- Chimera-users - RBVI Mailing Lists

Directly representing ellipsoids
by Thomas Ouldridge 26 Jul '10

26 Jul '10

Hi, I'm afraid I'm not a crystallographer/protein simulator, and so this question might seem quite naive. I run coarse-grained simulations, and I would like to represent the objects as ellipses in chimera. I have the position (which I am able to use) and the orientation that I would like my ellipses to take, encoded as a matrix relative to (x,y,z) cartesian coordinates. This matrix gives me the principal axes and radii of the ellipse. As I understand, Chimera is designed to display a "Thermal ellipsoid" - I would like this ellipsoid to have the axes and radii given by my matrix. However, it seems that the input (via pdb format files) is interpreted as an "anisotropic temperature factor", and I can't find a way to convert my matrix into the anisotropic temperature factor (I tried some papers online but they seemed to be talking in terms of transformations between lab frame and crystallographic frames, but I cannot see how that applies - what is my crystallographic frame?). In short, is there a way to convert my matrix into the "anisotropic temperature factor" representation so that Chimera can read it and convert it back? I did try just plugging in the matrix elements to the PDB file but got some weird ellipsoids out. Any help would be gratefully appreciated, Tom

2 1

Transparency doesn't look right
by Tom Goddard 26 Jul '10

26 Jul '10

Hi Mitalee This is a Chimera limitation. Two or transparent models will not be shown correctly. Transparency works correctly only when at most one model is transparent. You have the volume data displayed in "solid" style which is a kind of transparent rendering, and you have a surface model which is transparent. How defective the transparency looks depends on the order the models were opened in Chimera (or maybe it depends on which has higher model id number, don't recall). In any case, both orders look seriously wrong. If you reverse the order of opening your two models I think your surface will remain totally invisible until it becomes 0% transparent when it will suddenly appear. This limitation is a rather fundamental design problem in Chimera. Chimera draws the models one at a time. A model that is drawn after another model can only appear in front of the first model. Chimera first draws all opaque models, then draws all transparent models. If you look at the termite gut video I made http://www.cgl.ucsf.edu/chimera/animations/movies/termitegut.mov where surfaces fade in you'll see at the start of the fade in, a black blob suddenly appears representing the object. This is the same bad behavior you see in your case, but your surface is white (the background color) and is in front of the volume data making it look especially bad. This problem has arisen many times in, especially in movie making where transparency is used to fade objects in and out. I have an idea for a solution although it is not yet implemented. But we just hired Daren Weber to work on animation improvements in Chimera and perhaps he can try this. The idea is to enhance the movie command to add a "crossfade" option. You would display the volume, then use a command like "movie crossfade 25" then show the opaque surface. The command would take the image right before the command was issued and the next image and linearly blend them over 25 frames. This would be useful for many fade scenarios. It is limited in that it won't be able to have models moving and a fade occurring at the same time since that is not simply a linearly blending of two images. I'll see if Darren is interested in trying to add this if you are interested. If you do not want to wait for this, another option is to record your movie without the fade -- just have the surface suddenly appear. Then drop the movie into an video editing program like Final Cut and add the crossfade with that software. Tom > Hi Tom, > > I was using the surft command, trying to make a segment appear inside of a > cmap file. Basically, I have a cmap file open and visible, and I want to > show the segmented cell appear slowly. My problem is that when I set the > transparency of the segmented cell to 100 (i.e. surft 100 #0), it doesn't > exactly become transparent, or what I thought would be transparent. When I > enter this command, it makes the entire image transparent at that point > (so the shape of the segmented cell is preserved and matches the > background. I've attached an image of what I got as a result. Is there a > way to make preserve the cmap image and just make the segmented cell > overlay onto it without completely "removing" the section where the > segmented cell will appear? > > Thanks, > Mitalee

1 1

Question about match
by Ibrahim Moustafa 26 Jul '10

26 Jul '10

Dear Chimera developers, I have a question related to the ³match² command. I wanted to align 4 related proteins and I used the default in the match menu. The alignment is fine; but I have a question about the output in the reply log. In the log it says: ³evaluating superpositions across all 439 fully populated columns in the final alignment² Then the pair-wise RMSD between the different pairs (range from 0.7 1.6 A) are given. What is meant by 439 fully populated columns? Does it mean 439 C-alpha atoms for those amino acids in the fully occupied aligned columns? I¹m asking because I want to report these values of RMSD and I want to be more specific and state the number of atoms over which the RMSD value is being reported. P.S. The proteins vary in their length (461,462,460 and 470). Thanks for your reply in advance, Ibrahim

