non-matching column a color of my choice? Thanks, Sabuj Pattanayek

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