March 2015 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] FW: How to get prmtop file corresponding to a pdb file
by Mahendra B Thapa 18 Mar '15

18 Mar '15

Dear Dr. Victor, Thank you for reminding me about the protonation state of HIS. As a trial, I changed all HIS to HID and again repeated my previous steps. This time, I got some python track back errors. I suspect the source of error could be the initial pdb file which I used in chimera ; the pdb file was obtained from other software (like online server), so some atom names were different from that of AMBER. My goal was to get AMBER prmtop corresponding to pdb files which were generated by programs other than AMBER so that I could use ambertools. So, may I need to convert all such pdb files compatible with amber pdb format ? Thank you for help, Mahendra Thapa On Wed, Mar 18, 2015 at 5:08 AM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > ------------------------------ > *From:* Victor Muñoz > *Sent:* Wednesday, March 18, 2015 3:08:18 AM (UTC-06:00) Central America > *To:* Thapa, Mahendra (thapamb) > *Cc:* chimera-users(a)cgl.ucsf.edu > *Subject:* Re: [Chimera-users] How to get prmtop file corresponding to a > pdb file > > Dear Mahendra, > > The error is due to HIS not being the standard residue name for Histidine > in the Amber force field. In Amber, histidine residues are named either > HIE, HID or HIP depending on their protonation state ( > http://ambermd.org/Questions/HIS.html) Change the name of the histidines > on the PDB file accordingly to their protonation state and it should work > fine. > > Kind regards, > > Victor > > 2015-03-18 6:39 GMT+01:00 Mahendra B Thapa <thapamb(a)mail.uc.edu>: > >> Dear Chimera users, >> >> To get *Amber prmtop file* corresponding to a *pdb file using Chimera*, >> I did the following steps: >> 1] tools -> Amber -> write prmtop >> 2] In a pop-up window 'save file in chimera', I gave file name, say, >> aa.prmtop, then clicked save. >> 3] No charges message appeared, then I clicked 'Assign charges'. >> 4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other >> residues, then clicked ok. >> 5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in >> charge method >> 6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS. >> Check reply log for details. >> 7] In reply log, '*Failure running ANTECHEMBER for residue HIS*' seen. >> >> Any help in this issue will be a good help for me. >> >> Thank you. >> Mahendra Thapa >> University of Cincinnati,OH >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >

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on color zone
by Smith Liu 17 Mar '15

17 Mar '15

Dear All, I have a mrc file for a protein complex with a 3-fragment sheets (from A to B, from B to C, from C to D, and they were connected by H-bonds). Will you please introduce to me on how to use color zone to split to get the mrc file for each fragment of the sheets? I have tried to do it by myself, however I find the splitting was not done based on fragment, i.e., I cannot get the mrc file for each fragment of the sheets. I am looking forward to getting your reply. Smith

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Chimera tutorial at VIZBI conference in Boston on Tuesday, March 24
by Samuel Hertig 16 Mar '15

16 Mar '15

Dear Chimera users, In case you are interested in learning the basics of Chimera and if you can make it to Boston on March 24, the RBVI will be teaching a small Chimera tutorial as part of the Visualizing Biological Data (VIZBI) conference. Details and registration: http://www.vizbi.org/2015/Program/#Tuesday Best regards, Sam Hertig, PhD Postdoctoral researcher Resource for Biocomputing, Visualization, and Informatics University of California, San Francisco

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UCSF Chimera error: X Error of failed request: BadDrawable (invalid Pixmap or Window parameter)
by Muhammad Sufian 16 Mar '15

16 Mar '15

Dear all Chimera users, I tried to install following version of Chimera; chimera-1.10.1-linux_x86_64.bin but after installation, following error appeared after its execution; sufian@system01:/usr/local/chimera/bin> ./chimera X Error of failed request: BadDrawable (invalid Pixmap or Window parameter) Major opcode of failed request: 72 (X_PutImage) Resource id in failed request: 0x2200064 Serial number of failed request: 1357 Current serial number in output stream: 1363 I also tried to install Chimera 1.9, but got same error. My system specifications are; Processor: x86_64 Operating-system: GNU/Linux (OpenSUSE 12.1) Kernel: Linux 3.4.63-2.44-desktop Kindly guide me how to resolve this issue. Regards. Muhammad SufianM.Phil. scholar (Molecular Medicine),Computational Biology Laboratory,Lab no. P-103, PCMD-Extension,Dr. Panjwani Center for Molecular Medicine and Drug ResearchInternational Center for Chemical and Biological SciencesUniversity of Karachi, Karachi, Pakistan