2 2

protonated carboxyl group
by Elaine Meng 26 Jul '10

26 Jul '10

> right now I'm getting stuck on things like adding hydrogens (e.g. I would like a -COOH and not -COO group) Hi, We may make some changes to make this easier in the future, but for now here is the procedure: (a) change the atom type of the oxygen to be protonated to O3. This could be done by Ctrl-clicking to select that oxygen and then using the command: setattr a idatmType O3 sel (b) add hydrogens with command "addh" or the AddH tool (c) if this is in a "standard residue" (amino acid ASP or GLU) and you are also going to assign charges in Chimera, you will also need to adjust the names of the atoms so they will receive the correct Amber partial charge values. If the residue is ASP, you will need to make sure that the sidechain oxygen without the hydrogen is named OD1, the one with the hydrogen is named OD2, and the hydrogen itself is named HD2. If GLU, it is analogous except the names contain E instead of D. Show atom labels for that residue to see the current names (e.g. to show atom labels for residue 9 in chain A, use command: lab :9.a). To rename an atom, you could select it and use a command something like: setattr a name OD1 sel Once the names are correct, charge assignment will give you the correct Amber values for residue ASH (protonated ASP) or GLH (protonated GLU). 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

1 0

map normalization; ccp4 file saving
by Jean-Paul Armache 26 Jul '10

26 Jul '10

hello, i would like to pose two questions: 1. is there a way of adjusting one map so that it's adjusting to the levels of another map? i believe it should be achievable with "vop" command, but i am not sure whether the vop scale is the appropriate thing to use. 2. would it be possible to save the output map as a ccp4 map? currently you're permitting mrc saving, which is not that very much different from ccp4, so i was wondering if it was possible to add this feature. the difference is large enough so that coot does not allow for map loading of mrc files. best regards, jean-paul

2 1

Problem
by Reza Heidari 25 Jul '10

25 Jul '10

1 0

More on extracting data from the reply log
by Jean Didier Pie Marechal 21 Jul '10

