Tag Archives: dc

Conflicting SEQRES records

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Q:
I’m trying to visualize a morph between two structures. However, I’m prompted with the error message “Conflicting SEQRES records”. How may I resolve this?

A:
This is by far the most comment cause of failure. The server uses SEQRES data to determine the actual protein sequence. However, this frequently conflicts with the sequence intuited from ATOM records (including official PDB files from http://www.rcsb.org). If the server cannot automatically resolve these conflicts, it will fail. The easiest workaround to this is to submit files with SEQRES records deleted; if you supplied a PDB ID rather than a file you will need to download the proper file from the PDB, then modify and upload it. However, this may sometimes lead to other distortions, depending on the sequence numbering.

Preventing submissions on the morph server from becoming public

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Q:
I understand that, by default, the structures I submit to your morph server become public on your database. However, I am submitting coordinates that have not yet been published, or which are commercial. Thus, I’d prefer that my submission not be made public. Can you help me?

A:
We strongly discourage private submissions because they go against the spirit of the database, which is not only intended to provide free morphing to individual users, but also to serve as a browseable and searchable repository of morphs which are useful to others. We understand, however, that some morphs may reveal confidential information and so beyond moral suasion nothing prevents you from using the “Private” check box on our single- and multi-chain morph submission forms. This sets a flag in our database that tells our movie gallery page not to display the morph. Also, the search tool on our front page will not return it. The only way a member of the public could possibly find your morph is if they were able to intercept the email you got from our server with the link to it. We consider the probability that this will happen to be very low. Generally we cannot handle specific requests for further security unless as part of an official collaboration.

problems in compilation of libproteingeometry-2-3-1

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Q.
I am experiencing problems in trying to compile your package (libproteingeometry-2-3-1). I tried to compile it under Ubuntu-11.10 on a 32-bit VAIO centrino-based PC (gcc vers 4.6.1) and I got the following error message:

utypes.h:16:15: error: conflicting types for ‘float_t’
/usr/include/i386-linux-gnu/bits/mathdef.h:36:21: note: previous declaration of
‘float_t’ was here

Is it possible that this error is related CPPFLAGS settings?

I have also had difficulty compiling on an Intel i7 64-b machine under Ubuntu-11.10 with the same gcc version. This time the message was:

../src-lib/.libs/libproteingeometry: undefined reference to `sincos’ ../src-lib/.libs/libproteingeometry: undefined reference to `ceil’ ../src-lib/.libs/libproteingeometry: undefined reference to `atan2′ ../src-lib/.libs/libproteingeometry: undefined reference to `acos’ ../src-lib/.libs/libproteingeometry: undefined reference to `sin’ ../src-lib/.libs/libproteingeometry: undefined reference to `rint’ ../src-lib/.libs/libproteingeometry: undefined reference to `sqrtf’ ../src-lib/.libs/libproteingeometry: undefined reference to `pow’ ../src-lib/.libs/libproteingeometry: undefined reference to `sqrt’ ../src-lib/.libs/libproteingeometry: undefined reference to `floor’ collect2: ld returned 1 exit status

A.
This problem was resolved in a strange way. The package was compiled in the /usr/local dir of an Intel i5 machine, and all the compiled material was brought to the corresponding dir of an i7 computer. Almost the same had been done for a vaio 32-bit computer using a CD with the Ubuntu 9.10 version on another 32-bit system.

There may have been some collisions with environment flags set by the preceding compilation of other packages. In particular, Amber10 and Gromacs-4-5-5 had already been installed on the i7 and vaio.

Interaction Data set

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Q:

help of your paper “Redefining Nodes and Edges: Relating 3D Structures to Protein Networks Provides Insight
into their Evolution “. Now I need to get those protein in pfam which are involved in interaction and also the crystal structure of them.
I would be very grateful to you if you send me the link to access the more detail format of SIN v0.9 data.

A:

My understanding from your email is that you would like to know the Pfam IDs
and the corresponding crystal structures (ie, the PDB IDs) for the
interactions involved in the SIN. To do this, you will have to process two
separate datasets together, but this will not be difficult. Here are the
steps:

i) access the raw SIN data (http://networks.gersteinlab.org/structint/) At
this page, click on “composite dataset” under the download column for SIN
v0.9 data. This is a list of open reading frame IDs corresponding to each
interaction (the first and third columns), as well as whether the
interaction is taken from Pfam.
ii) open the text file I’ve attached with this email. Each row contains
several pieces of information, but what you would like to do is find the PDB
IDs (contained in the 2nd column) corresponding to each Ensembl Gene ID (the
first column). This Ensembl Gene ID is taken from (i) above.
I should mention that there are two problems with the procedure outlined
above.
The first is that I noticed it will not provide crystal structures for all
interactions. I’m not sure why this is the case. Secondly, for some
interactions, multiple crystal structures are available, and it is not clear
which structure was used in Pfam. Nitin (CC’ed to this email) may know how
to negotiate with these issues. If you are still having difficulty, please
contact Nitin or I again after further efforts to get the data you need.

morph server question

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Q:

I am currently using your server to morph two actin structures (open nucleotide cleft and closed). Besides morphing the two actin chains, I would also like to morph the bound ATP molecules. Although I can the two actin structures to morph, I cannot seem to figure out how to morph the ATPs. So basically my question is: can bound nucleotides be morphed? How should they be defined in the PDB filem which server to use, and should the morphs be done separately (i.e. protein and ATP as separate morphs)?

A:

Thank you for your query, and for using MolMovDB. Specifically, which server is it that you have been using, and what error message(s) are returned? It is sometimes the case that the formatting of the PDB files must be manually changed in certain ways, and this in and of itself can be a little tricky. If you like (and if you don’t mind), you may send the PDB files to me, and I will spend some time on trying to format them for the server. If all else fails, it may indeed be necessary to morph things separately, but combining the resultant morphs may be an endeavor on its own.

Finally (and importantly), I should point out that the PDB formats may not be the issue at all; it may be the case that that there is an issue with ATP constituting ‘heteroatoms’. Dealing with heteroatoms in our server is extremely difficult, and this is sometimes a result of the way in which they’re numbered in your input files. In addition, parameterizing heteroatoms using our interpolation software is very difficult (to the point that, if you do indeed obtain a morph, the resultant interpolation may be very questionable, so it may be a use-at-your-own-risk practice if the parameterization is not done properly).