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a question related to segment map
by Smith Liu 16 Mar '15

16 Mar '15

Dear All, After I segment a map into diffrent color, will you please tell me in detail how can I erase some specific parts of the map which I do not nee for some purpose? Smith

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Selecting just 1 carbohydrate chain
by Tein Leong (PG Research) 12 Mar '15

12 Mar '15

Hello, Thank you for the amazing programme. I’m using it for the first time and I can do most of the things I needed to do. I am writing to ask if it is possible to “color” just one carbohydrate chain ? I’m coloring an antibody crystal structure which is made up of two heavy chains. Each chain has a carbohydrate attached. I wanted to color both carbohydrate in different colors but I’m unable to do so. When I go to “Select” > “Residue” , the programme can only select all carbohydrate residues. Please advice. Thanks ! Best wishes, Tein Foong Leong PhD Student Jacqui Wood Cancer Centre, Level 7 Ninewells Hospital University of Dundee DD1 9SY The University of Dundee is a registered Scottish Charity, No: SC015096

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binned color ranges for scolor?
by Oliver Clarke 11 Mar '15

11 Mar '15

Hi all, I was wondering whether it is possible to use binned ranges for scolor? Specifically, I would like to color one volume by the density values of a second volume, but rather than using a continuous color palette, I would like to highlight several discrete bins with particular colors - e.g coloring all values between 2 and 4 red, and all values between 6 and 8 green, while leaving other voxels uncolored (or colored gray, for example). Is this currently possible? I couldn’t figure it out - both cmap and map range seem to give continuous coloring. Best, Oliver.

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How to lower the map size
by 李智海 09 Mar '15

09 Mar '15

Hi, Now I have a density map with a dimension of 820*820*820, it is too large for me to perform image processes with Chimera. So I was wondering whether there is a way to decrease the map size rather than re-reconstruct the map with bined particle image. please help me out! Thank you in advance! Zhihai Li

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Re: [Chimera-users] Request for support - UCSF Chimera
by Eric Pettersen 04 Mar '15

04 Mar '15

On Mar 4, 2015, at 10:14 AM, Nishant Ray Velagapudi <nishray(a)uw.edu> wrote: > Hello Mr. Petterson, > > I was looking for some help with using UCSF chimera and I was wondering if I can directly email you my question. If this is not the appropriate address, my apologies, and could you point me in the appropriate direction for support? Hi Nishant, You should probably send questions like these to the chimera-users mailing list. That way other people can benefit from the answer, and it also allows others to answer in the cases where I'm not really the best person for the question. > My issue is that I want to automate the process of creating and saving structure based sequence alignments. It has been simple to open the file and align them, but I am not sure how to save the .fasta alignment file out. Here is what I have so far: > > for fn in file_names: > replyobj.status("Processing: " + fn) > rc("open " + fn) > rc(mm #0 #1 show true) > rc("close " + fn) > > The bold line is the problematic one - is there any way to write out the resulting alignment file in a programmatic fashion? Yes. You can locate the MultAlign Viewer (MAV) instance using the code in this previous chimera-users mail: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html That message also describes how to save the alignment to a file, in conjunction with the info in this message: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010015.html You can search the chimera-users list from this page to see if your question has been asked previously: http://www.cgl.ucsf.edu/chimera/docs/feedback.html I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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concatenate
by sunyeping 04 Mar '15

04 Mar '15

Dear all,I am dealing with a EM map which is a double helical filament and composed of two protein chains winding each other. Each of the two chains is composed of multiple same protein subunits. Now I am trying to color one chain of the map with one color, and the other chain with another color. How should I do that?Besides, it is known that multiple such double helixes can constitute a longer helix by a head-to-tail way. I can open several helixes in chimera, but how to concatenate they correctly into a long helix?Could you help me with these questions?With many thanks! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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