21 Jul '10

Hi everyone, I want to write only a part of the reply log in a file. I was trying to use the script you gave to katrina months ago but I have a problem in parsing the reply log text output. If I understand correctly the reply log text is a raw text. I'd like to parse it in "lines" and then only write in the output file a intersting bit, like for example lines that contains "RMSD". I thought it would be enough to split text using the '\n' return character but that does not work. Could you give me a hand please? Best JD def save_reply_log(path): from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f= open(path, 'w') i=text.split("\n") f.close() save_reply_log("d:/tmplog.txt") Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Divendres, Juliol 16, 2010 7:33 pm Assumpte: Chimera-users Digest, Vol 87, Issue 13 > 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. Re: alignment + missing residues (Gesa Volkers) > 2. Re: alignment + missing residues (Gesa Volkers) > 3. Re: alignment + missing residues (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 16 Jul 2010 11:58:48 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402D58.7090906(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Eric, > > thanks for your suggestions. Unfortunately removing the SEQRES > record > did not help. I also downloaded and installed the new chimera- > version > today. The false numbering in the alignment still occurs. Also when > I > remove the SEQRES record and try with the new chimera version the > false > numbering appears. Quite annoying... The pdb-file is not in the > protein > data bank yet. > > Any more suggestions? Could I add "dummy atoms" in the structure? > > Thanks, > Gesa > > > > Eric Pettersen schrieb: > > On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > > > >> Dear All, > >> > >> I observed an issue with the alignment function of Chimera. > >> I loaded a crystal structure where in between a loop is not > modelled > >> due to low electron density- so these residues are missing in > the > >> structure and the numbering also has this gap. When I align this > >> structure with others, the missing residues are not recognized > and > >> chimera just overrides the numbering so after this loop all the > >> numbers in the alignment do not fit anymore to the residues they > >> should belong to although the structure and numberings are shown > in > >> the right way in the graphics window. How can I overcome this > issue? > >> Should I change the pdb-file? In which way? > >> > >> Thanks for all responses! > > > > Hi Gesa, > > I had a similar problem reported with 1JFF 12 days ago and > haven't yet > > worked on fixing it. It seems to only happen for a small subset > of > > structures. 1JFF has a missing loop and also exactly one missing > > residue at the N terminus. Is your structure like that? Is it a > > standard PDB entry (if so, what's the ID code)? I'll add you to > the > > recipient list for the ticket we have open in our bug database > for > > this (#8585) so you will be notified when it gets fixed. It'll > > probably be fairly soon. > > Until then the only workaround that occurs to me is for you to > remove > > the SEQRES records from the PDB file before you open it. Then > the > > Sequence viewer will depict only the residues physically present > in > > the structure -- no gaps (incorrect or otherwise) will be depicted. > > > > --Eric > > > > Eric Pettersen > > > > UCSF Computer Graphics Lab > > > > http://www.cgl.ucsf.edu > > > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 2 > Date: Fri, 16 Jul 2010 12:06:56 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402F40.2010604(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Additionally I downloaded 1JFF and did an alignment with another > tubulin-structure. And still the numbering does not recognize this > gap > between 34 and 61. > > Gesa Volkers schrieb: > > Dear Eric, > > > > thanks for your suggestions. Unfortunately removing the SEQRES > record > > did not help. I also downloaded and installed the new chimera- > version > > today. The false numbering in the alignment still occurs. Also > when I > > remove the SEQRES record and try with the new chimera version the > > false numbering appears. Quite annoying... The pdb-file is not in > the > > protein data bank yet. > > > > Any more suggestions? Could I add "dummy atoms" in the structure? > > > > Thanks, > > Gesa > > > > > > > > Eric Pettersen schrieb: > >> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >> > >>> Dear All, > >>> > >>> I observed an issue with the alignment function of Chimera. > >>> I loaded a crystal structure where in between a loop is not > modelled > >>> due to low electron density- so these residues are missing in > the > >>> structure and the numbering also has this gap. When I align > this > >>> structure with others, the missing residues are not recognized > and > >>> chimera just overrides the numbering so after this loop all the > >>> numbers in the alignment do not fit anymore to the residues > they > >>> should belong to although the structure and numberings are > shown in > >>> the right way in the graphics window. How can I overcome this > issue? > >>> Should I change the pdb-file? In which way? > >>> > >>> Thanks for all responses! > >> > >> Hi Gesa, > >> I had a similar problem reported with 1JFF 12 days ago and > haven't > >> yet worked on fixing it. It seems to only happen for a small > subset > >> of structures. 1JFF has a missing loop and also exactly one > missing > >> residue at the N terminus. Is your structure like that? Is it > a > >> standard PDB entry (if so, what's the ID code)? I'll add you to > the > >> recipient list for the ticket we have open in our bug database > for > >> this (#8585) so you will be notified when it gets fixed. It'll > >> probably be fairly soon. > >> Until then the only workaround that occurs to me is for you to > remove > >> the SEQRES records from the PDB file before you open it. Then > the > >> Sequence viewer will depict only the residues physically present > in > >> the structure -- no gaps (incorrect or otherwise) will be depicted. > >> > >> --Eric > >> > >> Eric Pettersen > >> > >> UCSF Computer Graphics Lab > >> > >> http://www.cgl.ucsf.edu > >> > >> > >> > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 10:32:39 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] alignment + missing residues > To: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <CF134751-B951-403B-B9E3-E441DB44644D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gesa, > I suspect you are using a Mac, since the daily builds failed last > night for the Mac platforms. You need to get a daily build dated > July > 16 or later. I tried opening the sequence view for 1JFF in one of > the > successful daily builds and it was correct, e.g.: > > > > You can see that the interior gap is correctly recognized now. > Hopefully the daily builds on the Mac platforms will work tonight. > > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > > Ah, the "remove SEQRES records" hack will only work for the single- > sequence viewer, not an alignment. I tested that in the 1.4.1 > release > and it indeed worked as I expected: > > > > The whole sequence is smushed together with no gaps, but the > correspondences are correct. You could then align additional > sequences to the smushed sequence and the correspondences would > remain > correct. Nonetheless it's probably simply better to wait for a > daily > build to succeed than to use the hack now. So make sure you check > the > date in the download table. If you still have problems with a > release > later than July 16, let me know. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jul 16, 2010, at 3:06 AM, Gesa Volkers wrote: > > > Additionally I downloaded 1JFF and did an alignment with another > > tubulin-structure. And still the numbering does not recognize > this > > gap between 34 and 61. > > > > Gesa Volkers schrieb: > >> Dear Eric, > >> > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > >> > >> Any more suggestions? Could I add "dummy atoms" in the structure? > >> > >> Thanks, > >> Gesa > >> > >> > >> > >> Eric Pettersen schrieb: > >>> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >>> > >>>> Dear All, > >>>> > >>>> I observed an issue with the alignment function of Chimera. > >>>> I loaded a crystal structure where in between a loop is not > >>>> modelled due to low electron density- so these residues are > >>>> missing in the structure and the numbering also has this gap. > >>>> When I align this structure with others, the missing residues > are > >>>> not recognized and chimera just overrides the numbering so > after > >>>> this loop all the numbers in the alignment do not fit anymore > to > >>>> the residues they should belong to although the structure and > >>>> numberings are shown in the right way in the graphics window. > How > >>>> can I overcome this issue? Should I change the pdb-file? In > which > >>>> way? > >>>> > >>>> Thanks for all responses! > >>> > >>> Hi Gesa, > >>> I had a similar problem reported with 1JFF 12 days ago and > haven't > >>> yet worked on fixing it. It seems to only happen for a small > >>> subset of structures. 1JFF has a missing loop and also exactly > > >>> one missing residue at the N terminus. Is your structure like > >>> that? Is it a standard PDB entry (if so, what's the ID code)? > >>> I'll add you to the recipient list for the ticket we have open > in > >>> our bug database for this (#8585) so you will be notified when > it > >>> gets fixed. It'll probably be fairly soon. > >>> Until then the only workaround that occurs to me is for you to > >>> remove the SEQRES records from the PDB file before you open it. > > >>> Then the Sequence viewer will depict only the residues > physically > >>> present in the structure -- no gaps (incorrect or otherwise) > will > >>> be depicted. > >>> > >>> --Eric > >>> > >>> Eric Pettersen > >>> > >>> UCSF Computer Graphics Lab > >>> > >>> http://www.cgl.ucsf.edu > >>> > >>> > >>> > >> > >> > > > > > > -- > > Gesa Volkers > > Institut f?r Biochemie, Molekulare Strukturbiologie > > Felix-Hausdorff-Stra?e 4 > > 17489 Greifswald > > Germany > > +49 (3834)-864392 > > > > > > > > >

2 1

Re: [Chimera-users] save density map relative to...
by Tom Goddard 20 Jul '10

20 Jul '10

Hi Jie, You want to save a map that has been rotated relative to another map so that when you open both maps later they align. The difficulty is that the common map file formats like MRC and Spider don't have any place in the file header to specify a rotation. There are two ways to work around this limitation. One is that Chimera does some special trickery and puts the rotation information into a "label" in MRC map files so that when it later reads the file it can restore it in the right position. The trouble is that no other software will recognize that rotated position -- only Chimera. Another difficulty is that Chimera won't record the rotated position when you fit one map in another. The reason for that is because Chimera saves the rotation of the map grid relative to the maps local coordinate system. But fitting doesn't change the orientation of the grid -- instead it moves the local coordinate system (the map coordinate axes move instead of the data moving). Each map has its own set of coordinate axes. I think it would be pretty easy to add a "save relative to" option to the Same Map As... dialog that would take account of both types of rotation. But again, the orientation would only be restored by Chimera. The second method is to resample the rotated map on the grid of the map you fit into and save that resampled map. This will allow other software to open the maps and show the correct alignment. The drawback here is that the resampled map may have degraded quality since it interpolated the original map (trilinear interpolation). The Chimera command to do that looks like vop resample #3 onGrid #2 Here #3 is the id number (shown in Favorites / Model Panel or the volume dialog) of the rotated map that was fit into map #2. This will make a new map that you can save and it will align with map #2 when opened in another session or with other software since they share identical grids. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample Tom > Hi Tom, > > Hope this email finds you well. This is Jie from Joachim Frank's lab. > We met at the UCSF molecular animation workshop. > > I am writing about the "save map as" function in Chimera. Is there a > way to save map relative to another map (like the option available in > "save PDB")? The fitting algorithm ("fit in map" function) in Chimera > is very good, and I sometimes use it to align two density maps. > However, I couldn't save the density map after it was shifted. If > there's no such option, is it possible to add it? > > Best regards, > > > -Jie >

1 0

Re: [Chimera-users] Chimera-users Digest, Vol 87, Issue 13
by Jean Didier Pie Marechal 20 Jul '10

20 Jul '10

Hi again, I'd like to do a mmaker for a region of space leading to something like this: mmaker #(ref-model and part of the selection) #(flex-model and part of the selection) So far I haven't found the correct syntax to do so but I am pretty sure we can do that. any help? Cheers JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Divendres, Juliol 16, 2010 7:33 pm Assumpte: Chimera-users Digest, Vol 87, Issue 13 > 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. Re: alignment + missing residues (Gesa Volkers) > 2. Re: alignment + missing residues (Gesa Volkers) > 3. Re: alignment + missing residues (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 16 Jul 2010 11:58:48 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402D58.7090906(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Eric, > > thanks for your suggestions. Unfortunately removing the SEQRES > record > did not help. I also downloaded and installed the new chimera- > version > today. The false numbering in the alignment still occurs. Also when > I > remove the SEQRES record and try with the new chimera version the > false > numbering appears. Quite annoying... The pdb-file is not in the > protein > data bank yet. > > Any more suggestions? Could I add "dummy atoms" in the structure? > > Thanks, > Gesa > > > > Eric Pettersen schrieb: > > On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > > > >> Dear All, > >> > >> I observed an issue with the alignment function of Chimera. > >> I loaded a crystal structure where in between a loop is not > modelled > >> due to low electron density- so these residues are missing in > the > >> structure and the numbering also has this gap. When I align this > >> structure with others, the missing residues are not recognized > and > >> chimera just overrides the numbering so after this loop all the > >> numbers in the alignment do not fit anymore to the residues they > >> should belong to although the structure and numberings are shown > in > >> the right way in the graphics window. How can I overcome this > issue? > >> Should I change the pdb-file? In which way? > >> > >> Thanks for all responses! > > > > Hi Gesa, > > I had a similar problem reported with 1JFF 12 days ago and > haven't yet > > worked on fixing it. It seems to only happen for a small subset > of > > structures. 1JFF has a missing loop and also exactly one missing > > residue at the N terminus. Is your structure like that? Is it a > > standard PDB entry (if so, what's the ID code)? I'll add you to > the > > recipient list for the ticket we have open in our bug database > for > > this (#8585) so you will be notified when it gets fixed. It'll > > probably be fairly soon. > > Until then the only workaround that occurs to me is for you to > remove > > the SEQRES records from the PDB file before you open it. Then > the > > Sequence viewer will depict only the residues physically present > in > > the structure -- no gaps (incorrect or otherwise) will be depicted. > > > > --Eric > > > > Eric Pettersen > > > > UCSF Computer Graphics Lab > > > > http://www.cgl.ucsf.edu > > > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 2 > Date: Fri, 16 Jul 2010 12:06:56 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402F40.2010604(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Additionally I downloaded 1JFF and did an alignment with another > tubulin-structure. And still the numbering does not recognize this > gap > between 34 and 61. > > Gesa Volkers schrieb: > > Dear Eric, > > > > thanks for your suggestions. Unfortunately removing the SEQRES > record > > did not help. I also downloaded and installed the new chimera- > version > > today. The false numbering in the alignment still occurs. Also > when I > > remove the SEQRES record and try with the new chimera version the > > false numbering appears. Quite annoying... The pdb-file is not in > the > > protein data bank yet. > > > > Any more suggestions? Could I add "dummy atoms" in the structure? > > > > Thanks, > > Gesa > > > > > > > > Eric Pettersen schrieb: > >> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >> > >>> Dear All, > >>> > >>> I observed an issue with the alignment function of Chimera. > >>> I loaded a crystal structure where in between a loop is not > modelled > >>> due to low electron density- so these residues are missing in > the > >>> structure and the numbering also has this gap. When I align > this > >>> structure with others, the missing residues are not recognized > and > >>> chimera just overrides the numbering so after this loop all the > >>> numbers in the alignment do not fit anymore to the residues > they > >>> should belong to although the structure and numberings are > shown in > >>> the right way in the graphics window. How can I overcome this > issue? > >>> Should I change the pdb-file? In which way? > >>> > >>> Thanks for all responses! > >> > >> Hi Gesa, > >> I had a similar problem reported with 1JFF 12 days ago and > haven't > >> yet worked on fixing it. It seems to only happen for a small > subset > >> of structures. 1JFF has a missing loop and also exactly one > missing > >> residue at the N terminus. Is your structure like that? Is it > a > >> standard PDB entry (if so, what's the ID code)? I'll add you to > the > >> recipient list for the ticket we have open in our bug database > for > >> this (#8585) so you will be notified when it gets fixed. It'll > >> probably be fairly soon. > >> Until then the only workaround that occurs to me is for you to > remove > >> the SEQRES records from the PDB file before you open it. Then > the > >> Sequence viewer will depict only the residues physically present > in > >> the structure -- no gaps (incorrect or otherwise) will be depicted. > >> > >> --Eric > >> > >> Eric Pettersen > >> > >> UCSF Computer Graphics Lab > >> > >> http://www.cgl.ucsf.edu > >> > >> > >> > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 10:32:39 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] alignment + missing residues > To: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <CF134751-B951-403B-B9E3-E441DB44644D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gesa, > I suspect you are using a Mac, since the daily builds failed last > night for the Mac platforms. You need to get a daily build dated > July > 16 or later. I tried opening the sequence view for 1JFF in one of > the > successful daily builds and it was correct, e.g.: > > > > You can see that the interior gap is correctly recognized now. > Hopefully the daily builds on the Mac platforms will work tonight. > > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > > Ah, the "remove SEQRES records" hack will only work for the single- > sequence viewer, not an alignment. I tested that in the 1.4.1 > release > and it indeed worked as I expected: > > > > The whole sequence is smushed together with no gaps, but the > correspondences are correct. You could then align additional > sequences to the smushed sequence and the correspondences would > remain > correct. Nonetheless it's probably simply better to wait for a > daily > build to succeed than to use the hack now. So make sure you check > the > date in the download table. If you still have problems with a > release > later than July 16, let me know. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jul 16, 2010, at 3:06 AM, Gesa Volkers wrote: > > > Additionally I downloaded 1JFF and did an alignment with another > > tubulin-structure. And still the numbering does not recognize > this > > gap between 34 and 61. > > > > Gesa Volkers schrieb: > >> Dear Eric, > >> > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > >> > >> Any more suggestions? Could I add "dummy atoms" in the structure? > >> > >> Thanks, > >> Gesa > >> > >> > >> > >> Eric Pettersen schrieb: > >>> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >>> > >>>> Dear All, > >>>> > >>>> I observed an issue with the alignment function of Chimera. > >>>> I loaded a crystal structure where in between a loop is not > >>>> modelled due to low electron density- so these residues are > >>>> missing in the structure and the numbering also has this gap. > >>>> When I align this structure with others, the missing residues > are > >>>> not recognized and chimera just overrides the numbering so > after > >>>> this loop all the numbers in the alignment do not fit anymore > to > >>>> the residues they should belong to although the structure and > >>>> numberings are shown in the right way in the graphics window. > How > >>>> can I overcome this issue? Should I change the pdb-file? In > which > >>>> way? > >>>> > >>>> Thanks for all responses! > >>> > >>> Hi Gesa, > >>> I had a similar problem reported with 1JFF 12 days ago and > haven't > >>> yet worked on fixing it. It seems to only happen for a small > >>> subset of structures. 1JFF has a missing loop and also exactly > > >>> one missing residue at the N terminus. Is your structure like > >>> that? Is it a standard PDB entry (if so, what's the ID code)? > >>> I'll add you to the recipient list for the ticket we have open > in > >>> our bug database for this (#8585) so you will be notified when > it > >>> gets fixed. It'll probably be fairly soon. > >>> Until then the only workaround that occurs to me is for you to > >>> remove the SEQRES records from the PDB file before you open it. > > >>> Then the Sequence viewer will depict only the residues > physically > >>> present in the structure -- no gaps (incorrect or otherwise) > will > >>> be depicted. > >>> > >>> --Eric > >>> > >>> Eric Pettersen > >>> > >>> UCSF Computer Graphics Lab > >>> > >>> http://www.cgl.ucsf.edu > >>> > >>> > >>> > >> > >> > > > > > > -- > > Gesa Volkers > > Institut f?r Biochemie, Molekulare Strukturbiologie > > Felix-Hausdorff-Stra?e 4 > > 17489 Greifswald > > Germany > > +49 (3834)-864392 > > > > > > > > >

3 2

alignment + missing residues
by Gesa Volkers 20 Jul '10

20 Jul '10

Dear All, I observed an issue with the alignment function of Chimera. I loaded a crystal structure where in between a loop is not modelled due to low electron density- so these residues are missing in the structure and the numbering also has this gap. When I align this structure with others, the missing residues are not recognized and chimera just overrides the numbering so after this loop all the numbers in the alignment do not fit anymore to the residues they should belong to although the structure and numberings are shown in the right way in the graphics window. How can I overcome this issue? Should I change the pdb-file? In which way? Thanks for all responses! -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

2 5